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Cui JH, Kwan JZJ, Faghihi A, Nguyen TF, Teves SS. Functional divergence of TBP homologs through distinct DNA-binding dynamics. Nucleic Acids Res 2025; 53:gkaf436. [PMID: 40396489 PMCID: PMC12093143 DOI: 10.1093/nar/gkaf436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 04/02/2025] [Accepted: 05/12/2025] [Indexed: 05/22/2025] Open
Abstract
The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to the increasingly complex gene expression regulation across evolutionary time. To determine the molecular mechanisms of species- and tissue-specificity for homologous TBPs, we examined the ability of yeast TBP and murine TBP paralogs to replace the endogenous TBP in mouse embryonic stem cells (mESCs). We show that, despite the high conservation in the DNA-binding domain among the homologs, they cannot fully rescue the lethality of TBP depletion in mESCs, which correlates with their inability to support RNA Pol III transcription. Furthermore, we show that the homologs differentially support stress-induced transcription reprogramming, with the divergent N-terminal domain playing a role in modulating changes in transcriptional response. Lastly, we show that the homologs have vastly different DNA binding dynamics, suggesting a potential mechanism for the distinct functional behavior observed among the homologs. Taken together, these data show a remarkable balance between flexibility and essentiality for the different functions of homologous TBP in eukaryotic transcription.
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Affiliation(s)
- Jieying H Cui
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T 1Z3, Canada
| | - James Z J Kwan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T 1Z3, Canada
| | - Armin Faghihi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T 1Z3, Canada
| | - Thomas F Nguyen
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T 1Z3, Canada
| | - Sheila S Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T 1Z3, Canada
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Li J, Zhang J, Zhao S, Wang Q, Liu R, Chen X, He Z. Combined metabolome and transcriptome analysis provides molecular insights into reproductive process in Chuanxiang Black and Landrace pigs. Front Genet 2025; 16:1501876. [PMID: 40092557 PMCID: PMC11906663 DOI: 10.3389/fgene.2025.1501876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 02/07/2025] [Indexed: 03/19/2025] Open
Abstract
Testes are crucial for male reproduction, and transcriptomic and metabolomic analyses can help identify genes and pathways linked to reproductive performance differences in pig breeds. The present study was conducted to identify the differentially expressed genes and differentially accumulated metabolites (DAMs) through transcriptomic and metabolomic analyses of testicular tissues in Chuanxiang Black and Landrace pigs. Six testis tissue samples from each pig breed were used for transcriptomic analysis. Further liquid chromatography-mass spectrometry analysis was performed for targeted metabolomic analysis to identify differential metabolites in both breeds. RNA-sequencing data identified a total of 6,233 DEGs, including 3,417 upregulated and 2,816 downregulated genes in Chuanxiang Black compared to Landrace pigs. Comparative pathway enrichment analyses revealed that many DEGs and DAMs were associated with critical reproductive pathways, especially those related to male gametogenesis, spermatogenesis, sexual reproduction, development, and reproductive processes. Three major pathways related to signal transduction (PI3K-Akt, Rap1, and MAPK signaling pathways), lipid metabolism (linoleic acid and arachidonic acid metabolism), and cytokine-cytokine receptor interaction were identified as differentially enriched pathways in Chuanxiang Black pigs. Differential circRNA target gene enrichment analysis revealed 4,179 DEGs, including 3,022 genes involved in biological processes, 477 in cellular components, and 680 in molecular functions. Differential analysis of miRNA between the two groups revealed 2,512 DEGs, including 1,628 upregulated and 884 downregulated genes. Both miRNA and circRNA were involved in enriched KEGG pathways mainly including signaling pathways (cAMP signaling pathways, calcium signaling pathways), endocrine secretion (aldosterone synthesis and secretion and GnRH secretion), and signaling molecules and interaction (ECM-receptor interaction). These findings revealed that both circRNA and miRNA play a crucial role in regulating the differential gene expression related to reproductive processes in Chuanxiang Black compared to Landrace pigs.
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Yi T, Wang C, Ye X, Lin J, Lin C, Qin F, Yang W, Ye Y, Ning D, Lan J, Li H, Luo C, Ma J, Wei Z. METTL16 inhibits pancreatic cancer proliferation and metastasis by promoting MROH8 RNA stability and inhibiting CAPN2 expression - experimental studies. Int J Surg 2024; 110:7701-7719. [PMID: 39434688 PMCID: PMC11634154 DOI: 10.1097/js9.0000000000002116] [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: 07/14/2024] [Accepted: 09/30/2024] [Indexed: 10/23/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) modification plays a crucial role in the progression of various cancers, including pancreatic cancer, by regulating gene expression. However, the specific mechanisms by which m6A affects pancreatic cancer metastasis remain unclear. This study aims to elucidate the role of METTL16, an m6A writer gene, in regulating core genes such as CAPN2 and MROH8, influencing tumor growth and metastasis. MATERIALS AND METHODS Transcriptomic data from pancreatic cancer patients in The Cancer Genome Atlas (TCGA) were analyzed to identify m6A-related genes. We performed correlation and survival analyses to uncover core genes influenced by m6A expression. Functional assays, including METTL16 knockdown and overexpression experiments, were conducted in pancreatic cancer cell lines, patient-derived organoids, and animal models. Immunofluorescence, co-immunoprecipitation (Co-IP), and m6A-specific quantitative PCR were used to validate protein interactions and m6A modifications. Chromatin immunoprecipitation (ChIP) analysis was utilized to investigate transcription factor binding at gene promoter regions. RESULTS METTL16 and METTL3 were identified as key m6A regulators associated with improved prognosis in pancreatic cancer patients ( P <0.05). CAPN2, CHMP2B, ITGA3, ITGA6, ITPR1, and RAC1 were identified as core genes linked to m6A expression, all significantly correlated with patient prognosis ( P <0.05). METTL16 overexpression significantly inhibited tumor growth and metastasis ( P <0.001) by downregulating CAPN2 through an indirect mechanism involving the transcription factor TBP and the gene MROH8. MROH8 negatively regulated CAPN2 by promoting TBP degradation, with METTL16 enhancing MROH8 mRNA stability through m6A modifications ( P <0.01). Functional assays demonstrated that METTL16 and YTHDC2 (an m6A reader) collaboratively enhanced MROH8 mRNA stability, thereby inhibiting CAPN2 expression and reducing tumor proliferation and metastasis ( P <0.001). CONCLUSION This study reveals a novel regulatory axis involving METTL16, MROH8, and TBP that modulates CAPN2 expression, contributing to the suppression of pancreatic cancer progression. The METTL16-MROH8-TBP-CAPN2 pathway offers potential therapeutic targets for pancreatic cancer treatment, highlighting the significance of m6A modifications in tumor regulation. Further clinical validation is needed to confirm these findings in human patients.
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Affiliation(s)
- Tingzhuang Yi
- Department of Oncology, Affiliated Hospital of YouJiang Medical University for Nationalities/Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Baise, Guangxi, People’s Republic of China
| | - Chunming Wang
- Department of Hepatopancreatobiliary & Vascular Surgery, The Second Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Xia Ye
- Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Jie Lin
- Department of Oncology, Affiliated Hospital of YouJiang Medical University for Nationalities/Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Baise, Guangxi, People’s Republic of China
| | - Cheng Lin
- Department of Oncology, Affiliated Hospital of YouJiang Medical University for Nationalities/Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Baise, Guangxi, People’s Republic of China
| | - Fengzhen Qin
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Wanlin Yang
- Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Yulu Ye
- Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Dengchong Ning
- Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Jinyan Lan
- Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Huafu Li
- Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, UK
| | - Chunying Luo
- Department of Oncology, Affiliated Hospital of YouJiang Medical University for Nationalities/Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Baise, Guangxi, People’s Republic of China
| | - Jian Ma
- Department of Hepatobiliary Surgery, Jining Public Health Medical Center, Jining, People’s Republic of China
| | - Zhongheng Wei
- Department of Oncology, Affiliated Hospital of YouJiang Medical University for Nationalities/Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Baise, Guangxi, People’s Republic of China
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Vilstrup AP, Gupta A, Rasmussen AJ, Ebert A, Riedelbauch S, Lukassen MV, Hayashi R, Andersen P. A germline PAF1 paralog complex ensures cell type-specific gene expression. Genes Dev 2024; 38:866-886. [PMID: 39332828 PMCID: PMC11535153 DOI: 10.1101/gad.351930.124] [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: 05/15/2024] [Accepted: 08/27/2024] [Indexed: 09/29/2024]
Abstract
Animal germline development and fertility rely on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream from such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here, we show that efficient termination of tTAF-activated transcription relies on testis-specific paralogs of canonical polymerase-associated factor 1 complex (PAF1C) proteins, which form a testis-specific PAF1C (tPAF). Consequently, tPAF mutants show aberrant expression of hundreds of downstream genes due to read-in transcription. Furthermore, tPAF facilitates expression of Y-linked male fertility factor genes and thus serves to maintain spermatocyte-specific gene expression. Consistently, tPAF is required for the segregation of meiotic chromosomes and male fertility. Supported by comparative in vivo protein interaction assays, we provide a mechanistic model for the functional divergence of tPAF and the PAF1C and identify transcription termination as a developmentally regulated process required for germline-specific gene expression.
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Affiliation(s)
- Astrid Pold Vilstrup
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Archica Gupta
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Anna Jon Rasmussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Anja Ebert
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Sebastian Riedelbauch
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Rippei Hayashi
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory 2601, Australia;
| | - Peter Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
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Sharma S, Kapoor S, Ansari A, Tyagi AK. The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses. Crit Rev Biochem Mol Biol 2024; 59:267-309. [PMID: 39361782 PMCID: PMC12051360 DOI: 10.1080/10409238.2024.2408562] [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: 05/31/2024] [Revised: 09/03/2024] [Accepted: 09/21/2024] [Indexed: 10/05/2024]
Abstract
In eukaryotes, general transcription factors (GTFs) enable recruitment of RNA polymerase II (RNA Pol II) to core promoters to facilitate initiation of transcription. Extensive research in mammals and yeast has unveiled their significance in basal transcription as well as in diverse biological processes. Unlike mammals and yeast, plant GTFs exhibit remarkable degree of variability and flexibility. This is because plant GTFs and GTF subunits are often encoded by multigene families, introducing complexity to transcriptional regulation at both cellular and biological levels. This review provides insights into the general transcription mechanism, GTF composition, and their cellular functions. It further highlights the involvement of RNA Pol II-related GTFs in plant development and stress responses. Studies reveal that GTFs act as important regulators of gene expression in specific developmental processes and help equip plants with resilience against adverse environmental conditions. Their functions may be direct or mediated through their cofactor nature. The versatility of GTFs in controlling gene expression, and thereby influencing specific traits, adds to the intricate complexity inherent in the plant system.
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Affiliation(s)
- Shivam Sharma
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Sanjay Kapoor
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, USA
| | - Akhilesh Kumar Tyagi
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Wu R, Jia Q, Guo Y, Lin Y, Liu J, Chen J, Yan Q, Yuan N, Xue C, Chen X, Yuan X. Characterization of TBP and TAFs in Mungbean ( Vigna radiata L.) and Their Potential Involvement in Abiotic Stress Response. Int J Mol Sci 2024; 25:9558. [PMID: 39273505 PMCID: PMC11394781 DOI: 10.3390/ijms25179558] [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: 08/02/2024] [Revised: 08/31/2024] [Accepted: 09/01/2024] [Indexed: 09/15/2024] Open
Abstract
The TATA-box binding protein (TBP) and TBP-associated factors (TAFs) constitute the transcription factor IID (TFIID), a crucial component of RNA polymerase II, essential for transcription initiation and regulation. Several TFIID subunits are shared with the Spt-Ada-Gcn5-acetyltransferase (SAGA) coactivator complex. Recent research has revealed the roles of TBP and TAFs in organogenesis and stress adaptation. In this study, we identified 1 TBP and 21 putative TAFs in the mungbean genome, among which VrTAF5, VrTAF6, VrTAF8, VrTAF9, VrTAF14, and VrTAF15 have paralogous genes. Their potential involvement in abiotic stress responses was also investigated here, including high salinity, water deficit, heat, and cold. The findings indicated that distinct genes exerted predominant influences in the response to different abiotic stresses through potentially unique mechanisms. Specifically, under salt stress, VrTBP, VrTAF2, and VrTAF15-1 were strongly induced, while VrTAF10, VrTAF11, and VrTAF13 acted as negative regulators. In the case of water-deficit stress, it was likely that VrTAF1, VrTAF2, VrTAF5-2, VrTAF9, and VrTAF15-1 were primarily involved. Additionally, in response to changes in ambient temperature, it was possible that genes such as VrTAF5-1, VrTAF6-1, VrTAF9-2, VrTAF10, VrTAF13, VrTAF14b-2, and VrTAF15-1 might play a dominant role. This comprehensive exploration of VrTBP and VrTAFs can offer a new perspective on understanding plant stress responses and provide valuable insights into breeding improvement.
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Affiliation(s)
- Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiyuan Jia
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingjian Guo
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jinyang Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Na Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.W.); (Q.J.); (Y.G.); (Y.L.); (J.L.); (J.C.); (Q.Y.); (N.Y.); (C.X.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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Wang B, Mount S. Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR Genom Bioinform 2024; 6:lqae099. [PMID: 39131816 PMCID: PMC11310860 DOI: 10.1093/nargab/lqae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/13/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of distinct alternative motifs, or are best described by base composition. Here we apply the latent Dirichlet allocation (LDA) mixture model to nucleotide sequences. Using positions in an alignment of human or Drosophila splice sites as samples, we show that LDA readily identifies motifs, including such elusive cases as the intron branch site. Using whole sequences with positional k-mers as features, LDA can identify sequence subtypes enriched in long vs. short introns. LDA with bulk k-mers can reliably distinguish reading frame and species of origin in coding sequences from humans and Drosophila. We find that LDA is a useful model for describing heterogeneous signals, for assigning individual sequences to subtypes, and for identifying and characterizing sequences that do not fit recognized subtypes. Because LDA topic models are interpretable, they also aid the discovery of new motifs, even those present in a small fraction of samples. In summary, LDA can identify and characterize signals in nucleotide sequences, including candidate regulatory factors involved in biological processes.
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Affiliation(s)
- Bixuan Wang
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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8
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Du D, Zhong F, Liu L. Enhancing recognition and interpretation of functional phenotypic sequences through fine-tuning pre-trained genomic models. J Transl Med 2024; 22:756. [PMID: 39135093 PMCID: PMC11318145 DOI: 10.1186/s12967-024-05567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 08/03/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Decoding human genomic sequences requires comprehensive analysis of DNA sequence functionality. Through computational and experimental approaches, researchers have studied the genotype-phenotype relationship and generate important datasets that help unravel complicated genetic blueprints. Thus, the recently developed artificial intelligence methods can be used to interpret the functions of those DNA sequences. METHODS This study explores the use of deep learning, particularly pre-trained genomic models like DNA_bert_6 and human_gpt2-v1, in interpreting and representing human genome sequences. Initially, we meticulously constructed multiple datasets linking genotypes and phenotypes to fine-tune those models for precise DNA sequence classification. Additionally, we evaluate the influence of sequence length on classification results and analyze the impact of feature extraction in the hidden layers of our model using the HERV dataset. To enhance our understanding of phenotype-specific patterns recognized by the model, we perform enrichment, pathogenicity and conservation analyzes of specific motifs in the human endogenous retrovirus (HERV) sequence with high average local representation weight (ALRW) scores. RESULTS We have constructed multiple genotype-phenotype datasets displaying commendable classification performance in comparison with random genomic sequences, particularly in the HERV dataset, which achieved binary and multi-classification accuracies and F1 values exceeding 0.935 and 0.888, respectively. Notably, the fine-tuning of the HERV dataset not only improved our ability to identify and distinguish diverse information types within DNA sequences but also successfully identified specific motifs associated with neurological disorders and cancers in regions with high ALRW scores. Subsequent analysis of these motifs shed light on the adaptive responses of species to environmental pressures and their co-evolution with pathogens. CONCLUSIONS These findings highlight the potential of pre-trained genomic models in learning DNA sequence representations, particularly when utilizing the HERV dataset, and provide valuable insights for future research endeavors. This study represents an innovative strategy that combines pre-trained genomic model representations with classical methods for analyzing the functionality of genome sequences, thereby promoting cross-fertilization between genomics and artificial intelligence.
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Affiliation(s)
- Duo Du
- School of Basic Medical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Fan Zhong
- School of Basic Medical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Lei Liu
- School of Basic Medical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
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Elpek GO. Tata-box-binding protein-associated factor 15 as a new potential marker in gastrointestinal tumors. World J Gastroenterol 2024; 30:3367-3372. [PMID: 39091718 PMCID: PMC11290397 DOI: 10.3748/wjg.v30.i28.3367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 07/24/2024] Open
Abstract
In this editorial, the roles of tata-box-binding protein-associated factor 15 (TAF15) in oncogenesis, tumor behavior, and as a therapeutic target in cancers in the context of gastrointestinal (GI) tumors are discussed concerning the publication by Guo et al. TAF15 is a member of the FET protein family with a comprehensive range of cellular processes. Besides, evidence has shown that TAF15 is involved in many diseases, including cancers. TAF15 contributes to carcinogenesis and tumor behavior in many tumors. Besides, its relationship with the mitogen-activated protein kinases (MAPK) signaling pathway makes TAF15 a new target for therapy. Although, the fact that there is few studies investigating the expression of TAF15 constitutes a potential limitation in GI system, the association of TAF15 expression with aggressive tumor behavior and, similar to other organ tumors, the influence of TAF15 on the MAPK signaling pathway emphasize that this protein could serve as a new molecular biomarker to predict tumor behavior and target therapeutic intervention in GI cancers. In conclusion, more studies should be performed to better understand the prognostic and therapeutic role of TAF15 in GI tumors, especially in tumors resistant to therapy.
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Affiliation(s)
- Gulsum Ozlem Elpek
- Department of Pathology, Akdeniz University Medical School, Antalya 07070, Türkiye
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10
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Tan Y, Huang Y, Xu C, Huang X, Li S, Yin Z. Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson). BMC Genomics 2024; 25:357. [PMID: 38600449 PMCID: PMC11005167 DOI: 10.1186/s12864-024-10281-7] [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: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production. RESULTS We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction. CONCLUSION Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.
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Affiliation(s)
- Yuting Tan
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Yunyan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Chunhui Xu
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Shibao Li
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Zhaozheng Yin
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China.
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11
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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12
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Ricci S, Pacífico C, Kreuzer-Redmer S, Castillo-Lopez E, Rivera-Chacon R, Sener-Aydemir A, Rossi G, Galosi L, Biagini L, Schwartz-Zimmermann HE, Berthiller F, Reisinger N, Petri RM, Zebeli Q. Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle. FEMS Microbiol Ecol 2024; 100:fiae006. [PMID: 38281064 PMCID: PMC10858391 DOI: 10.1093/femsec/fiae006] [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: 04/17/2023] [Revised: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.
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Affiliation(s)
- Sara Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Susanne Kreuzer-Redmer
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Ezequias Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Raul Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Arife Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Livio Galosi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Lucia Biagini
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Heidi E Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, 3430 Tulln an der Donau, Austria
| | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, 3430 Tulln an der Donau, Austria
| | - Nicole Reisinger
- dsm-firmenich,
Animal Health and Nutrition R&D Center, Technopark 1, 3430 Tulln an der Donau, Austria
| | - Renee M Petri
- Agriculture and Agri-Food Canada,
Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec J1M 0C8, Canada
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
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13
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Kwan JZ, Nguyen TF, Teves SS. TBP facilitates RNA Polymerase I transcription following mitosis. RNA Biol 2024; 21:42-51. [PMID: 38958280 PMCID: PMC11225926 DOI: 10.1080/15476286.2024.2375097] [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] [Revised: 04/09/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.
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Affiliation(s)
- James Z.J. Kwan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Thomas F. Nguyen
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sheila S. Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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14
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Du T, Li M, Chen L, Shao Y, Wang Y, Wang H, Ma J, Yao B. Compound heterozygous mutations in TBPL2 were identified in an infertile woman with impaired ovarian folliculogenesis. J Assist Reprod Genet 2023; 40:2945-2950. [PMID: 37804378 PMCID: PMC10656374 DOI: 10.1007/s10815-023-02961-2] [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: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023] Open
Abstract
OBJECTIVE A 32-year-old female was diagnosed with unexplained primary infertility for 10 years. She had roughly normal basal hormone levels, but her basal follicle-stimulating hormone (FSH) levels were elevated. In addition, the level of anti-Mullerian hormone was within the normal range, and she had undergone two failed oocyte collection attempts. We aimed to investigate the genetic cause of female infertility in patients with impaired ovarian folliculogenesis. METHODS Genomic DNA was extracted from the peripheral blood of the patient and her family members. Whole-exome sequencing was performed on the patient, and TBPL2 mutations were identified and confirmed by Sanger sequencing. The Exome Aggregation Consortium (ExAC) Browser and Genome Aggregation Database (gnomAD) Browser Beta were used to search the allele frequencies of the variants in the general population. The harmfulness of the mutations was analyzed by SIFT, Mutation Taster, and CADD software. RESULT One novel mutation, c.802C > T (p. Arg268Ter), and one known variant, c.788 + 3A > G (p. Arg233Ter), in TBPL2 were identified in the infertile family. Compound heterozygous mutations in TBPL2 may be the cause of impaired ovarian folliculogenesis, failure of superovulation, and infertility. CONCLUSIONS We identified compound heterozygous mutations in TBPL2 that caused impaired ovarian folliculogenesis, failure of superovulation, and infertility in patients. These findings suggest an important role for compound heterozygous mutations in TBPL2 and expand the mutational spectrum of TBPL2, which might provide a new precise diagnostic marker for female infertility.
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Affiliation(s)
- Tian Du
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China
| | - Meiling Li
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China
| | - Li Chen
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China
| | - Yong Shao
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China
| | - Yichun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Hui Wang
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China
| | - Jinzhao Ma
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China.
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China.
| | - Bing Yao
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Southeast University, Nanjing, 210002, Jiangsu, China.
- Center of Reproductive Medicine, Affiliated Hospital of Medical School, Jinling Hospital, Nanjing University, Nanjing, 21002, Jiangsu, China.
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15
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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16
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Jin J, Ren P, Li X, Zhang Y, Yang W, Ma Y, Lai M, Yu C, Zhang S, Zhang YL. Ovulatory signal-triggered chromatin remodeling in ovarian granulosa cells by HDAC2 phosphorylation activation-mediated histone deacetylation. Epigenetics Chromatin 2023; 16:11. [PMID: 37076890 PMCID: PMC10116676 DOI: 10.1186/s13072-023-00485-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/07/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Epigenetic reprogramming is involved in luteinizing hormone (LH)-induced ovulation; however, the underlying mechanisms are largely unknown. RESULTS We here observed a rapid histone deacetylation process between two waves of active transcription mediated by the follicle-stimulating hormone (FSH) and the LH congener human chorionic gonadotropin (hCG), respectively. Analysis of the genome-wide H3K27Ac distribution in hCG-treated granulosa cells revealed that a rapid wave of genome-wide histone deacetylation remodels the chromatin, followed by the establishment of specific histone acetylation for ovulation. HDAC2 phosphorylation activation coincides with histone deacetylation in mouse preovulatory follicles. When HDAC2 was silenced or inhibited, histone acetylation was retained, leading to reduced gene transcription, retarded cumulus expansion, and ovulation defect. HDAC2 phosphorylation was associated with CK2α nuclear translocation, and inhibition of CK2α attenuated HDAC2 phosphorylation, retarded H3K27 deacetylation, and inactivated the ERK1/2 signaling cascade. CONCLUSIONS This study demonstrates that the ovulatory signal erases histone acetylation through activation of CK2α-mediated HDAC2 phosphorylation in granulosa cells, which is an essential prerequisite for subsequent successful ovulation.
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Affiliation(s)
- Jiamin Jin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Peipei Ren
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Xiang Li
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Yinyi Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Weijie Yang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Yerong Ma
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Mengru Lai
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China
| | - Chao Yu
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Songying Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China.
| | - Yin-Li Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, 310016, China.
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17
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Bioinformatic Data Mining for Candidate Drugs Affecting Risk of Bisphosphonate-Related Osteonecrosis of the Jaw (BRONJ) in Cancer Patients. DISEASE MARKERS 2022; 2022:3348480. [PMID: 36157219 PMCID: PMC9492334 DOI: 10.1155/2022/3348480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Background. Bisphosphonate-related osteonecrosis of the jaw (BRONJ) leads to significant morbidity. Other coadministered drugs may modulate the risk for BRONJ. The present study aimed to leverage bioinformatic data mining to identify drugs that potentially modulate the risk of BRONJ in cancer. Methods. A GEO gene expression dataset of peripheral blood mononuclear cells related to BRONJ in multiple myeloma patients was downloaded, and differentially expressed genes (DEGs) in patients with BRONJ versus those without BRONJ were identified. A protein-protein interaction network of the DEGs was constructed using experimentally validated interactions in the STRING database. Overrepresented Gene Ontology (GO) molecular function terms and KEGG pathways in the network were analysed. Network topology was determined, and ‘hub genes’ with degree ≥2 in the network were identified. Known drug targets of the hub genes were mined from the ‘drug gene interaction database’ (DGIdb) and labelled as candidate drugs affecting the risk of BRONJ. Results. 751 annotated DEGs (
,
) were obtained from the microarray gene expression dataset GSE7116. A PPI network with 633 nodes and 168 edges was constructed. Data mining for drugs interacting with 49 gene nodes was performed. 37 drug interactions were found for 9 of the hub genes including TBP, TAF1, PPP2CA, PRPF31, CASP8, UQCRB, ACTR2, CFLAR, and FAS. Interactions were found for several established and novel anticancer chemotherapeutic, kinase inhibitor, caspase inhibitor, antiangiogenic, and immunomodulatory agents. Aspirin, metformin, atrovastatin, thrombin, androgen and antiandrogen drugs, progesterone, Vitamin D, and Ginsengoside 20(S)-Protopanaxadiol were also documented. Conclusions. A bioinformatic data mining strategy identified several anticancer, immunomodulator, and other candidate drugs that may affect the risk of BRONJ in cancer patients.
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18
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Yang P, Chen T, Wu K, Hou Z, Zou Y, Li M, Zhang X, Xu J, Zhao H. A homozygous variant in TBPL2 was identified in women with oocyte maturation defects and infertility. Hum Reprod 2021; 36:2011-2019. [PMID: 33893736 DOI: 10.1093/humrep/deab094] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION What are the genetic causes of oocyte maturation defects? SUMMARY ANSWER A homozygous splicing variant (c.788 + 3A>G) in TATA-box binding protein like 2 (TBPL2) was identified as a contributory genetic factor in oocyte maturation defects. WHAT IS KNOWN ALREADY TBPL2, a vertebrate oocyte-specific general transcription factor, is essential for oocyte development. TBPL2 variants have not been studied in human oocyte maturation defects. STUDY DESIGN, SIZE, DURATION Two infertile families characterized by oocyte maturation defects were recruited for whole-exome sequencing (WES). PARTICIPANTS/MATERIALS, SETTING, METHODS Genomic DNA was extracted from peripheral blood for WES analysis. Sanger sequencing was performed for data validation. Pathogenicity of variants was predicted by in silico analysis. Minigene assay and single-oocyte RNA sequencing were performed to investigate the effects of the variant on mRNA integrity and oocyte transcriptome, respectively. MAIN RESULTS AND THE ROLE OF CHANCE A homozygous splicing variant (c.788 + 3A>G) in TBPL2 was identified in two unrelated families characterized by oocyte maturation defects. Haplotype analysis indicated that the disease allele of Families 1 and 2 was independent. The variant disrupted the integrity of TBPL2 mRNA. Transcriptome sequencing of affected oocytes showed that vital genes for oocyte maturation and fertilization were widely and markedly downregulated, suggesting that a mutation in the transcriptional factor, TBPL2, led to global gene alterations in oocytes. LIMITATIONS, REASONS FOR CAUTION Limitations include the lack of direct functional evidence. Owing to the scarcity of human oocyte samples, only two immature MI oocytes were obtained from the patients, and we could only investigate the effect of the mutation at the transcriptional level by high-throughput sequencing technology. No extra oocytes were obtained to assess the transcriptional activity of the mutant oocytes by immunofluorescence, or investigate the effects on the binding of TBPL2 caused by the mutation. WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight a critical role of TBPL2 in female reproduction and identify a homozygous splicing mutation in TBPL2 that might be related to defects in human oocyte maturation. This information will facilitate the genetic diagnosis of infertile individuals with repeated failures of IVF, providing a basis for genetic counseling. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the National Key Research and Development Program of China (2018YFC1004000, 2017YFC1001504 and 2017YFC1001600), the National Natural Science Foundation of China (81871168, 31900409 and 31871509), the Foundation for Distinguished Young Scholars of Shandong Province (JQ201816), the Innovative Research Team of High-Level Local Universities in Shanghai (SSMU-ZLCX20180401) and the Fundamental Research Funds of Shandong University. The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Ping Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Tailai Chen
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Keliang Wu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Yang Zou
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Mei Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - XinZe Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Junting Xu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
| | - Han Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Shandong Key Laboratory of Reproductive Medicine, Jinan, China
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Gong Y, Zhang Y, Li B, Xiao Y, Zeng Q, Xu K, Duan Y, He J, Ma H. Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig. BIOLOGY 2021; 10:310. [PMID: 33917834 PMCID: PMC8068270 DOI: 10.3390/biology10040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022]
Abstract
Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only CAV1, PACSIN2, and CDC42 in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA-mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.
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Affiliation(s)
- Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
- Ningxiang Pig Farm of Dalong Livestock Technology Co. Ltd., Ningxiang 410600, China
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Yehui Duan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
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20
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Ho KH, Patrizi A. Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus. Sci Rep 2021; 11:3278. [PMID: 33558629 PMCID: PMC7870894 DOI: 10.1038/s41598-021-82800-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023] Open
Abstract
Choroid plexus (ChP), a vascularized secretory epithelium located in all brain ventricles, plays critical roles in development, homeostasis and brain repair. Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular and useful technique for measuring gene expression changes and also widely used in ChP studies. However, the reliability of RT-qPCR data is strongly dependent on the choice of reference genes, which are supposed to be stable across all samples. In this study, we validated the expression of 12 well established housekeeping genes in ChP in 2 independent experimental paradigms by using popular stability testing algorithms: BestKeeper, DeltaCq, geNorm and NormFinder. Rer1 and Rpl13a were identified as the most stable genes throughout mouse ChP development, while Hprt1 and Rpl27 were the most stable genes across conditions in a mouse sensory deprivation experiment. In addition, Rpl13a, Rpl27 and Tbp were mutually among the top five most stable genes in both experiments. Normalisation of Ttr and Otx2 expression levels using different housekeeping gene combinations demonstrated the profound effect of reference gene choice on target gene expression. Our study emphasized the importance of validating and selecting stable housekeeping genes under specific experimental conditions.
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Affiliation(s)
- Kim Hoa Ho
- Schaller Research Group, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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21
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A recurrent mutation in TBPL2 causes diminished ovarian reserve and female infertility. J Genet Genomics 2020; 47:785-788. [PMID: 33541821 DOI: 10.1016/j.jgg.2020.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
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22
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Parra-Marín O, López-Pacheco K, Hernández R, López-Villaseñor I. The highly diverse TATA box-binding proteins among protists: A review. Mol Biochem Parasitol 2020; 239:111312. [PMID: 32771681 DOI: 10.1016/j.molbiopara.2020.111312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Transcription is the first step of gene expression regulation and is a fundamental mechanism for establishing the viability and development of a cell. The TATA box-binding protein (TBP) interaction with a TATA box in a promoter is one of the best studied mechanisms in transcription initiation. TBP is a transcription factor that is highly conserved from archaea to humans and is essential for the transcription initiated by each of the three RNA polymerases. In addition, the discovery of TBP-related factor 1 (TRF1) and other factors related to TBP shed light on the variability among transcription initiation complexes, thus demonstrating that the compositions of these complexes are, in fact, more complicated than originally believed. Despite these facts, the majority of studies on transcription have been performed on animal, plant and fungal cells, which serve as canonical models, and information regarding protist cells is relatively scarce. The aim of this work is to review the diversity of the TBPs that have been documented in protists and describe some of the specific features that differentiate them from their counterparts in higher eukaryotes.
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Affiliation(s)
- Olivia Parra-Marín
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Karla López-Pacheco
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico.
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23
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Bylino OV, Ibragimov AN, Shidlovskii YV. Evolution of Regulated Transcription. Cells 2020; 9:E1675. [PMID: 32664620 PMCID: PMC7408454 DOI: 10.3390/cells9071675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
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Affiliation(s)
- Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
| | - Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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24
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TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes. Stem Cell Res Ther 2020; 11:196. [PMID: 32448362 PMCID: PMC7245780 DOI: 10.1186/s13287-020-01711-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mesendodermal formation during early gastrulation requires the expression of lineage-specific genes, while the regulatory mechanisms during this process have not yet been fully illustrated. TATA box-binding protein (TBP) and TBP-like factors are general transcription factors responsible for the transcription initiation by recruiting the preinitiation complex to promoter regions. However, the role of TBP family members in the regulation of mesendodermal specification remains largely unknown. METHODS We used an in vitro mesendodermal differentiation system of human embryonic stem cells (hESCs), combining with the microarray and quantitative polymerase chain reaction (qRT-PCR) analysis, loss of function and gain of function to determine the function of the TBP family member TBP-related factor 3 (TRF3) during mesendodermal differentiation of hESCs. The chromatin immunoprecipitation (ChIP) and biochemistry analysis were used to determine the binding of TRF3 to the promoter region of key mesendodermal genes. RESULTS The mesendodermal differentiation of hESCs was confirmed by the microarray gene expression profile, qRT-PCR, and immunocytochemical staining. The expression of TRF3 mRNA was enhanced during mesendodermal differentiation of hESCs. The TRF3 deficiency did not affect the pluripotent marker expression, alkaline phosphatase activity, and cell cycle distribution of undifferentiated hESCs or the expression of early neuroectodermal genes during neuroectodermal differentiation. During the mesendodermal differentiation, the expression of pluripotency markers decreased in both wild-type and TRF3 knockout (TRF3-/-) cells, while the TRF3 deficiency crippled the expression of the mesendodermal markers. The reintroduction of TRF3 into the TRF3-/- hESCs rescued inhibited mesendodermal differentiation. Mechanistically, the TRF3 binding profile was significantly shifted to the mesendodermal specification during mesendodermal differentiation of hESCs based on the ChIP-seq data. Moreover, ChIP and ChIP-qPCR analysis showed that TRF3 was enriched at core promoter regions of mesendodermal developmental genes, EOMESODERMIN, BRACHYURY, mix paired-like homeobox, and GOOSECOID homeobox, during mesendodermal differentiation of hESCs. CONCLUSIONS These results reveal that the TBP family member TRF3 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation. However, it directs mesendodermal lineage commitment of hESCs via specifically promoting the transcription of key mesendodermal transcription factors. These findings provide new insights into the function and mechanisms of the TBP family member in hESC early lineage specification.
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25
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Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. Nat Commun 2020; 11:2384. [PMID: 32404905 PMCID: PMC7221094 DOI: 10.1038/s41467-020-16182-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
TATA-box binding protein (TBP) is required for every single transcription event in archaea and eukaryotes. It binds DNA and harbors two repeats with an internal structural symmetry that show sequence asymmetry. At various times in evolution, TBP has acquired multiple interaction partners and different organisms have evolved TBP paralogs with additional protein regions. Together, these observations raise questions of what molecular determinants (i.e. key residues) led to the ability of TBP to acquire new interactions, resulting in an increasingly complex transcriptional system in eukaryotes. We present a comprehensive study of the evolutionary history of TBP and its interaction partners across all domains of life, including viruses. Our analysis reveals the molecular determinants and suggests a unified and multi-stage evolutionary model for the functional innovations of TBP. These findings highlight how concerted chemical changes on a conserved structural scaffold allow for the emergence of complexity in a fundamental biological process. The TATA-box binding protein (TBP) is required for transcription initiation in archaea and eukaryotes. Here the authors delineate how TBP’s function has evolved new functional features through context-dependent interactions with various protein partners.
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26
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Rodriguez Barreto D, Garcia de Leaniz C, Verspoor E, Sobolewska H, Coulson M, Consuegra S. DNA Methylation Changes in the Sperm of Captive-Reared Fish: A Route to Epigenetic Introgression in Wild Populations. Mol Biol Evol 2020; 36:2205-2211. [PMID: 31180510 PMCID: PMC6759066 DOI: 10.1093/molbev/msz135] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or transgenerational epigenetic modifications in Atlantic salmon. We found that the sperm of wild and captive-reared males differed in methylated regions consistent with early epigenetic signatures of domestication. Some of the epigenetic marks that differed between hatchery and wild males affected genes related to transcription, neural development, olfaction, and aggression, and were maintained in the offspring beyond developmental reprogramming. Our findings suggest that rearing in captivity may trigger epigenetic modifications in the sperm of hatchery fish that could explain the rapid phenotypic and genetic changes observed among hybrid fish. Epigenetic introgression via fish sperm represents a previously unappreciated mechanism that could compromise locally adapted fish populations.
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Affiliation(s)
| | | | - Eric Verspoor
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Halina Sobolewska
- Noahgene Ltd, The e-Centre, Cooperage Way Business Village, Alloa, United Kingdom
| | - Mark Coulson
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Sofia Consuegra
- Biosciences Department, College of Science, Swansea University, Swansea, United Kingdom
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27
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Lu H, Wang L, Li S, Pan C, Cheng K, Luo Y, Xu H, Tian B, Zhao Y, Hua Y. Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO. Nucleic Acids Res 2019; 47:9925-9933. [PMID: 31410466 PMCID: PMC6765133 DOI: 10.1093/nar/gkz720] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.
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Affiliation(s)
- Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Shengjie Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Chaoming Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuxia Luo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
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28
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González-Bermúdez L, Anglada T, Genescà A, Martín M, Terradas M. Identification of reference genes for RT-qPCR data normalisation in aging studies. Sci Rep 2019; 9:13970. [PMID: 31562345 PMCID: PMC6764958 DOI: 10.1038/s41598-019-50035-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/29/2019] [Indexed: 01/10/2023] Open
Abstract
Aging is associated with changes in gene expression levels that affect cellular functions and predispose to age-related diseases. The use of candidate genes whose expression remains stable during aging is required to correctly address the age-associated variations in expression levels. Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) has become a powerful approach for sensitive gene expression analysis. Reliable RT-qPCR assays rely on the normalisation of the results to stable reference genes. Taken these data together, here we evaluated the expression stability of eight frequently used reference genes in three aging models: oncogene-induced senescence (OIS), in vitro and in vivo aging. Using NormFinder and geNorm algorithms, we identified that the most stable reference gene pairs were PUM1 and TBP in OIS, GUSB and PUM1 for in vitro aging and GUSB and OAZ1 for in vivo aging. To validate these candidates, we used them to normalise the expression data of CDKN1A, APOD and TFRC genes, whose expression is known to be affected during OIS, in vitro and in vivo aging. This study demonstrates that accurate normalisation of RT-qPCR data is crucial in aging research and provides a specific subset of stable reference genes for future aging studies.
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Affiliation(s)
- Lourdes González-Bermúdez
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Teresa Anglada
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Genescà
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marta Martín
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Mariona Terradas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
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29
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The RNA Polymerase II Core Promoter in Drosophila. Genetics 2019; 212:13-24. [PMID: 31053615 DOI: 10.1534/genetics.119.302021] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/05/2019] [Indexed: 11/18/2022] Open
Abstract
Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.
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30
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An in vitro characterisation of the Trichomonas vaginalis TATA box-binding proteins (TBPs). Parasitol Res 2019; 118:3019-3031. [DOI: 10.1007/s00436-019-06438-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/22/2019] [Indexed: 10/26/2022]
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31
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Kurshakova MM, Nabirochkina EN, Georgieva SG, Kopytova DV. TRF4, the novel TBP-related protein of Drosophila melanogaster, is concentrated at the endoplasmic reticulum and copurifies with proteins participating in the processes associated with endoplasmic reticulum. J Cell Biochem 2019; 120:7927-7939. [PMID: 30426565 DOI: 10.1002/jcb.28070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023]
Abstract
Understanding the functions of TBP-related factors is essential for studying chromatin assembly and transcription regulation in higher eukaryotes. The novel TBP-related protein-coding gene, trf4, was described in Drosophila melanogaster. trf4 is found only in Drosophila and has likely originated in Drosophila common ancestor. TRF4 protein has a distant homology with TBP and TRF2 in the region of TBP-like domain and is evolutionarily conserved among distinct Drosophila species, which indicates its functional significance. TRF4 is widely expressed in D. melanogaster with high levels of its expression being observed in testes. Interestingly enough, TRF4 has become a cytoplasmic protein having lost nuclear localization signal sequence. TRF4 is concentrated at the endoplasmic reticulum (ER) and copurifies with the proteins participating in the ER-associated processes. We suggest that trf4 gene is an example of homolog neofunctionalization by protein subcellular relocalization pathway, where the subcellular relocalization of gene product of duplicated gene leads to the new functions in ER-associated processes.
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Affiliation(s)
- Maria M Kurshakova
- Department of transcription factors of eukaryotes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Nabirochkina
- Department of transcription factors of eukaryotes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia G Georgieva
- Department of transcription factors of eukaryotes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daria V Kopytova
- Department of transcription factors of eukaryotes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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32
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Transcription initiation factor TBP: old friend new questions. Biochem Soc Trans 2019; 47:411-423. [DOI: 10.1042/bst20180623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/14/2022]
Abstract
Abstract
In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.
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33
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Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R. A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. eLife 2018; 7:35621. [PMID: 29939130 PMCID: PMC6037474 DOI: 10.7554/elife.35621] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/23/2018] [Indexed: 12/18/2022] Open
Abstract
Maintenance of transcription programs is challenged during mitosis when chromatin becomes condensed and transcription is silenced. How do the daughter cells re-establish the original transcription program? Here, we report that the TATA-binding protein (TBP), a key component of the core transcriptional machinery, remains bound globally to active promoters in mouse embryonic stem cells during mitosis. Using live-cell single-molecule imaging, we observed that TBP mitotic binding is highly stable, with an average residence time of minutes, in stark contrast to typical TFs with residence times of seconds. To test the functional effect of mitotic TBP binding, we used a drug-inducible degron system and found that TBP promotes the association of RNA Polymerase II with mitotic chromosomes, and facilitates transcriptional reactivation following mitosis. These results suggest that the core transcriptional machinery promotes efficient transcription maintenance globally.
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Affiliation(s)
- Sheila S Teves
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Luye An
- Department of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, United States
| | - Aarohi Bhargava-Shah
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Liangqi Xie
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Berkeley, United States
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34
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Danks GB, Navratilova P, Lenhard B, Thompson EM. Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. BMC Genomics 2018; 19:164. [PMID: 29482522 PMCID: PMC6389100 DOI: 10.1186/s12864-018-4504-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/28/2018] [Indexed: 01/28/2023] Open
Abstract
Background Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Results Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. Conclusions Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa. Electronic supplementary material The online version of this article (10.1186/s12864-018-4504-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma B Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.
| | - Pavla Navratilova
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway
| | - Boris Lenhard
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Eric M Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway. .,Department of Biology, University of Bergen, Bergen, N-5006, Norway.
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35
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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36
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Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. Mol Neurobiol 2017; 55:1871-1904. [PMID: 28233272 DOI: 10.1007/s12035-017-0427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/26/2017] [Indexed: 01/31/2023]
Abstract
Adaptability to a variety of environmental conditions is a prominent feature of Homo sapiens. We hypothesize that this feature can be explained by evolutionary changes in gene promoters active in the brain prefrontal cortex leading to a more flexible gene regulation network. The genotype-dependent range of gene expression can be broader in humans than in other higher primates. Thus, we searched for specific signatures of evolutionary changes in promoter architectures of multiple hominid genes, including the genes active in human cortical neurons that may indicate an increase of variability of gene expression rather than just changes in the level of expression, such as downregulation or upregulation of the genes. We performed a whole-genome search for genetic-based alterations that may impact gene regulation "flexibility" in a process of hominids evolution, such as (i) CpG dinucleotide content, (ii) predicted nucleosome-DNA dissociation constant, and (iii) predicted affinities for TATA-binding protein (TBP) in gene promoters. We tested all putative promoter regions across the human genome and especially gene promoters in active chromatin state in neurons of prefrontal cortex, the brain region critical for abstract thinking and social and behavioral adaptation. Our data imply that the origin of modern man has been associated with an increase of flexibility of promoter-driven gene regulation in brain. In contrast, after splitting from the ancestral lineages of H. sapiens, the evolution of ape species is characterized by reduced flexibility of gene promoter functioning, underlying reduced variability of the gene expression.
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37
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TRF2 is recruited to the pre-initiation complex as a testis-specific subunit of TFIIA/ALF to promote haploid cell gene expression. Sci Rep 2016; 6:32069. [PMID: 27576952 PMCID: PMC5006001 DOI: 10.1038/srep32069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/28/2016] [Indexed: 11/08/2022] Open
Abstract
Mammalian genomes encode two genes related to the TATA-box binding protein (TBP), TBP-related factors 2 and 3 (TRF2 and TRF3). Male Trf2−/− mice are sterile and characterized by arrested spermatogenesis at the transition from late haploid spermatids to early elongating spermatids. Despite this characterization, the molecular function of murine Trf2 remains poorly characterized and no direct evidence exists to show that it acts as a bona fide chromatin-bound transcription factor. We show here that Trf2 forms a stable complex with TFIIA or the testis expressed paralogue ALF chaperoned in the cytoplasm by heat shock proteins. We demonstrate for the first time that Trf2 is recruited to active haploid cell promoters together with Tbp, Taf7l and RNA polymerase II. RNA-seq analysis identifies a set of genes activated in haploid spermatids during the first wave of spermatogenesis whose expression is down-regulated by Trf2 inactivation. We therefore propose that Trf2 is recruited to the preinitiation complex as a testis-specific subunit of TFIIA/ALF that cooperates with Tbp and Taf7l to promote haploid cell gene expression.
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38
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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39
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Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJC. Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development 2016; 143:1340-50. [PMID: 26952988 PMCID: PMC4852510 DOI: 10.1242/dev.127936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/24/2016] [Indexed: 12/15/2022]
Abstract
Embryonic development relies on activating and repressing regulatory influences that are faithfully integrated at the core promoter of individual genes. In vertebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and two TBP-related factors. In Xenopus embryos, the three TBP family factors are all essential for development and are required for expression of distinct subsets of genes. Here, we report on a non-canonical TBP family-insensitive (TFI) mechanism of transcription initiation that involves mesoderm and organizer gene expression. Using TBP family single- and triple-knockdown experiments, α-amanitin treatment, transcriptome profiling and chromatin immunoprecipitation, we found that TFI gene expression cannot be explained by functional redundancy, is supported by active transcription and shows normal recruitment of the initiating form of RNA polymerase II to the promoter. Strikingly, recruitment of Gcn5 (also known as Kat2a), a co-activator that has been implicated in transcription initiation, to TFI gene promoters is increased upon depletion of TBP family factors. TFI genes are part of a densely connected TBP family-insensitive T-box-Otx2-Gsc interaction network. The results indicate that this network of genes bound by Vegt, Eomes, Otx2 and Gsc utilizes a novel, flexible and non-canonical mechanism of transcription that does not require TBP or TBP-related factors. Highlighted article: A network of embryonic genes, many of which are expressed in the mesoderm and the organiser, can initiate transcription through a non-canonical mechanism.
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Affiliation(s)
- Emese Gazdag
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ulrike G Jacobi
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
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40
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Malecova B, Dall'Agnese A, Madaro L, Gatto S, Coutinho Toto P, Albini S, Ryan T, Tora L, Puri PL. TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells. eLife 2016; 5. [PMID: 26880551 PMCID: PMC4775216 DOI: 10.7554/elife.12534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/21/2016] [Indexed: 02/07/2023] Open
Abstract
Change in the identity of the components of the transcription pre-initiation complex is proposed to control cell type-specific gene expression. Replacement of the canonical TFIID-TBP complex with TRF3/TBP2 was reported to be required for activation of muscle-gene expression. The lack of a developmental phenotype in TBP2 null mice prompted further analysis to determine whether TBP2 deficiency can compromise adult myogenesis. We show here that TBP2 null mice have an intact regeneration potential upon injury and that TBP2 is not expressed in established C2C12 muscle cell or in primary mouse MuSCs. While TFIID subunits and TBP are downregulated during myoblast differentiation, reduced amounts of these proteins form a complex that is detectable on promoters of muscle genes and is essential for their expression. This evidence demonstrates that TBP2 does not replace TBP during muscle differentiation, as previously proposed, with limiting amounts of TFIID-TBP being required to promote muscle-specific gene expression. DOI:http://dx.doi.org/10.7554/eLife.12534.001 The muscles that allow animal’s to move are built predominantly of cells called myofibers. Like other specialized cell types, these myofibers develop via a regulated set of events called differentiation. In adults, this phenomenon occurs when muscles regenerate after an injury, and new myofibers differentiate from so-called satellite cells that already reside within the muscles. Differentiation is regulated at the genetic level, and the development of myofibers relies on the activation of muscle-specific genes. A gene’s expression is typically controlled via a nearby regulatory region of DNA called a promoter that can be recognized by various molecular machines made from protein complexes. In most adult tissues, such regulatory machineries contain a complex called TFIID. Previously it was reported that the TFIID complex was eliminated from cells during muscle differentiation, and that an alternative protein complex called TBP2/TAF3 recognizes and regulates the promoters of muscle-specific genes. However, Malecova et al. have now discovered that TFIID is actually present, albeit at reduced amounts, in differentiated muscles and that it drives the activation of muscle-specific genes during differentiation. Further experiments also showed that the TBP2 protein is not required for differentiation of muscle cells or for the regeneration of injured muscles, and is actually absent in muscle cells. Further studies are now needed to explore how the TFIID-containing complex works with other regulatory protein complexes that are known to help make muscle-specific genes accessible to TFIID. It will also be important to study the relationship between the down-regulation of TFIID components and the activation of muscle-specific genes that typically occurs in mature myofbers. Together these efforts will allow the various aspects of gene regulation to be integrated, which will help provide a more complete understanding of the process of muscle differentiation. DOI:http://dx.doi.org/10.7554/eLife.12534.002
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Affiliation(s)
- Barbora Malecova
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Alessandra Dall'Agnese
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Luca Madaro
- Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Sole Gatto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Paula Coutinho Toto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Sonia Albini
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Tammy Ryan
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Làszlò Tora
- Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CU de Strasbourg, France
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
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41
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Ravarani CNJ, Chalancon G, Breker M, de Groot NS, Babu MM. Affinity and competition for TBP are molecular determinants of gene expression noise. Nat Commun 2016; 7:10417. [PMID: 26832815 PMCID: PMC4740812 DOI: 10.1038/ncomms10417] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
Cell-to-cell variation in gene expression levels (noise) generates phenotypic diversity and is an important phenomenon in evolution, development and disease. TATA-box binding protein (TBP) is an essential factor that is required at virtually every eukaryotic promoter to initiate transcription. While the presence of a TATA-box motif in the promoter has been strongly linked with noise, the molecular mechanism driving this relationship is less well understood. Through an integrated analysis of multiple large-scale data sets, computer simulation and experimental validation in yeast, we provide molecular insights into how noise arises as an emergent property of variable binding affinity of TBP for different promoter sequences, competition between interaction partners to bind the same surface on TBP (to either promote or disrupt transcription initiation) and variable residence times of TBP complexes at a promoter. These determinants may be fine-tuned under different conditions and during evolution to modulate eukaryotic gene expression noise.
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Affiliation(s)
- Charles N J Ravarani
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guilhem Chalancon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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42
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Song C, Ortiz-Urquiza A, Ying SH, Zhang JX, Keyhani NO. Interaction between TATA-Binding Protein (TBP) and Multiprotein Bridging Factor-1 (MBF1) from the Filamentous Insect Pathogenic Fungus Beauveria bassiana. PLoS One 2015; 10:e0140538. [PMID: 26466369 PMCID: PMC4605657 DOI: 10.1371/journal.pone.0140538] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/28/2015] [Indexed: 01/27/2023] Open
Abstract
TATA-binding protein (TBP) is a ubiquitous component of eukaryotic transcription factors that acts to nucleate assembly and position pre-initiation complexes. Multiprotein bridging factor 1 (MBF1) is thought to interconnect TBP with gene specific transcriptional activators, modulating transcriptional networks in response to specific signal and developmental programs. The insect pathogen, Beauveria bassiana, is a cosmopolitan fungus found in most ecosystems where it acts as an important regulator of insect populations and can form intimate associations with certain plants. In order to gain a better understanding of the function of MBF1 in filamentous fungi, its interaction with TBP was demonstrated. The MBF1 and TBP homologs in B. bassiana were cloned and purified from a heterologous E. coli expression system. Whereas purified BbTBP was shown to be able to bind oligonucleotide sequences containing the TATA-motif (Kd ≈ 1.3 nM) including sequences derived from the promoters of the B. bassiana chitinase and protease genes. In contrast, BbMBF1 was unable to bind to these same target sequences. However, the formation of a ternary complex between BbMBF1, BbTBP, and a TATA-containing target DNA sequence was seen in agarose gel electrophoretic mobility shift assays (EMSA). These data indicate that BbMBF1 forms direct interactions with BbTBP, and that the complex is capable of binding to DNA sequences containing TATA-motifs, confirming that BbTBP can link BbMBF1 to target sequences as part of the RNA transcriptional machinery in fungi.
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Affiliation(s)
- Chi Song
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Bldg 981, Museum Rd., Gainesville, FL 32611, United States of America
| | - Almudena Ortiz-Urquiza
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Bldg 981, Museum Rd., Gainesville, FL 32611, United States of America
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin-Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China
| | - Nemat O. Keyhani
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Bldg 981, Museum Rd., Gainesville, FL 32611, United States of America
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43
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Koster M, Snel B, Timmers H. Genesis of Chromatin and Transcription Dynamics in the Origin of Species. Cell 2015; 161:724-36. [DOI: 10.1016/j.cell.2015.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 11/15/2022]
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44
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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45
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Abstract
Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (Pol II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.
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Key Words
- BREd, downstream TFIIB recognition element
- BREu, upstream TFIIB recognition element
- ChIP, Chromatin immunoprecipitation
- DPE
- DPE, downstream core promoter element
- Inr, initiator
- MTE, motif ten element
- PIC, preinitiation complex
- Pol II, RNA polymerase II
- RNA Pol II transcription
- TAF, TBP-associated factor
- TBP, TATA-box binding protein
- TBP-related factors
- TCT
- TFIIA (transcription factor, RNA polymerase II A)
- TFIIB (transcription factor, RNA polymerase II B)
- TFIID (transcription factor, RNA polymerase II D)
- TRF, TATA-box-binding protein-related factor
- TRF2
- TSS, transcription start site
- core promoter elements/motifs
- embryonic development
- histone gene cluster
- ribosomal protein genes
- spermiogenesis
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Affiliation(s)
- Yonathan Zehavi
- a The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan , 5290002 , Israel
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46
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Abstract
Kadonaga and colleagues present novel molecular insights into TATA-box-binding protein (TBP) family members and the evolution of complex animal body plans. They demonstrate that the TBP-related factor 2 (TRF2), which activates TATA-less core promoters, first arose in a common ancestor to the bilaterians and hypothesize that this new TRF2-based transcription system facilitated the evolution of bilateria. The development of a complex body plan requires a diversity of regulatory networks. Here we consider the concept of TATA-box-binding protein (TBP) family proteins as “system factors” that each supports a distinct set of transcriptional programs. For instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream core promoter element (DPE) motif. These findings led us to investigate the evolution of TRF2. TBP occurs in Archaea and eukaryotes, but TRF2 evolved prior to the emergence of the bilateria and subsequent to the evolutionary split between bilaterians and nonbilaterian animals. Unlike TBP, TRF2 does not bind to the TATA box and could thus function as a new system factor that is largely independent of TBP. We postulate that this TRF2-based system served as the foundation for new transcriptional programs, such as those involved in triploblasty and body plan development, that facilitated the evolution of bilateria.
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Affiliation(s)
- Sascha H C Duttke
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Russell F Doolittle
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA;
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47
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Abstract
Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator.
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Jullien J, Miyamoto K, Pasque V, Allen GE, Bradshaw CR, Garrett NJ, Halley-Stott RP, Kimura H, Ohsumi K, Gurdon JB. Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming. Mol Cell 2014; 55:524-36. [PMID: 25066233 PMCID: PMC4156308 DOI: 10.1016/j.molcel.2014.06.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/15/2014] [Accepted: 06/12/2014] [Indexed: 12/31/2022]
Abstract
Nuclear transfer to oocytes is an efficient way to transcriptionally reprogram somatic nuclei, but its mechanisms remain unclear. Here, we identify a sequence of molecular events that leads to rapid transcriptional reprogramming of somatic nuclei after transplantation to Xenopus oocytes. RNA-seq analyses reveal that reprogramming by oocytes results in a selective switch in transcription toward an oocyte rather than pluripotent type, without requiring new protein synthesis. Time-course analyses at the single-nucleus level show that transcriptional reprogramming is induced in most transplanted nuclei in a highly hierarchical manner. We demonstrate that an extensive exchange of somatic- for oocyte-specific factors mediates reprogramming and leads to robust oocyte RNA polymerase II binding and phosphorylation on transplanted chromatin. Moreover, genome-wide binding of oocyte-specific linker histone B4 supports its role in transcriptional reprogramming. Thus, our study reveals the rapid, abundant, and stepwise loading of oocyte-specific factors onto somatic chromatin as important determinants for successful reprogramming.
Xenopus oocytes induce an oocyte transcription pattern in mouse nuclei in 2 days Reprogramming requires a switch from somatic to oocyte transcriptional components Unusually high amounts of oocyte-derived RNA polymerase II drive reprogramming The pattern of oocyte linker histone binding to somatic chromatin is revealed
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Affiliation(s)
- Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Kei Miyamoto
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Vincent Pasque
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - George E Allen
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Charles R Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Nigel J Garrett
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Richard P Halley-Stott
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Keita Ohsumi
- Laboratory of Molecular Genetics, Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - John B Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK.
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49
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Wang YL, Duttke SHC, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev 2014; 28:1550-5. [PMID: 24958592 PMCID: PMC4102762 DOI: 10.1101/gad.245662.114] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The TCT core promoter element is present in most ribosomal protein (RP) genes in Drosophila and humans. Here we show that TBP (TATA box-binding protein)-related factor TRF2, but not TBP, is required for transcription of the TCT-dependent RP genes. In cells, TCT-dependent transcription, but not TATA-dependent transcription, increases or decreases upon overexpression or depletion of TRF2. In vitro, purified TRF2 activates TCT but not TATA promoters. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) experiments revealed the preferential localization of TRF2 at TCT versus TATA promoters. Hence, a specialized TRF2-based RNA polymerase II system functions in the synthesis of RPs and complements the RNA polymerase I and III systems.
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Affiliation(s)
- Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sascha H C Duttke
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Kai Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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50
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Decker KB, Hinton DM. Transcription Regulation at the Core: Similarities Among Bacterial, Archaeal, and Eukaryotic RNA Polymerases. Annu Rev Microbiol 2013; 67:113-39. [DOI: 10.1146/annurev-micro-092412-155756] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kimberly B. Decker
- Unit on Microbial Pathogenesis, Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Deborah M. Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892;
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