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Friedson B, Willis SD, Shcherbik N, Campbell AN, Cooper KF. The CDK8 kinase module: A novel player in the transcription of translation initiation and ribosomal genes. Mol Biol Cell 2025; 36:ar2. [PMID: 39565680 PMCID: PMC11742111 DOI: 10.1091/mbc.e24-04-0164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 11/05/2024] [Accepted: 11/12/2024] [Indexed: 11/22/2024] Open
Abstract
Survival following stress is dependent upon reprogramming transcription and translation. Communication between these programs following stress is critical for adaptation but is not clearly understood. The Cdk8 kinase module (CKM) of the Mediator complex modulates the transcriptional response to various stresses. Its involvement in regulating translational machinery has yet to be elucidated, highlighting an existing gap in knowledge. Here, we report that the CKM positively regulates a subset of ribosomal protein (RP) and translation initiation factor (TIF)-encoding genes under physiological conditions in Saccharomyces cerevisiae. In mouse embryonic fibroblasts and HCT116 cells, the CKM regulates unique sets of RP and TIF genes, demonstrating some conservation of function across species. In yeast, this is mediated by Cdk8 phosphorylation of one or more transcription factors which control RP and TIF expression. Conversely, the CKM is disassembled following nutrition stress, permitting repression of RP and TIF genes. The CKM also plays a transcriptional role important for promoting cell survival, particularly during translational machinery stress triggered by ribosome-targeting antibiotics. Furthermore, in mammalian cells, the activity of CDK8 and its paralogue, CDK19, promotes cell survival following ribosome inhibition. These results provide mechanistic insights into the CKM's role in regulating expression of a subset of genes associated with translation.
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Affiliation(s)
- Brittany Friedson
- Department of Molecular Biology, Virtual Health College of Medicine and Life Sciences, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Stephen D. Willis
- Department of Molecular Biology, Virtual Health College of Medicine and Life Sciences, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Natalia Shcherbik
- Department of Molecular Biology, Virtual Health College of Medicine and Life Sciences, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Alicia N. Campbell
- Department of Molecular Biology, Virtual Health College of Medicine and Life Sciences, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Katrina F. Cooper
- Department of Molecular Biology, Virtual Health College of Medicine and Life Sciences, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
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2
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Fauqueux J, Boussion S, Thuillier C, Meurisse E, Lacombe D, Willems M, Piton A, Ait-Yahya E, Ghoumid J, Smol T. Splice site variants in the canonical donor site of MED13L exon 7 lead to intron retention in patients with MED13L syndrome. J Med Genet 2024; 61:1040-1044. [PMID: 39181712 DOI: 10.1136/jmg-2024-110154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
Pathogenic variants in the MED13L gene are associated with the autosomal dominant MED13L syndrome, which is characterised by global developmental delay and cardiac malformations. We investigated two heterozygous MED13L variants located at the canonical donor splice site motif of exon 7: c.1009+1G>C and c.1009+5G>C. We report that in silico predictions suggested two possible outcomes: exon 7 skipping, resulting in loss of the phosphodegron motif essential for MED13L regulation, or activation of a cryptic donor site in intron 7, leading to intron retention. RNA analysis confirmed that both variants affected the exon 7 splice donor site, resulting in the retention of 73 bp of intron 7. This retention caused a frameshift and premature translation termination, consistent with haploinsufficiency. Our results highlight the importance of combining predictive and experimental approaches to understand the functional impact of splice site variants. These insights into the molecular consequences of MED13L variants provide a deeper understanding of the genetic basis of MED13L syndrome.
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Affiliation(s)
| | - Simon Boussion
- Univ. Lille, ULR7364 RADEME, Lille, France
- CHU Lille, Clinique de Génétique, Lille, France
| | | | | | - Didier Lacombe
- Univ. Bordeaux, UMR1211 - MRGM - Maladies Rares Génétique et Métabolisme, Bordeaux, France
- CHU Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Marjolaine Willems
- CHU Montpellier, Département de Génétique Médicale, Centre de Référence Anomalies du Développement, Montpellier, France
- Univ. Montpellier, Inserm, Institute for Neurosciences of Montpellier, Montpellier, France
| | - Amélie Piton
- IGBMC, Neurogenetics and Translational Medicine, Illkirch-Graffenstaden, France
- CHU Strasbourg, Laboratoire de Diagnostic Génétique, Strasbourg, France
| | - Emilie Ait-Yahya
- CHU Lille, Unité de Bio-informatique, Plateau de Biologie-Moléculaire, Lille, France
| | - Jamal Ghoumid
- Univ. Lille, ULR7364 RADEME, Lille, France
- CHU Lille, Clinique de Génétique, Lille, France
| | - Thomas Smol
- Univ. Lille, ULR7364 RADEME, Lille, France
- CHU Lille, Institut de Génétique Médicale, Lille, France
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3
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Chao TC, Chen SF, Kim HJ, Tang HC, Tseng HC, Xu A, Palao L, Khadka S, Li T, Huang MF, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Mol Cell 2024; 84:3932-3949.e10. [PMID: 39321804 PMCID: PMC11832219 DOI: 10.1016/j.molcel.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/05/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024]
Abstract
The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function.
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Affiliation(s)
- Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hsiang-Ching Tseng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Subash Khadka
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA; Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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4
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Maji S, Waseem M, Sharma MK, Singh M, Singh A, Dwivedi N, Thakur P, Cooper DG, Bisht NC, Fassler JS, Subbarao N, Khurana JP, Bhavesh NS, Thakur JK. MediatorWeb: a protein-protein interaction network database for the RNA polymerase II Mediator complex. FEBS J 2024; 291:3938-3960. [PMID: 38975839 DOI: 10.1111/febs.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 04/24/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
The protein-protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue-level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.
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Grants
- BT/PR40146/BTIS/137/4/2020 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR40169/BTIS/137/71/2023 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/27/2021 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/26/2021 Department of Biotechnology, Ministry of Science and Technology, India
- SERB, Government of India
- ICMR
- Council of Scientific and Industrial Research, India
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Affiliation(s)
- Sourobh Maji
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohd Waseem
- National Institute of Plant Genome Research, New Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Maninder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Anamika Singh
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nidhi Dwivedi
- National Institute of Plant Genome Research, New Delhi, India
| | - Pallabi Thakur
- National Institute of Plant Genome Research, New Delhi, India
| | - David G Cooper
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN, USA
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra P Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jitendra Kumar Thakur
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- National Institute of Plant Genome Research, New Delhi, India
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Mitchel MW, Turner S, Walsh LK, Torene RI, Myers SM, Taylor CM. MED13L-related disorder characterized by severe motor speech impairment. RESEARCH SQUARE 2024:rs.3.rs-4790993. [PMID: 39257968 PMCID: PMC11384029 DOI: 10.21203/rs.3.rs-4790993/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Background MED13L-related disorder is associated with intellectual disability, motor delay, and speech deficits. Previous studies have focused on broad clinical descriptions of individuals, but limited information regarding specific speech diagnoses and results of direct testing has been published to date. We conducted deep phenotyping to characterize the speech, language, motor, cognitive, and adaptive phenotypes of individuals with MED13L-related disorder. Methods In this cross-sectional study, we administered standardized articulation, language, motor, and cognitive testing to 17 children and adolescents (mean age 9y 9m; SD 4y 5m; range 4y 2m to 19y 7m). In-person testing was supplemented with broad developmental, medical, and behavioral information collected virtually from a cohort of 67 individuals. Results All individuals who completed in-person articulation testing met diagnostic criteria for speech apraxia, dysarthria, or both. Language impairment was present in all of the in-person cohort and almost all (97%) of the virtual cohort. Those who were able to complete motor testing demonstrated significant deficits in visual motor integration (mean 57.08, SD 9.26). Full scale IQs fell in the borderline to intellectual disability range, consistent with reported cognitive impairment in 97% of the virtual cohort. Notable medical features included hypotonia (83%), vision problems (72%), recurrent otitis media (58%), gastrointestinal problems (57%), and seizures (31%). Conclusions MED13L-related disorder is characterized by a high rate of motor speech disorders that occur in the context of globally impaired motor, language, and cognitive skills. Children would benefit from intensive, individualized speech therapy and the early adoption of augmentative communication strategies.
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Chen SF, Chao TC, Kim HJ, Tang HC, Khadka S, Li T, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601608. [PMID: 39005267 PMCID: PMC11244988 DOI: 10.1101/2024.07.01.601608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.
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Li X, Liu M, Xing Y, Niu Y, Liu TH, Sun JL, Liu Y, Hemba-Waduge RUS, Ji JY. Distinct effects of CDK8 module subunits on cellular growth and proliferation in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591924. [PMID: 38746212 PMCID: PMC11092604 DOI: 10.1101/2024.04.30.591924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Mediator complex, composed of about 30 conserved subunits, plays a pivotal role in facilitating RNA polymerase II-dependent transcription in eukaryotes. Within this complex, the CDK8 kinase module (CKM), comprising Med12, Med13, CDK8, and CycC (Cyclin C), serves as a dissociable subcomplex that modulates the activity of the small Mediator complex. Genetic studies in Drosophila have revealed distinct phenotypes of CDK8-CycC and Med12-Med13 mutations, yet the underlying mechanism has remained unknown. Here, using Drosophila as a model organism, we show that depleting CDK8-CycC enhances E2F1 target gene expression and promotes cell-cycle progression. Conversely, depletion of Med12-Med13 affects the expression of ribosomal protein genes and fibrillarin, indicating a more severe reduction in ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Moreover, we found that the stability of CDK8 and CycC relies on Med12 and Med13, with a mutually interdependent relationship between Med12 and Med13. Furthermore, CycC stability depends on the other three CKM subunits. These findings reveal distinct roles for CKM subunits in vivo , with Med12-Med13 disruption exerting a more pronounced impact on ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Significance The CDK8 kinase module (CKM), comprising CDK8, CycC, Med12, and Med13, is essential in the Mediator complex for RNA polymerase II-dependent transcription in eukaryotes. While expected to function jointly, CKM subunit mutations result in distinct phenotypes in Drosophila . This study investigates the mechanisms driving these differing effects. Our analysis reveals the role of Med12-Med13 pair in regulating ribosomal biogenesis and cellular growth, contrasting with the involvement of CDK8-CycC in E2F1-dependent cell-cycle progression. Additionally, an asymmetric interdependence in the stability of CDK8-CycC and Med12-Med13 was observed. CKM mutations or overexpression are associated with cancers and cardiovascular diseases. Our findings underscore the distinct impacts of CKM mutations on cellular growth and proliferation, advancing our understanding of their diverse consequences in vivo .
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8
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Yang JH, Liu ZG, Liu CL, Zhang MR, Jia YL, Zhai QX, He MF, He N, Qiao JD. MED12 variants associated with X-linked recessive partial epilepsy without intellectual disability. Seizure 2024; 116:30-36. [PMID: 36894399 DOI: 10.1016/j.seizure.2023.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The MED12 gene encodes mediator complex subunit 12, which is a component of the mediator complex involved in the transcriptional regulation of nearly all RNA polymerase II-dependent genes. MED12 variants have previously been associated with developmental disorders with or without nonspecific intellectual disability. This study aims to explore the association between MED12 variants and epilepsy. MATERIALS AND METHODS Trios-based whole-exome sequencing was performed in a cohort of 349 unrelated cases with partial (focal) epilepsy without acquired causes. The genotype-phenotype correlations of MED12 variants were analyzed. RESULTS Five hemizygous missense MED12 variants, including c.958A>G/p.Ile320Val, c.1757G>A/p.Ser586Asn, c.2138C>T/p.Pro713Leu, c.3379T>C/p.Ser1127Pro, and c.4219A>C/p.Met1407Leu were identified in five unrelated males with partial epilepsy. All patients showed infrequent focal seizures and achieved seizure free without developmental abnormalities or intellectual disability. All the hemizygous variants were inherited from asymptomatic mothers (consistent with the X-linked recessive inheritance pattern) and were absent in the general population. The two variants with damaging hydrogen bonds were associated with early-onset seizures. Further genotype-phenotype analysis revealed that congenital anomaly disorder (Hardikar syndrome) was associated with (de novo) destructive variants in an X-linked dominant inheritance pattern, whereas epilepsy was associated with missense variants in an X-linked recessive inheritance pattern. Phenotypic features of intellectual disability appeared as the intermediate phenotype in terms of both genotype and inheritance. Epilepsy-related variants were located at the MED12-LCEWAV domain and the regions between MED12-LCEWAV and MED12-POL. CONCLUSION MED12 is a potentially causative gene for X-linked recessive partial epilepsy without developmental or intellectual abnormalities. The genotype-phenotype correlation of MED12 variants explains the phenotypic variations and can help the genetic diagnosis.
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Affiliation(s)
- Jie-Hua Yang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China; Department of Neurology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhi-Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Chun-Ling Liu
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Rui Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan-Lu Jia
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qiong-Xiang Zhai
- Department of pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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Schiano C, Luongo L, Maione S, Napoli C. Mediator complex in neurological disease. Life Sci 2023; 329:121986. [PMID: 37516429 DOI: 10.1016/j.lfs.2023.121986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Neurological diseases, including traumatic brain injuries, stroke (haemorrhagic and ischemic), and inherent neurodegenerative diseases cause acquired disability in humans, representing a leading cause of death worldwide. The Mediator complex (MED) is a large, evolutionarily conserved multiprotein that facilities the interaction between transcription factors and RNA Polymerase II in eukaryotes. Some MED subunits have been found altered in the brain, although their specific functions in neurodegenerative diseases are not fully understood. Mutations in MED subunits were associated with a wide range of genetic diseases for MED12, MED13, MED13L, MED20, MED23, MED25, and CDK8 genes. In addition, MED12 and MED23 were deregulated in the Alzheimer's Disease. Interestingly, most of the genomic mutations have been found in the subunits of the kinase module. To date, there is only one evidence on MED1 involvement in post-stroke cognitive deficits. Although the underlying neurodegenerative disorders may be different, we are confident that the signal cascades of the biological-cognitive mechanisms of brain adaptation, which begin after brain deterioration, may also differ. Here, we analysed relevant studies in English published up to June 2023. They were identified through a search of electronic databases including PubMed, Medline, EMBASE and Scopus, including search terms such as "Mediator complex", "neurological disease", "brains". Thematic content analysis was conducted to collect and summarize all studies demonstrating MED alteration to understand the role of this central transcriptional regulatory complex in the brain. Improved and deeper knowledge of the regulatory mechanisms in neurological diseases can increase the ability of physicians to predict onset and progression, thereby improving diagnostic care and providing appropriate treatment decisions.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy.
| | - Livio Luongo
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Sabatino Maione
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy; Clinical Department of Internal Medicine and Specialistic Units, Division of Clinical Immunology and Immunohematology, Transfusion Medicine, and Transplant Immunology (SIMT), Regional Reference Laboratory of Transplant Immunology (LIT), Azienda Universitaria Policlinico (AOU), Italy
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10
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Prokop JW, Jdanov V, Savage L, Morris M, Lamb N, VanSickle E, Stenger CL, Rajasekaran S, Bupp CP. Computational and Experimental Analysis of Genetic Variants. Compr Physiol 2022; 12:3303-3336. [PMID: 35578967 DOI: 10.1002/cphy.c210012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Vladislav Jdanov
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lane Savage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.,Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
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11
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Fan J, Bellon M, Ju M, Zhao L, Wei M, Fu L, Nicot C. Clinical significance of FBXW7 loss of function in human cancers. Mol Cancer 2022; 21:87. [PMID: 35346215 PMCID: PMC8962602 DOI: 10.1186/s12943-022-01548-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
FBXW7 (F-Box and WD Repeat Domain Containing 7) (also referred to as FBW7 or hCDC4) is a component of the Skp1-Cdc53 / Cullin-F-box-protein complex (SCF/β-TrCP). As a member of the F-box protein family, FBXW7 serves a role in phosphorylation-dependent ubiquitination and proteasome degradation of oncoproteins that play critical role(s) in oncogenesis. FBXW7 affects many regulatory functions involved in cell survival, cell proliferation, tumor invasion, DNA damage repair, genomic instability and telomere biology. This thorough review of current literature details how FBXW7 expression and functions are regulated through multiple mechanisms and how that ultimately drives tumorigenesis in a wide array of cell types. The clinical significance of FBXW7 is highlighted by the fact that FBXW7 is frequently inactivated in human lung, colon, and hematopoietic cancers. The loss of FBXW7 can serve as an independent prognostic marker and is significantly correlated with the resistance of tumor cells to chemotherapeutic agents and poorer disease outcomes. Recent evidence shows that genetic mutation of FBXW7 differentially affects the degradation of specific cellular targets resulting in a distinct and specific pattern of activation/inactivation of cell signaling pathways. The clinical significance of FBXW7 mutations in the context of tumor development, progression, and resistance to therapies as well as opportunities for targeted therapies is discussed.
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Affiliation(s)
- Jingyi Fan
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute; Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.,Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Marcia Bellon
- Department of Pathology and Laboratory Medicine, Center for Viral Pathogenesis, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute; Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
| | - Christophe Nicot
- Department of Pathology and Laboratory Medicine, Center for Viral Pathogenesis, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA.
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12
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Thirmanne HN, Wu F, Janssens DH, Swanger J, Diab A, Feldman H, Amezquita RA, Gottardo R, Paddison PJ, Henikoff S, Clurman BE. Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations. eLife 2022; 11:74338. [PMID: 35225231 PMCID: PMC8926403 DOI: 10.7554/elife.74338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/16/2022] [Indexed: 11/30/2022] Open
Abstract
The Fbw7 ubiquitin ligase targets many proteins for proteasomal degradation, which include oncogenic transcription factors (TFs) (e.g., c-Myc, c-Jun, and Notch). Fbw7 is a tumor suppressor and tumors often contain mutations in FBXW7, the gene that encodes Fbw7. The complexity of its substrate network has obscured the mechanisms of Fbw7-associated tumorigenesis, yet this understanding is needed for developing therapies. We used an integrated approach employing RNA-Seq and high-resolution mapping (cleavage under target and release using nuclease) of histone modifications and TF occupancy (c-Jun and c-Myc) to examine the combinatorial effects of misregulated Fbw7 substrates in colorectal cancer (CRC) cells with engineered tumor-associated FBXW7 null or missense mutations. Both Fbw7 mutations caused widespread transcriptional changes associated with active chromatin and altered TF occupancy: some were common to both Fbw7 mutant cell lines, whereas others were mutation specific. We identified loci where both Jun and Myc were coregulated by Fbw7, suggesting that substrates may have synergistic effects. One coregulated gene was CIITA, the master regulator of MHC Class II gene expression. Fbw7 loss increased MHC Class II expression and Fbw7 mutations were correlated with increased CIITA expression in TCGA colorectal tumors and cell lines, which may have immunotherapeutic implications for Fbw7-associated cancers. Analogous studies in neural stem cells in which FBXW7 had been acutely deleted closely mirrored the results in CRC cells. Gene set enrichment analyses revealed Fbw7-associated pathways that were conserved across both cell types that may reflect fundamental Fbw7 functions. These analyses provide a framework for understanding normal and neoplastic context-specific Fbw7 functions.
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Affiliation(s)
| | - Feinan Wu
- Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Derek H Janssens
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jherek Swanger
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Ahmed Diab
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Heather Feldman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Robert A Amezquita
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Bruce E Clurman
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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13
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Chang KT, Jezek J, Campbell AN, Stieg DC, Kiss ZA, Kemper K, Jiang P, Lee HO, Kruger WD, van Hasselt PM, Strich R. Aberrant cyclin C nuclear release induces mitochondrial fragmentation and dysfunction in MED13L syndrome fibroblasts. iScience 2022; 25:103823. [PMID: 35198885 PMCID: PMC8844603 DOI: 10.1016/j.isci.2022.103823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/02/2021] [Accepted: 01/21/2022] [Indexed: 12/25/2022] Open
Abstract
MED13L syndrome is a haploinsufficiency developmental disorder characterized by intellectual disability, heart malformation, and hypotonia. MED13L controls transcription by tethering the cyclin C-Cdk8 kinase module (CKM) to the Mediator complex. In addition, cyclin C has CKM-independent roles in the cytoplasm directing stress-induced mitochondrial fragmentation and regulated cell death. Unstressed MED13L S1497 F/fs patient fibroblasts exhibited aberrant cytoplasmic cyclin C localization, mitochondrial fragmentation, and a 6-fold reduction in respiration. In addition, the fibroblasts exhibited reduced mtDNA copy number, reduction in mitochondrial membrane integrity, and hypersensitivity to oxidative stress. Finally, transcriptional analysis of MED13L mutant fibroblasts revealed reduced mRNA levels for several genes necessary for normal mitochondrial function. Pharmacological or genetic approaches preventing cyclin C-mitochondrial localization corrected the fragmented mitochondrial phenotype and partially restored organelle function. In conclusion, this study found that mitochondrial dysfunction is an underlying defect in cells harboring the MED13L S1497 F/fs allele and identified cyclin C mis-localization as the likely cause. These results provide a new avenue for understanding this disorder.
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Affiliation(s)
- Kai-Ti Chang
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Jan Jezek
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Alicia N Campbell
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Zachary A Kiss
- Department of Medicine, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Kevin Kemper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Ping Jiang
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Hyung-Ok Lee
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Peter M van Hasselt
- Department of Metabolic and Endocrine Disease, University of Utrecht Medical Center, Utrecht, 3584 CX, the Netherlands
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
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14
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The Mediator kinase module: an interface between cell signaling and transcription. Trends Biochem Sci 2022; 47:314-327. [DOI: 10.1016/j.tibs.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
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15
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Lan H, Sun Y. Tumor Suppressor FBXW7 and Its Regulation of DNA Damage Response and Repair. Front Cell Dev Biol 2021; 9:751574. [PMID: 34760892 PMCID: PMC8573206 DOI: 10.3389/fcell.2021.751574] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/05/2021] [Indexed: 12/21/2022] Open
Abstract
The proper DNA damage response (DDR) and repair are the central molecular mechanisms for the maintenance of cellular homeostasis and genomic integrity. The abnormality in this process is frequently observed in human cancers, and is an important contributing factor to cancer development. FBXW7 is an F-box protein serving as the substrate recognition component of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase. By selectively targeting many oncoproteins for proteasome-mediated degradation, FBXW7 acts as a typical tumor suppressor. Recent studies have demonstrated that FBXW7 also plays critical roles in the process of DDR and repair. In this review, we first briefly introduce the processes of protein ubiquitylation by SCFFBXW7 and DDR/repair, then provide an overview of the molecular characteristics of FBXW7. We next discuss how FBXW7 regulates the process of DDR and repair, and its translational implication. Finally, we propose few future perspectives to further elucidate the role of FBXW7 in regulation of a variety of biological processes and tumorigenesis, and to design a number of approaches for FBXW7 reactivation in a subset of human cancers for potential anticancer therapy.
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Affiliation(s)
- Huiyin Lan
- Department of Thoracic Radiation Oncology, Zhejiang Cancer Hospital, Cancer Hospital of University of Chinese Academy of Sciences, Hangzhou, China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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16
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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17
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Lee JEA, Parsons LM, Quinn LM. MYC function and regulation in flies: how Drosophila has enlightened MYC cancer biology. AIMS GENETICS 2021. [DOI: 10.3934/genet.2014.1.81] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractProgress in our understanding of the complex signaling events driving human cancer would have been unimaginably slow without discoveries from Drosophila genetic studies. Significantly, many of the signaling pathways now synonymous with cancer biology were first identified as a result of elegant screens for genes fundamental to metazoan development. Indeed the name given to many core cancer-signaling cascades tells of their history as developmental patterning regulators in flies—e.g. Wingless (Wnt), Notch and Hippo. Moreover, astonishing insight has been gained into these complex signaling networks, and many other classic oncogenic signaling networks (e.g. EGFR/RAS/RAF/ERK, InR/PI3K/AKT/TOR), using sophisticated fly genetics. Of course if we are to understand how these signaling pathways drive cancer, we must determine the downstream program(s) of gene expression activated to promote the cell and tissue over growth fundamental to cancer. Here we discuss one commonality between each of these pathways: they are all implicated as upstream activators of the highly conserved MYC oncogene and transcription factor. MYC can drive all aspects of cell growth and cell cycle progression during animal development. MYC is estimated to be dysregulated in over 50% of all cancers, underscoring the importance of elucidating the signals activating MYC. We also discuss the FUBP1/FIR/FUSE system, which acts as a ‘cruise control’ on the MYC promoter to control RNA Polymerase II pausing and, therefore, MYC transcription in response to the developmental signaling environment. Importantly, the striking conservation between humans and flies within these major axes of MYC regulation has made Drosophila an extremely valuable model organism for cancer research. We therefore discuss how Drosophila studies have helped determine the validity of signaling pathways regulating MYC in vivo using sophisticated genetics, and continue to provide novel insight into cancer biology.
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Affiliation(s)
- Jue Er Amanda Lee
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Linda May Parsons
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Leonie M. Quinn
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
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18
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van de Plassche SR, de Brouwer APM. MED12-Related (Neuro)Developmental Disorders: A Question of Causality. Genes (Basel) 2021; 12:663. [PMID: 33925166 PMCID: PMC8146938 DOI: 10.3390/genes12050663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
MED12 is a member of the Mediator complex that is involved in the regulation of transcription. Missense variants in MED12 cause FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome, as well as non-syndromic intellectual disability (ID) in hemizygous males. Recently, female patients with de novo missense variants and de novo protein truncating variants in MED12 were described, resulting in a clinical spectrum centered around ID and Hardikar syndrome without ID. The missense variants are found throughout MED12, whether they are inherited in hemizygous males or de novo in females. They can result in syndromic or nonsyndromic ID. The de novo nonsense variants resulting in Hardikar syndrome that is characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, are found more N-terminally, whereas the more C-terminally positioned variants are de novo protein truncating variants that cause a severe, syndromic phenotype consisting of ID, facial dysmorphism, short stature, skeletal abnormalities, feeding difficulties, and variable other abnormalities. This broad range of distinct phenotypes calls for a method to distinguish between pathogenic and non-pathogenic variants in MED12. We propose an isogenic iNeuron model to establish the unique gene expression patterns that are associated with the specific MED12 variants. The discovery of these patterns would help in future diagnostics and determine the causality of the MED12 variants.
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Affiliation(s)
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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19
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Roliński M, Montaldo NP, Aksu ME, Fordyce Martin S, Brambilla A, Kunath N, Johansen J, Erlandsen S, Liabbak NB, Rian K, Bjørås M, Sætrom P, van Loon B. Loss of Mediator complex subunit 13 (MED13) promotes resistance to alkylation through cyclin D1 upregulation. Nucleic Acids Res 2021; 49:1470-1484. [PMID: 33444446 PMCID: PMC7897519 DOI: 10.1093/nar/gkaa1289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 12/19/2022] Open
Abstract
Alkylating drugs are among the most often used chemotherapeutics. While cancer cells frequently develop resistance to alkylation treatments, detailed understanding of mechanisms that lead to the resistance is limited. Here, by using genome-wide CRISPR-Cas9 based screen, we identify transcriptional Mediator complex subunit 13 (MED13) as a novel modulator of alkylation response. The alkylation exposure causes significant MED13 downregulation, while complete loss of MED13 results in reduced apoptosis and resistance to alkylating agents. Transcriptome analysis identified cyclin D1 (CCND1) as one of the highly overexpressed genes in MED13 knock-out (KO) cells, characterized by shorter G1 phase. MED13 is able to bind to CCND1 regulatory elements thus influencing the expression. The resistance of MED13 KO cells is directly dependent on the cyclin D1 overexpression, and its down-regulation is sufficient to re-sensitize the cells to alkylating agents. We further demonstrate the therapeutic potential of MED13-mediated response, by applying combinatory treatment with CDK8/19 inhibitor Senexin A. Importantly, the treatment with Senexin A stabilizes MED13, and in combination with alkylating agents significantly reduces viability of cancer cells. In summary, our findings identify novel alkylation stress response mechanism dependent on MED13 and cyclin D1 that can serve as basis for development of innovative therapeutic strategies.
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Affiliation(s)
- Miłosz Roliński
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Nicola Pietro Montaldo
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Merdane Ezgi Aksu
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Sarah L Fordyce Martin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Alessandro Brambilla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Nicolas Kunath
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Jostein Johansen
- Bioinformatics core facility - BioCore; Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Sten Even Erlandsen
- Genomics core facility, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Nina-Beate Liabbak
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Kristin Rian
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
- Department of Microbiology, Oslo University Hospital, 0027 Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
- Bioinformatics core facility - BioCore; Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- Department of Computer Science, Faculty of Information Technology and Electrical Engineering, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Barbara van Loon
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
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20
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Zhou W, Cai H, Li J, Xu H, Wang X, Men H, Zheng Y, Cai L. Potential roles of mediator Complex Subunit 13 in Cardiac Diseases. Int J Biol Sci 2021; 17:328-338. [PMID: 33390853 PMCID: PMC7757031 DOI: 10.7150/ijbs.52290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022] Open
Abstract
Mediator complex subunit 13 (MED13, previously known as THRAP1 and TRAP240) is a subunit of the cyclin-dependent kinase 8 (CDK8) kinase module in the eukaryotic mediator complex. MED13 has been known to play critical roles in cell cycle, development, and growth. The purpose of this review is to comprehensively discuss its newly identified potential roles in myocardial energy metabolism and non-metabolic cardiovascular diseases. Evidence indicates that cardiac MED13 mainly participates in the regulation of nuclear receptor signaling, which drives the transcription of genes involved in modulating cardiac and systemic energy homeostasis. MED13 is also associated with several pathological conditions, such as metabolic syndrome and thyroid disease-associated heart failure. Therefore, MED13 constitutes a potential therapeutic target for the regulation of metabolic disorders and other cardiovascular diseases.
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Affiliation(s)
- Wenqian Zhou
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - He Cai
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China
| | - Jia Li
- Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA.,Department of Nephrology, the First Hospital of Jilin University, Changchun 130021, China
| | - He Xu
- Department of Respiratory Medicine, the First Hospital of Jilin University (Eastern Division), Changchun 130031, China
| | - Xiang Wang
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - Hongbo Men
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - Yang Zheng
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China
| | - Lu Cai
- Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA.,Department of Pharmacology and Toxicology, the University of Louisville, Louisville, KY 40202, USA
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21
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Straub J, Venigalla S, Newman JJ. Mediator's Kinase Module: A Modular Regulator of Cell Fate. Stem Cells Dev 2020; 29:1535-1551. [PMID: 33161841 DOI: 10.1089/scd.2020.0164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multi-subunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules. One critical module of the Mediator complex is the kinase module consisting of four subunits: MED12, MED13, CDK8, and CCNC. The kinase module exists in variable association with the 26-subunit Mediator core and affects transcription through phosphorylation of transcription factors and by controlling Mediator structure and function. Many studies have shown the kinase module to be a key player in the maintenance of stem cells that is distinct from a general role in transcription. Genetic studies have revealed that dysregulation of this kinase subunit contributes to the development of many human diseases. In this review, we discuss the importance of the Mediator kinase module by examining how this module functions with the more recently identified transcriptional super-enhancers, how changes in the kinase module and its activity can lead to the development of human disease, and the role of this unique module in directing and maintaining cell state. As we look to use stem cells to understand human development and treat human disease through both cell-based therapies and tissue engineering, we need to remain aware of the on-going research and address critical gaps in knowledge related to the molecular mechanisms that control cell fate.
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Affiliation(s)
- Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
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22
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Zhu Y, Huang P, Guo P, Chong L, Yu G, Sun X, Hu T, Li Y, Hsu CC, Tang K, Zhou Y, Zhao C, Gao W, Tao WA, Mengiste T, Zhu JK. CDK8 is associated with RAP2.6 and SnRK2.6 and positively modulates abscisic acid signaling and drought response in Arabidopsis. THE NEW PHYTOLOGIST 2020; 228:1573-1590. [PMID: 32619295 DOI: 10.1111/nph.16787] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
CDK8 is a key subunit of Mediator complex, a large multiprotein complex that is a fundamental part of the conserved eukaryotic transcriptional machinery. However, the biological functions of CDK8 in plant abiotic stress responses remain largely unexplored. Here, we demonstrated CDK8 as a critical regulator in the abscisic acid (ABA) signaling and drought response pathways in Arabidopsis. Compared to wild-type, cdk8 mutants showed reduced sensitivity to ABA, impaired stomatal apertures and hypersensitivity to drought stress. Transcriptomic and chromatin immunoprecipitation analysis revealed that CDK8 positively regulates the transcription of several ABA-responsive genes, probably through promoting the recruitment of RNA polymerase II to their promoters. We discovered that both CDK8 and SnRK2.6 interact physically with an ERF/AP2 transcription factor RAP2.6, which can directly bind to the promoters of RD29A and COLD-REGULATED 15A (COR15A) with GCC or DRE elements, thereby promoting their expression. Importantly, we also showed that CDK8 is essential for the ABA-induced expression of RAP2.6 and RAP2.6-mediated upregulation of ABA-responsive genes, indicating that CDK8 could link the SnRK2.6-mediated ABA signaling to RNA polymerase II to promote immediate transcriptional response to ABA and drought signals. Overall, our data provide new insights into the roles of CDK8 in modulating ABA signaling and drought responses.
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Affiliation(s)
- Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Pengcheng Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Pengcheng Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Gaobo Yu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163711, China
| | - Xiaoli Sun
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163711, China
| | - Tao Hu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Gao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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23
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De Nardi L, Faletra F, D'Adamo AP, Bianco AMR, Athanasakis E, Bruno I, Barbi E. Could the MED13 mutations manifest as a Kabuki-like syndrome? Am J Med Genet A 2020; 185:584-590. [PMID: 33258286 DOI: 10.1002/ajmg.a.61994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 10/24/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
MED13-related disorder is a new neurodevelopmental disorder recently described in literature, which belongs to the group of CDK8-kinase module genes-associated conditions. It is characterized by variable intellectual disability and/or developmental delays, especially in language. Autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), eye or vision problems, hypotonia, mild congenital hearth abnormalities and dysmorphisms have been described among individuals with MED13 mutations. We report the case of a 13-year-old girl who received a previous clinical diagnosis of Kabuki syndrome (KS) without mutations in classic KS genes. After a whole exome sequencing (WES) analysis a de novo missense mutation in MED13 (c.C979T; p.Pro327Ser) was found. This variant has been once described in literature as accountable for a novel neurodevelopmental disorder. The aim of this report is to improve clinical delineation of MED13-related condition and to explore differences and similarities between KS spectrum and MED13-related disorders.
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Affiliation(s)
| | - Flavio Faletra
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Adamo Pio D'Adamo
- University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | | | | | - Irene Bruno
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Egidio Barbi
- University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
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24
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Wu D, Zhang Z, Chen X, Yan Y, Liu X. Angel or Devil ? - CDK8 as the new drug target. Eur J Med Chem 2020; 213:113043. [PMID: 33257171 DOI: 10.1016/j.ejmech.2020.113043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022]
Abstract
Cyclin-dependent kinase 8 (CDK8) plays an momentous role in transcription regulation by forming kinase module or transcription factor phosphorylation. A large number of evidences have identified CDK8 as an important factor in cancer occurrence and development. In addition, CDK8 also participates in the regulation of cancer cell stress response to radiotherapy and chemotherapy, assists tumor cell invasion, metastasis, and drug resistance. Therefore, CDK8 is regarded as a promising target for cancer therapy. Most studies in recent years supported the role of CDK8 as a carcinogen, however, under certain conditions, CDK8 exists as a tumor suppressor. The functional diversity of CDK8 and its exceptional role in different types of cancer have aroused great interest from scientists but even more controversy during the discovery of CDK8 inhibitors. In addition, CDK8 appears to be an effective target for inflammation diseases and immune system disorders. Therefore, we summarized the research results of CDK8, involving physiological/pathogenic mechanisms and the development status of compounds targeting CDK8, provide a reference for the feasibility evaluation of CDK8 as a therapeutic target, and guidance for researchers who are involved in this field for the first time.
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Affiliation(s)
- Dan Wu
- School of Biological Engineering, Hefei Technology College, Hefei, 238000, PR China
| | - Zhaoyan Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Yaoyao Yan
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xinhua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China.
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25
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Stieg DC, Cooper KF, Strich R. The extent of cyclin C promoter occupancy directs changes in stress-dependent transcription. J Biol Chem 2020; 295:16280-16291. [PMID: 32934007 DOI: 10.1074/jbc.ra120.015215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a detachable Mediator subunit composed of cyclin C and one each of paralogs Cdk8/Cdk19, Med12/Med12L, and Med13/Med13L. Our previous RNA-Seq studies demonstrated that cyclin C represses a subset of hydrogen peroxide-induced genes under normal conditions but is involved in activating other loci following stress. Here, we show that cyclin C directs this transcriptional reprograming through changes in its promoter occupancy. Following peroxide stress, cyclin C promoter occupancy increased for genes it activates while decreasing at loci it represses under normal conditions. Promoter occupancy of other CKM components generally mirrored cyclin C, indicating that the CKM moves as a single unit. It has previously been shown that some cyclin C leaves the nucleus following cytotoxic stress to induce mitochondrial fragmentation and apoptosis. We observed that CKM integrity appeared compromised at a subset of repressed promoters, suggesting a source of cyclin C that is targeted for nuclear release. Interestingly, mTOR inhibition induced a new pattern of cyclin C promoter occupancy indicating that this control is fine-tuned to the individual stress. Using inhibitors, we found that Cdk8 kinase activity is not required for CKM movement or repression but was necessary for full gene activation. In conclusion, this study revealed that different stress stimuli elicit specific changes in CKM promoter occupancy correlating to altered transcriptional outputs. Finally, although CKM components were recruited or expelled from promoters as a unit, heterogeneity was observed at individual promoters, suggesting a mechanism to generate gene- and stress-specific responses.
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Affiliation(s)
- David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA.
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26
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Zhang N, Song Y, Xu Y, Liu J, Shen Y, Zhou L, Yu J, Yang M. MED13L integrates Mediator-regulated epigenetic control into lung cancer radiosensitivity. Am J Cancer Res 2020; 10:9378-9394. [PMID: 32802198 PMCID: PMC7415817 DOI: 10.7150/thno.48247] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
To date, efforts to improve non-small-cell lung cancer (NSCLC) outcomes with increased radiation dose have not been successful. Identification of novel druggable targets that are capable to modulate NSCLC radiosensitivity may provide a way forward. Mediator complex is implicated in gene expression control, but it remains unclear how Mediator dysfunction is involved in cancer radiotherapy. Methods: The biologic functions of miR-4497, MED13L and PRKCA in NSCLC radiosensitivity were examined through biochemical assays including gene expression profilling, cell proliferation assay, colony formation assay, wound healing assay, transwell assay, dual luciferase reporter assay, xenograft models, immunoprecipitation, and chromatin immunoprecipitation sequencing. Clinical implications of miR-4497, MED13L and PRKCA in radiosensitivity were evaluated in NSCLC patients treated with concurrent chemoradiotherapy or radiotherapy alone. Results: We found that radiation can trigger disassemble of Mediator complex via silencing of MED13L by miR-4497 in NSCLC. Although not interrupting structure integrity of the core Mediator or the CDK8 kinase module, suppression of MED13L attenuated their physical interactions and reduced recruitment of acetyltransferase P300 to chromatin via Mediator. Silencing of MED13L therefore diminishes global H3K27ac signals written by P300, activities of enhancer and/or promoters and expression of multiple oncogenes, especially PRKCA. Inhibition of PRKCA expression potentiates the killing effect of radiotherapy in vitro and in vivo. Remarkably, high PRKCA expression in NSCLC tissues is correlated with poor prognosis of patients received radiotherapy. Conclusions: Our study linking PRKCA to radiosensitivity through a novel mechanism may enable the rational targeting of PRKCA to unlock therapeutic potentials of NSCLC.
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27
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Kuang Y, Golan O, Preusse K, Cain B, Christensen CJ, Salomone J, Campbell I, Okwubido-Williams FV, Hass MR, Yuan Z, Eafergan N, Moberg KH, Kovall RA, Kopan R, Sprinzak D, Gebelein B. Enhancer architecture sensitizes cell specific responses to Notch gene dose via a bind and discard mechanism. eLife 2020; 9:53659. [PMID: 32297857 PMCID: PMC7213981 DOI: 10.7554/elife.53659] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/15/2020] [Indexed: 11/13/2022] Open
Abstract
Notch pathway haploinsufficiency can cause severe developmental syndromes with highly variable penetrance. Currently, we have a limited mechanistic understanding of phenotype variability due to gene dosage. Here, we unexpectedly found that inserting an enhancer containing pioneer transcription factor sites coupled to Notch dimer sites can induce a subset of Notch haploinsufficiency phenotypes in Drosophila with wild type Notch gene dose. Using Drosophila genetics, we show that this enhancer induces Notch phenotypes in a Cdk8-dependent, transcription-independent manner. We further combined mathematical modeling with quantitative trait and expression analysis to build a model that describes how changes in Notch signal production versus degradation differentially impact cellular outcomes that require long versus short signal duration. Altogether, these findings support a 'bind and discard' mechanism in which enhancers with specific binding sites promote rapid Cdk8-dependent Notch turnover, and thereby reduce Notch-dependent transcription at other loci and sensitize tissues to gene dose based upon signal duration.
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Affiliation(s)
- Yi Kuang
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, United States
| | - Ohad Golan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Kristina Preusse
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, United States
| | - Collin J Christensen
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, United States.,Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Ian Campbell
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, United States
| | | | - Matthew R Hass
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Nathanel Eafergan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, United States
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States
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28
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Yumimoto K, Nakayama KI. Recent insight into the role of FBXW7 as a tumor suppressor. Semin Cancer Biol 2020; 67:1-15. [PMID: 32113998 DOI: 10.1016/j.semcancer.2020.02.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/15/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022]
Abstract
FBXW7 (also known as Fbw7, Sel10, hCDC4, or hAgo) is a tumor suppressor and the most frequently mutated member of the F-box protein family in human cancers. FBXW7 functions as the substrate recognition component of an SCF-type E3 ubiquitin ligase. It specifically controls the proteasome-mediated degradation of many oncoproteins such as c-MYC, NOTCH, KLF5, cyclin E, c-JUN, and MCL1. In this review, we summarize the molecular and biological features of FBXW7 and its substrates as well as the impact of mutations of FBXW7 on cancer development. We also address the clinical potential of anticancer therapy targeting FBXW7.
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Affiliation(s)
- Kanae Yumimoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan.
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29
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Zhang N, Xu J, Liu X, Liang W, Xin M, Du J, Hu Z, Peng H, Guo W, Ni Z, Sun Q, Yao Y. Identification of HSP90C as a substrate of E3 ligase TaSAP5 through ubiquitylome profiling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110170. [PMID: 31481192 DOI: 10.1016/j.plantsci.2019.110170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
Protein ubiquitination is a major post-translational modification important for diverse biological processes. In wheat (Triticum aestivum) and Arabidopsis thaliana, STRESS-ASSOCIATED PROTEIN 5 (SAP5) is involved in drought tolerance, acting as an E3 ubiquitin ligase to target DRIP and MBP-1 for degradation. To identify further target proteins of SAP5, we implemented two independent approaches in this work. We used ubiquitylome capture with a di-Gly-Lys antibody-based peptide enrichment and affinity purification with a polyubiquitin antibody coupled with mass spectrometry to elucidate the SAP5-dependent ubiquitylation of its target proteins in response to osmotic stress. Wild type or TaSAP5-overexpressing Arabidopsis line, which was more tolerant to osmotic stress according to our previous study, were used here. We identified HSP90C (chloroplast heat shock protein 90) as a substrate of TaSAP5. Further biochemical experiments indicated that TaSAP5 interacts with HSP90C and mediates its degradation by the 26S proteasome. Our work also demonstrates that ubiquitylome profiling is an effective approach to search for substrates of the TaSAP5 E3 ubiquitin ligase when heterologously expressed in Arabidopsis.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jing Xu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wenxing Liang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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30
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Fiore D, Piscopo C, Proto MC, Vasaturo M, Dal Piaz F, Fusco BM, Pagano C, Laezza C, Bifulco M, Gazzerro P. N6-Isopentenyladenosine Inhibits Colorectal Cancer and Improves Sensitivity to 5-Fluorouracil-Targeting FBXW7 Tumor Suppressor. Cancers (Basel) 2019; 11:cancers11101456. [PMID: 31569395 PMCID: PMC6826543 DOI: 10.3390/cancers11101456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022] Open
Abstract
N6-isopentenyladenosine has been shown to exert potent in vitro antitumor activity on different human cancers, including colorectal cancer. Although some potential biochemical targets have been identified, its precise mechanism of action remains unclear. We found that N6-isopentenyladenosine affects colorectal cancer proliferation in in vitro models carrying different mutational status of FBXW7 and TP53 genes, and in HCT116 xenografts in SCID mice, by increasing the expression of the well-established tumor suppressor FBXW7, a component of the SCF-E3 ubiquitin ligase complex that promotes degradation of various oncoproteins and transcription factors, such as c-Myc, SREBP and Mcl1. Corroborating our previous studies, we identified for the first time the FBXW7/SREBP/FDPS axis as a target of the compound. Pull down of ubiquitinated proteins, immunoprecipitation and luciferase assays, reveal that through the increase of FBXW7/c-Myc binding, N6-isopentenyladenosine induces the ubiquitination of c-Myc, inhibiting its transcriptional activity. Moreover, in FBXW7- and TP53-wild type cells, N6-isopentenyladenosine strongly synergizes with 5-Fluorouracil to inhibit colon cancer growth in vitro. Our results provide novel insights into the molecular mechanism of N6-isopentenyladenosine, revealing its multi-targeting antitumor action, in vitro and in vivo. Restoring of FBXW7 tumor-suppressor represents a valid therapeutic tool, enabling N6-isopentenyladenosine as optimizable compound for patient-personalized therapies in colorectal cancer.
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Affiliation(s)
- Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy.
| | - Chiara Piscopo
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy.
- PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy.
| | - Michele Vasaturo
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy.
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Baronissi (Salerno), Italy.
| | | | - Cristina Pagano
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Chiara Laezza
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
- Institute of Endocrinology and Experimental Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), 80131 Naples, Italy.
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy.
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31
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Youn DY, Xiaoli AM, Kwon H, Yang F, Pessin JE. The subunit assembly state of the Mediator complex is nutrient-regulated and is dysregulated in a genetic model of insulin resistance and obesity. J Biol Chem 2019; 294:9076-9083. [PMID: 31028171 PMCID: PMC6556571 DOI: 10.1074/jbc.ra119.007850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 01/22/2023] Open
Abstract
The Mediator complex plays a critical role in the regulation of transcription by linking transcription factors to RNA polymerase II. By examining mouse livers, we have found that in the fasted state, the Mediator complex exists primarily as an approximately 1.2-MDa complex, consistent with the size of the large Mediator complex, whereas following feeding, it converts to an approximately 600-kDa complex, consistent with the size of the core Mediator complex. This dynamic change is due to the dissociation and degradation of the kinase module that includes the MED13, MED12, cyclin-dependent kinase 8 (CDK8), and cyclin C (CCNC) subunits. The dissociation and degradation of the kinase module are dependent upon nutrient activation of mTORC1 that is necessary for the induction of lipogenic gene expression because pharmacological or genetic inhibition of mTORC1 in the fed state restores the kinase module. The degradation but not dissociation of the kinase module depends upon the E3 ligase, SCFFBW7 In addition, genetically insulin-resistant and obese db/db mice in the fasted state displayed elevated lipogenic gene expression and loss of the kinase module that was reversed following mTORC1 inhibition. These data demonstrate that the assembly state of the Mediator complex undergoes physiologic regulation during normal cycles of fasting and feeding in the mouse liver. Furthermore, the assembly state of the Mediator complex is dysregulated in states of obesity and insulin resistance.
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Affiliation(s)
- Dou Yeon Youn
- From the Departments of Medicine
- Molecular Pharmacology and
| | - Alus M Xiaoli
- From the Departments of Medicine
- Developmental and Molecular Biology, and
| | - Hyokjoon Kwon
- the Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901
| | - Fajun Yang
- From the Departments of Medicine
- Developmental and Molecular Biology, and
- the Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Jeffrey E Pessin
- From the Departments of Medicine,
- Molecular Pharmacology and
- the Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461 and
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Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts. G3-GENES GENOMES GENETICS 2019; 9:1901-1908. [PMID: 31036676 PMCID: PMC6553531 DOI: 10.1534/g3.119.400077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The transcriptional changes that occur in response to oxidative stress help direct the decision to maintain cell viability or enter a cell death pathway. Cyclin C-Cdk8 is a conserved kinase that associates with the RNA polymerase II Mediator complex that stimulates or represses transcription depending on the locus. In response to oxidative stress, cyclin C, but not Cdk8, displays partial translocation into the cytoplasm. These findings open the possibility that cyclin C relocalization is a regulatory mechanism governing oxidative stress-induced transcriptional changes. In the present study, the cyclin C-dependent transcriptome was determined and compared to transcriptional changes occurring in oxidatively stressed Mus musculus embryonic fibroblasts. We observed a similar number (∼2000) of genes up or downregulated in oxidatively stressed cells. Induced genes include cellular repair/survival factors while repressed loci were generally involved in proliferation or differentiation. Depleting cyclin C in unstressed cells produced an approximately equal number of genes (∼2400) that were repressed by, or whose transcription required, cyclin C. Consistent with the possibility that cyclin C nuclear release contributes to transcriptional remodeling in response to oxidative stress, we found that 37% cyclin C-dependent genes were downregulated following stress. Moreover, 20% of cyclin C- repressed genes were induced in response to stress. These findings are consistent with a model that cyclin C relocalization to the cytoplasm, and corresponding inactivation of Cdk8, represents a regulatory mechanism to repress and stimulate transcription of stress-responsive genes.
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Wang Y, An Y, Ma Y, Guo J. F-box/WD-40 repeat-containing protein 7: A potential target in the progression and treatment of gastrointestinal malignancy. Oncol Lett 2019; 17:3625-3634. [PMID: 30881487 PMCID: PMC6403509 DOI: 10.3892/ol.2019.10036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/21/2019] [Indexed: 12/21/2022] Open
Abstract
Cancer is a principal cause of human morbidity and mortality, with gastrointestinal malignancies, in particular, resulting in a marked number of tumor-associated mortalities. The progression of gastrointestinal malignancy is regulated by a variety of aberrantly expressed proteins, a number of which facilitate tumor progression, whereas, others function as tumor suppressors. The detection of such proteins not only contributes to the early diagnosis of cancer, they may additionally serve as potential therapeutic targets. In normal tissues, numerous proteins encoded by proto-oncoproteins are degraded by ubiquitylation enzymes, consisting of F-box/WD-40 repeat-containing protein 7 (Fbw7) and other proteins, thus avoiding tumorigenesis and maintaining homeostasis. In tumor tissues, the downregulation of Fbw7, caused by various factors, leads to disorders in ubiquitinase synthesis, which may induce tumor progression and chemoresistance, particularly in gastrointestinal malignancy. Therefore, an in-depth study of the regulatory mechanisms involved in disorders of Fbw7 expression and the role of Fbw7 in chemoresistance of gastrointestinal tumors may suggest improvements for early diagnostic screening and targeted therapy.
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Affiliation(s)
- Yizhi Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Yang An
- Department of Anesthesia, First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yi Ma
- Department of Thoracic Surgery, First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Junchao Guo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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Sardar S, Kerr A, Vaartjes D, Moltved ER, Karosiene E, Gupta R, Andersson Å. The oncoprotein TBX3 is controlling severity in experimental arthritis. Arthritis Res Ther 2019; 21:16. [PMID: 30630509 PMCID: PMC6329118 DOI: 10.1186/s13075-018-1797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Development of autoimmune diseases is the result of a complex interplay between hereditary and environmental factors, with multiple genes contributing to the pathogenesis in human disease and in experimental models for disease. The T-box protein 3 is a transcriptional repressor essential during early embryonic development, in the formation of bone and additional organ systems, and in tumorigenesis. METHODS With the aim to find novel genes important for autoimmune inflammation, we have performed genetic studies of collagen-induced arthritis (CIA), a mouse experimental model for rheumatoid arthritis. RESULTS We showed that a small genetic fragment on mouse chromosome 5, including Tbx3 and three additional protein-coding genes, is linked to severe arthritis and high titers of anti-collagen antibodies. Gene expression studies have revealed differential expression of Tbx3 in B cells, where low expression was accompanied by a higher B cell response upon B cell receptor stimulation in vitro. Furthermore, we showed that serum TBX3 levels rise concomitantly with increasing severity of CIA. CONCLUSIONS From these results, we suggest that TBX3 is a novel factor important for the regulation of gene transcription in the immune system and that genetic polymorphisms, resulting in lower expression of Tbx3, are contributing to a more severe form of CIA and high titers of autoantibodies. We also propose TBX3 as a putative diagnostic biomarker for rheumatoid arthritis.
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Affiliation(s)
- Samra Sardar
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Nordic Bioscience A/S, Copenhagen, Denmark
| | - Alish Kerr
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Nuritas, Dublin, Ireland
| | - Daniëlle Vaartjes
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Riis Moltved
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: IQVIA, Copenhagen, Denmark Denmark
| | - Edita Karosiene
- Department of Bio and Health Informatics, Kemitorvet 208, Technical University of Denmark, Lyngby, Denmark
- Present address: Novo Nordisk A/S, Copenhagen, Denmark
| | - Ramneek Gupta
- Department of Bio and Health Informatics, Kemitorvet 208, Technical University of Denmark, Lyngby, Denmark
| | - Åsa Andersson
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Rydberg Laboratory of Applied Sciences, ETN, Halmstad University, Halmstad, Sweden
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Ježek J, Smethurst DGJ, Stieg DC, Kiss ZAC, Hanley SE, Ganesan V, Chang KT, Cooper KF, Strich R. Cyclin C: The Story of a Non-Cycling Cyclin. BIOLOGY 2019; 8:biology8010003. [PMID: 30621145 PMCID: PMC6466611 DOI: 10.3390/biology8010003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
The class I cyclin family is a well-studied group of structurally conserved proteins that interact with their associated cyclin-dependent kinases (Cdks) to regulate different stages of cell cycle progression depending on their oscillating expression levels. However, the role of class II cyclins, which primarily act as transcription factors and whose expression remains constant throughout the cell cycle, is less well understood. As a classic example of a transcriptional cyclin, cyclin C forms a regulatory sub-complex with its partner kinase Cdk8 and two accessory subunits Med12 and Med13 called the Cdk8-dependent kinase module (CKM). The CKM reversibly associates with the multi-subunit transcriptional coactivator complex, the Mediator, to modulate RNA polymerase II-dependent transcription. Apart from its transcriptional regulatory function, recent research has revealed a novel signaling role for cyclin C at the mitochondria. Upon oxidative stress, cyclin C leaves the nucleus and directly activates the guanosine 5’-triphosphatase (GTPase) Drp1, or Dnm1 in yeast, to induce mitochondrial fragmentation. Importantly, cyclin C-induced mitochondrial fission was found to increase sensitivity of both mammalian and yeast cells to apoptosis. Here, we review and discuss the biology of cyclin C, focusing mainly on its transcriptional and non-transcriptional roles in tumor promotion or suppression.
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Affiliation(s)
- Jan Ježek
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Daniel G J Smethurst
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - David C Stieg
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Z A C Kiss
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Sara E Hanley
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Vidyaramanan Ganesan
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Kai-Ti Chang
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Katrina F Cooper
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Randy Strich
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
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Abstract
The Mediator-associated kinases CDK8 and CDK19 function in the context of three additional proteins: CCNC and MED12, which activate CDK8/CDK19 kinase function, and MED13, which enables their association with the Mediator complex. The Mediator kinases affect RNA polymerase II (pol II) transcription indirectly, through phosphorylation of transcription factors and by controlling Mediator structure and function. In this review, we discuss cellular roles of the Mediator kinases and mechanisms that enable their biological functions. We focus on sequence-specific, DNA-binding transcription factors and other Mediator kinase substrates, and how CDK8 or CDK19 may enable metabolic and transcriptional reprogramming through enhancers and chromatin looping. We also summarize Mediator kinase inhibitors and their therapeutic potential. Throughout, we note conserved and divergent functions between yeast and mammalian CDK8, and highlight many aspects of kinase module function that remain enigmatic, ranging from potential roles in pol II promoter-proximal pausing to liquid-liquid phase separation.
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Affiliation(s)
- Charli B Fant
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
| | - Dylan J Taatjes
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
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Desbois M, Crawley O, Evans PR, Baker ST, Masuho I, Yasuda R, Grill B. PAM forms an atypical SCF ubiquitin ligase complex that ubiquitinates and degrades NMNAT2. J Biol Chem 2018; 293:13897-13909. [PMID: 29997255 DOI: 10.1074/jbc.ra118.002176] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/13/2018] [Indexed: 12/20/2022] Open
Abstract
PHR (PAM/Highwire/RPM-1) proteins are conserved RING E3 ubiquitin ligases that function in developmental processes, such as axon termination and synapse formation, as well as axon degeneration. At present, our understanding of how PHR proteins form ubiquitin ligase complexes remains incomplete. Although genetic studies indicate NMNAT2 is an important mediator of PHR protein function in axon degeneration, it remains unknown how PHR proteins inhibit NMNAT2. Here, we decipher the biochemical basis for how the human PHR protein PAM, also called MYCBP2, forms a noncanonical Skp/Cullin/F-box (SCF) complex that contains the F-box protein FBXO45 and SKP1 but lacks CUL1. We show FBXO45 does not simply function in substrate recognition but is important for assembly of the PAM/FBXO45/SKP1 complex. Interestingly, we demonstrate a novel role for SKP1 as an auxiliary component of the target recognition module that enhances binding of FBXO45 to NMNAT2. Finally, we provide biochemical evidence that PAM polyubiquitinates NMNAT2 and regulates NMNAT2 protein stability and degradation by the proteasome.
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Affiliation(s)
- Muriel Desbois
- From the Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458 and
| | - Oliver Crawley
- From the Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458 and
| | - Paul R Evans
- the Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458
| | - Scott T Baker
- From the Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458 and
| | - Ikuo Masuho
- From the Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458 and
| | - Ryohei Yasuda
- the Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458
| | - Brock Grill
- From the Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458 and
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Priyadarshini R, Hussain M, Attri P, Kaur E, Tripathi V, Priya S, Dhapola P, Saha D, Madhavan V, Chowdhury S, Sengupta S. BLM Potentiates c-Jun Degradation and Alters Its Function as an Oncogenic Transcription Factor. Cell Rep 2018; 24:947-961.e7. [DOI: 10.1016/j.celrep.2018.06.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 05/07/2018] [Accepted: 06/25/2018] [Indexed: 12/16/2022] Open
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Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. BIOCHEMISTRY (MOSCOW) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
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Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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40
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Dimitrova E, Kondo T, Feldmann A, Nakayama M, Koseki Y, Konietzny R, Kessler BM, Koseki H, Klose RJ. FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. eLife 2018; 7:e37084. [PMID: 29809150 PMCID: PMC5997449 DOI: 10.7554/elife.37084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/26/2018] [Indexed: 01/05/2023] Open
Abstract
CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.
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Affiliation(s)
- Emilia Dimitrova
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Takashi Kondo
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | | | - Manabu Nakayama
- Department of Technology DevelopmentKazusa DNA Research InstituteKisarazuJapan
| | - Yoko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Rebecca Konietzny
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
- CRESTJapan Science and Technology AgencyKawaguchiJapan
| | - Robert J Klose
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
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Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P, Simon MEH, Smith R, Hurst JA, McLaughlin H, Person R, Crunk A, Wangler MF, Streff H, Symonds JD, Zuberi SM, Elliott KS, Sanders VR, Masunga A, Hopkin RJ, Dubbs HA, Ortiz-Gonzalez XR, Pfundt R, Brunner HG, Fisher SE, Kleefstra T, Cooper GM. De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder. Hum Genet 2018; 137:375-388. [PMID: 29740699 PMCID: PMC5973976 DOI: 10.1007/s00439-018-1887-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/21/2018] [Indexed: 01/15/2023]
Abstract
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.
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Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Krysta L Engel
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paulien Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Jane A Hurst
- Great Ormond Street Hospital for Children, London, UK
| | | | | | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | | | - Victoria R Sanders
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Abigail Masunga
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell Rep 2018; 20:2201-2214. [PMID: 28854368 PMCID: PMC5583477 DOI: 10.1016/j.celrep.2017.08.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 07/06/2017] [Accepted: 07/24/2017] [Indexed: 12/15/2022] Open
Abstract
Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average enabled the de novo construction of a functional protein correlation network, which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.
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Affiliation(s)
| | - Steven P Williams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Clara Alsinet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Nanne Aben
- Division of Molecular Carcinogenesis, Computational Cancer Biology, the Netherlands Cancer Institute, Amsterdam 1066, the Netherlands
| | - Fatemeh Zamanzad Ghavidel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Computational Cancer Biology, the Netherlands Cancer Institute, Amsterdam 1066, the Netherlands
| | - Michael Schubert
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Stacey Price
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - James C Wright
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lu Yu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Mi Yang
- Faculty of Medicine, Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52057, Germany
| | - Rodrigo Dienstmann
- Computational Oncology, Sage Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA; Oncology Data Science Group, Vall d'Hebron Institute of Oncology, Barcelona 08035, Spain
| | - Justin Guinney
- Computational Oncology, Sage Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Mercedes Pardo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, Computational Cancer Biology, the Netherlands Cancer Institute, Amsterdam 1066, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft 2628, the Netherlands
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Faculty of Medicine, Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52057, Germany
| | - Ultan McDermott
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jyoti S Choudhary
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK.
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Smol T, Petit F, Piton A, Keren B, Sanlaville D, Afenjar A, Baker S, Bedoukian EC, Bhoj EJ, Bonneau D, Boudry-Labis E, Bouquillon S, Boute-Benejean O, Caumes R, Chatron N, Colson C, Coubes C, Coutton C, Devillard F, Dieux-Coeslier A, Doco-Fenzy M, Ewans LJ, Faivre L, Fassi E, Field M, Fournier C, Francannet C, Genevieve D, Giurgea I, Goldenberg A, Green AK, Guerrot AM, Heron D, Isidor B, Keena BA, Krock BL, Kuentz P, Lapi E, Le Meur N, Lesca G, Li D, Marey I, Mignot C, Nava C, Nesbitt A, Nicolas G, Roche-Lestienne C, Roscioli T, Satre V, Santani A, Stefanova M, Steinwall Larsen S, Saugier-Veber P, Picker-Minh S, Thuillier C, Verloes A, Vieville G, Wenzel M, Willems M, Whalen S, Zarate YA, Ziegler A, Manouvrier-Hanu S, Kalscheuer VM, Gerard B, Ghoumid J. MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype. Neurogenetics 2018; 19:93-103. [PMID: 29511999 DOI: 10.1007/s10048-018-0541-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/17/2018] [Indexed: 12/30/2022]
Abstract
Molecular anomalies in MED13L, leading to haploinsufficiency, have been reported in patients with moderate to severe intellectual disability (ID) and distinct facial features, with or without congenital heart defects. Phenotype of the patients was referred to "MED13L haploinsufficiency syndrome." Missense variants in MED13L were already previously described to cause the MED13L-related syndrome, but only in a limited number of patients. Here we report 36 patients with MED13L molecular anomaly, recruited through an international collaboration between centers of expertise for developmental anomalies. All patients presented with intellectual disability and severe language impairment. Hypotonia, ataxia, and recognizable facial gestalt were frequent findings, but not congenital heart defects. We identified seven de novo missense variations, in addition to protein-truncating variants and intragenic deletions. Missense variants clustered in two mutation hot-spots, i.e., exons 15-17 and 25-31. We found that patients carrying missense mutations had more frequently epilepsy and showed a more severe phenotype. This study ascertains missense variations in MED13L as a cause for MED13L-related intellectual disability and improves the clinical delineation of the condition.
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Affiliation(s)
- T Smol
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France.,University of Lille, EA 7364-RADEME, Lille, France
| | - F Petit
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - A Piton
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - B Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - D Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - A Afenjar
- Service de Génétique, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - S Baker
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E C Bedoukian
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E J Bhoj
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - D Bonneau
- Service de Génétique, CHU d'Angers, Angers, France
| | - E Boudry-Labis
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - S Bouquillon
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - O Boute-Benejean
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - R Caumes
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - N Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - C Colson
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - C Coubes
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - C Coutton
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - F Devillard
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Dieux-Coeslier
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - M Doco-Fenzy
- Service de Génétique, EA3801, SFR-CAP Santé, CHU de Reims, Reims, France
| | - L J Ewans
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - L Faivre
- Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement, CHU Dijon, Dijon, France.,Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - M Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - C Fournier
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - C Francannet
- Service de Génétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - D Genevieve
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - I Giurgea
- Service de Génétique, Hôpital Trousseau, AP-HP, Paris, France
| | - A Goldenberg
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - A K Green
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - A M Guerrot
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - D Heron
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - B Isidor
- Service de Génétique Médicale, Unité de Génétique Clinique, CHU de Nantes, Nantes, France
| | - B A Keena
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - B L Krock
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - P Kuentz
- Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - N Le Meur
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - G Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Li
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - I Marey
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Nava
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - A Nesbitt
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - G Nicolas
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - C Roche-Lestienne
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - T Roscioli
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - V Satre
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Santani
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - S Steinwall Larsen
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - P Saugier-Veber
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - S Picker-Minh
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - C Thuillier
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - A Verloes
- Unité Fonctionnelle de Génétique Clinique, Hôpital Robert Debré, AP-HP, Paris, France
| | - G Vieville
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - M Wenzel
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Willems
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - S Whalen
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - Y A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Ziegler
- Service de Génétique, CHU d'Angers, Angers, France
| | - S Manouvrier-Hanu
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - V M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - B Gerard
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jamal Ghoumid
- University of Lille, EA 7364-RADEME, Lille, France. .,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France.
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Amoasii L, Olson EN, Bassel-Duby R. Control of Muscle Metabolism by the Mediator Complex. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a029843. [PMID: 28432117 DOI: 10.1101/cshperspect.a029843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exercise represents an energetic challenge to whole-body homeostasis. In skeletal muscle, exercise activates a variety of signaling pathways that culminate in the nucleus to regulate genes involved in metabolism and contractility; however, much remains to be learned about the transcriptional effectors of exercise. Mediator is a multiprotein complex that links signal-dependent transcription factors and other transcriptional regulators with the basal transcriptional machinery, thereby serving as a transcriptional "hub." In this article, we discuss recent studies highlighting the role of Mediator subunits in metabolic regulation and glucose metabolism, as well as exercise responsiveness. Elucidation of the roles of Mediator subunits in metabolic control has revealed new mechanisms and molecular targets for the modulation of metabolism and metabolic disorders.
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Affiliation(s)
- Leonela Amoasii
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 7539-9148
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 7539-9148
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 7539-9148
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Jiménez-Romero S, Carrasco-Salas P, Benítez-Burraco A. Language and Cognitive Impairment Associated with a Novel p.Cys63Arg Change in the MED13L Transcriptional Regulator. Mol Syndromol 2018; 9:83-91. [PMID: 29593475 DOI: 10.1159/000485638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in the MED13L gene, which encodes a subunit of a transcriptional regulatory complex, result in a complex phenotype entailing physical and cognitive anomalies. Deep language impairment has been reported in affected individuals, mostly in patients with copy number variations. We report on a child with a nonsynonymous p.Cys63Arg change in MED13L (chr12:116675396A>G, GRCh37) who exhibits profound language impairment in the expressive domain, cognitive delay, behavioral disturbances, and an autism-like phenotype. Because of the brain areas in which MED13L is expressed and because of the functional links between MED13L and the products of selected candidate genes for cognitive disorders involving language deficits, the proband's linguistic phenotype may result from changes in a functional network important for language development and evolution.
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Affiliation(s)
- Salud Jiménez-Romero
- Maimónides Institute of Biomedical Research, Córdoba, Spain.,Department of Psychology, University of Córdoba, Córdoba, Spain
| | | | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
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Abstract
Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.
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Affiliation(s)
- Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, Commissariat à l'énergie Atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), University Paris Sud, University Paris Saclay, F-91198 Gif-sur-Yvette, France
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Stieg DC, Willis SD, Ganesan V, Ong KL, Scuorzo J, Song M, Grose J, Strich R, Cooper KF. A complex molecular switch directs stress-induced cyclin C nuclear release through SCF Grr1-mediated degradation of Med13. Mol Biol Cell 2017; 29:363-375. [PMID: 29212878 PMCID: PMC5996960 DOI: 10.1091/mbc.e17-08-0493] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/22/2017] [Accepted: 12/01/2017] [Indexed: 02/03/2023] Open
Abstract
In response to oxidative stress, cells must choose either to live or to die. Here we show that the E3 ligase SCFGrr1 mediates the destruction of Med13, which releases cyclin C into the cytoplasm and results in cell death. The Med13 SCF degron is most likely primed by the Cdk8 kinase and marked for destruction by the MAPK Slt2. In response to oxidative stress, cells decide whether to mount a survival or cell death response. The conserved cyclin C and its kinase partner Cdk8 play a key role in this decision. Both are members of the Cdk8 kinase module, which, with Med12 and Med13, associate with the core mediator complex of RNA polymerase II. In Saccharomyces cerevisiae, oxidative stress triggers Med13 destruction, which thereafter releases cyclin C into the cytoplasm. Cytoplasmic cyclin C associates with mitochondria, where it induces hyperfragmentation and regulated cell death. In this report, we show that residues 742–844 of Med13’s 600–amino acid intrinsic disordered region (IDR) both directs cyclin C-Cdk8 association and serves as the degron that mediates ubiquitin ligase SCFGrr1-dependent destruction of Med13 following oxidative stress. Here, cyclin C-Cdk8 phosphorylation of Med13 most likely primes the phosphodegron for destruction. Next, pro-oxidant stimulation of the cell wall integrity pathway MAP kinase Slt2 initially phosphorylates cyclin C to trigger its release from Med13. Thereafter, Med13 itself is modified by Slt2 to stimulate SCFGrr1-mediated destruction. Taken together, these results support a model in which this IDR of Med13 plays a key role in controlling a molecular switch that dictates cell fate following exposure to adverse environments.
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Affiliation(s)
- David C Stieg
- Department of Molecular Biology, Graduate School of Biological Sciences, Rowan University, Stratford, NJ 08084
| | - Stephen D Willis
- Department of Molecular Biology, Graduate School of Biological Sciences, Rowan University, Stratford, NJ 08084
| | - Vidyaramanan Ganesan
- Department of Molecular Biology, Graduate School of Biological Sciences, Rowan University, Stratford, NJ 08084
| | - Kai Li Ong
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Joseph Scuorzo
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Mia Song
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084
| | - Julianne Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biological Sciences, Rowan University, Stratford, NJ 08084
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biological Sciences, Rowan University, Stratford, NJ 08084
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Gordon CT, Chopra M, Oufadem M, Alibeu O, Bras M, Boddaert N, Bole-Feysot C, Nitschké P, Abadie V, Lyonnet S, Amiel J. MED13L
loss-of-function variants in two patients with syndromic Pierre Robin sequence. Am J Med Genet A 2017; 176:181-186. [DOI: 10.1002/ajmg.a.38536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/06/2017] [Accepted: 10/15/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Christopher T. Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
| | - Maya Chopra
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
| | - Myriam Oufadem
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
| | - Olivier Alibeu
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Genomics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Marc Bras
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Bioinformatics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Nathalie Boddaert
- Service de Radiologie Pédiatrique; Hôpital Necker-Enfants Malades, AP-HP; Paris France
- INSERM U1000 and UMR 1163; Institut Imagine; Paris France
| | - Christine Bole-Feysot
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Genomics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Bioinformatics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Véronique Abadie
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Service de Pédiatrie Générale; Hôpital Necker-Enfants Malades, AP-HP; Paris France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
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49
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Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol 2017; 27:765-783. [DOI: 10.1016/j.tcb.2017.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
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50
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Abstract
In eukaryotes, RNA polymerase II (pol II) transcribes all protein-coding genes and many noncoding RNAs. Whereas many factors contribute to the regulation of pol II activity, the Mediator complex is required for expression of most, if not all, pol II transcripts. Structural characterization of Mediator is challenging due to its large size (∼20 subunits in yeast and 26 subunits in humans) and conformational flexibility. However, recent studies have revealed structural details at higher resolution. Here, we summarize recent findings and place in context with previous results, highlighting regions within Mediator that are important for regulating its structure and function.
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Affiliation(s)
- Thomas M Harper
- From the Department of Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Dylan J Taatjes
- From the Department of Biochemistry, University of Colorado, Boulder, Colorado 80303
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