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Pinhal D, Gonçalves LDB, Campos VF, Patton JG. Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation. Cell Mol Life Sci 2025; 82:197. [PMID: 40347284 PMCID: PMC12065703 DOI: 10.1007/s00018-025-05663-3] [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: 12/04/2024] [Revised: 02/20/2025] [Accepted: 03/17/2025] [Indexed: 05/12/2025]
Abstract
miRNA arm switching is a pivotal regulatory mechanism that allows organisms to fine-tune gene expression by selectively utilizing either the 5p or 3p strand of a miRNA duplex. This process, conserved across species, facilitates adaptive responses to developmental cues, environmental changes, and disease states. By dynamically altering strand selection, arm switching reshapes gene regulatory networks, contributing to phenotypic diversity and evolutionary innovation. Despite its growing recognition, the mechanisms driving arm switching-such as thermodynamic properties and enzyme-mediated processing-remain incompletely understood. This review synthesizes current findings, highlighting arm switching as a highly conserved mechanism with profound implications for the evolution of regulatory networks. We explore how this phenomenon expands miRNA functionality, drives phenotypic plasticity, and co-evolves with miRNA gene duplications to fuel the diversification of biological functions across taxa.
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Affiliation(s)
- Danillo Pinhal
- Genomics and Molecular Evolution Laboratory, Department of Chemical and Biological Sciences, Institute of Biosciences, DCQB, IBB, UNESP, Botucatu, SP, CEP 18618-689, Brazil.
| | - Leandro de B Gonçalves
- Genomics and Molecular Evolution Laboratory, Department of Chemical and Biological Sciences, Institute of Biosciences, DCQB, IBB, UNESP, Botucatu, SP, CEP 18618-689, Brazil
| | - Vinícius F Campos
- Structural Genomics Laboratory, Graduate Program in Biotechnology, Technological Development Center, Federal University of Pelotas, Pelotas, RS, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
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2
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Jouravleva K, Zamore PD. A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals. Nat Rev Mol Cell Biol 2025; 26:347-370. [PMID: 39856370 DOI: 10.1038/s41580-024-00818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2024] [Indexed: 01/27/2025]
Abstract
Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals.
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Affiliation(s)
- Karina Jouravleva
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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3
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Zhang C, Ma R, Liu W, Ma S, Wang Z, Sun Z. MicroRNAs from Yishen Tongluo formula can repair sperm DNA damage caused by benzo( a)pyrene. PHARMACEUTICAL BIOLOGY 2024; 62:781-789. [PMID: 39435988 PMCID: PMC11497566 DOI: 10.1080/13880209.2024.2417002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 10/04/2024] [Accepted: 10/10/2024] [Indexed: 10/23/2024]
Abstract
CONTEXT Plant microRNAs (miRNAs) present in Yishen Tongluo formula (YSTL, a traditional Chinese herbal medicine formula) are considered as potential therapeutic drugs for reducing the sperm DNA fragmentation index (DFI). OBJECTIVE To study the effectiveness of plant miRNAs in YSTL for repairing mouse sperm DNA damage caused by benzo(a)pyrene (BaP). METHODS AND MATERIALS Twenty-four male SPF ICR (CD1) mice were divided into control, BaP and YSTL groups. A BaP-induced (100 mg/kg) sperm DNA damage model was established in the BaP and YSTL groups, and the mice in the YSTL group were treated with YSTL (23.78 g/kg) for 8 weeks. Sperm DFI was determined via a sperm chromatin structure assay (SCSA). MicroRNAs in the testes of the mice were analysed via RNA-seq, and the top four plant miRNAs were screened, identified and overexpressed in GC cells. The effects of plant miRNAs on the viability and DNA integrity of GC cells exposed to benzo(a)pyrene diol epoxide (BPDE) (1 μM) were tested using CCK8 and comet assays. RESULTS Compared with that of the BaP group, the DFI of the YSTL group decreased (9.57% vs. 18.54%, F = 18.645, p = 0.0236). miR166-y, miR894-x, miR822-x and miR396-x were screened. The CCK8 and comet assays revealed that the DFI of the mimic group was significantly lower than that of the BPDE (IC50 = 1.006 μM) group, with the most significant difference in the miR396-x group. DISCUSSION AND CONCLUSIONS Plant miRNAs such as miR396-x can penetrate the blood-testis barrier through the digestive system to repair sperm DNA.
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Affiliation(s)
- Chenming Zhang
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, Henan, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Ruimin Ma
- Traditional Chinese Medicine (ZHONG JING) School, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Wenbang Liu
- Traditional Chinese Medicine (ZHONG JING) School, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Sicheng Ma
- Traditional Chinese Medicine (ZHONG JING) School, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Zulong Wang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Zixue Sun
- Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan, China
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Wang PY, Bartel DP. The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. Mol Cell 2024; 84:2918-2934.e11. [PMID: 39025072 PMCID: PMC11371465 DOI: 10.1016/j.molcel.2024.06.026] [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: 09/26/2023] [Revised: 05/03/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that, for different guide-RNA sequences, slicing rates of perfectly complementary bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Wang PY, Bartel DP. The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.15.562437. [PMID: 38766062 PMCID: PMC11100590 DOI: 10.1101/2023.10.15.562437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, slicing rates of perfectly complementary, bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y. Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David P. Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Lead contact
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Hynes C, Kakumani PK. Regulatory role of RNA-binding proteins in microRNA biogenesis. Front Mol Biosci 2024; 11:1374843. [PMID: 38567098 PMCID: PMC10985210 DOI: 10.3389/fmolb.2024.1374843] [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: 01/22/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3' untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically involves core catalytic proteins, namely, Drosha and Dicer, and several other RNA-binding proteins (RBPs) that recognize and interact with miRNA precursors and/or their intermediates, and mature miRNAs along with their interacting proteins. The series of RNA-protein and protein-protein interactions are critical to maintaining miRNA expression levels and their function, underlying a variety of cellular processes. Throughout this article, we review RBPs that play a role in miRNA biogenesis and focus on their association with components of the miRNA pathway with functional consequences in the processing and generation of mature miRNAs.
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Affiliation(s)
| | - Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
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7
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Szelągowski A, Kozakiewicz M. A Glance at Biogenesis and Functionality of MicroRNAs and Their Role in the Neuropathogenesis of Parkinson's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:7759053. [PMID: 37333462 PMCID: PMC10270766 DOI: 10.1155/2023/7759053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/20/2023]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNA transcripts. Mammalian miRNA coding sequences are located in introns and exons of genes encoding various proteins. As the central nervous system is the largest source of miRNA transcripts in living organisms, miRNA molecules are an integral part of the regulation of epigenetic activity in physiological and pathological processes. Their activity depends on many proteins that act as processors, transporters, and chaperones. Many variants of Parkinson's disease have been directly linked to specific gene mutations which in pathological conditions are cumulated resulting in the progression of neurogenerative changes. These mutations can often coexist with specific miRNA dysregulation. Dysregulation of different extracellular miRNAs has been confirmed in many studies on the PD patients. It seems reasonable to conduct further research on the role of miRNAs in the pathogenesis of Parkinson's disease and their potential use in future therapies and diagnosis of the disease. This review presents the current state of knowledge about the biogenesis and functionality of miRNAs in the human genome and their role in the neuropathogenesis of Parkinson's disease (PD)-one of the most common neurodegenerative disorders. The article also describes the process of miRNA formation which can occur in two ways-the canonical and noncanonical one. However, the main focus was on miRNA's use in in vitro and in vivo studies in the context of pathophysiology, diagnosis, and treatment of PD. Some issues, especially those regarding the usefulness of miRNAs in PD's diagnostics and especially its treatment, require further research. More standardization efforts and clinical trials on miRNAs are needed.
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Affiliation(s)
- Adam Szelągowski
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
| | - Mariusz Kozakiewicz
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
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Brancaccio R, Murdaca G, Casella R, Loverre T, Bonzano L, Nettis E, Gangemi S. miRNAs' Cross-Involvement in Skin Allergies: A New Horizon for the Pathogenesis, Diagnosis and Therapy of Atopic Dermatitis, Allergic Contact Dermatitis and Chronic Spontaneous Urticaria. Biomedicines 2023; 11:1266. [PMID: 37238937 PMCID: PMC10216116 DOI: 10.3390/biomedicines11051266] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/29/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Skin inflammation is a common underlying feature of atopic dermatitis, allergic contact dermatitis and chronic spontaneous urticaria. The pathogenetic mechanisms have not been fully elucidated. The purpose of this study was to examine whether miRNA, by regulating inflammatory mechanisms through the modulation of innate and adaptive immune responses, could play a major role in the pathogenesis of these skin conditions. We conducted a narrative review using the Pubmed and Embase scientific databases and search engines to find the most relevant miRNAs related to the pathophysiology, severity and prognosis of skin conditions. The studies show that miRNAs are involved in the pathogenesis and regulation of atopic dermatitis and can reveal an atopic predisposition or indicate disease severity. In chronic spontaneous urticaria, different miRNAs which are over-expressed during urticaria exacerbations not only play a role in the possible response to therapy or remission, but also serve as a marker of chronic autoimmune urticaria and indicate associations with other autoimmune diseases. In allergic contact dermatitis, miRNAs are upregulated in inflammatory lesions and expressed during the sensitization phase of allergic response. Several miRNAs have been identified as potential biomarkers of these chronic skin conditions, but they are also possible therapeutic targets.
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Affiliation(s)
- Raffaele Brancaccio
- Dermatology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42122 Reggio nell’Emilia, Italy
| | - Giuseppe Murdaca
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy
- Department of Internal Medicine, Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Rossella Casella
- Department of Emergency and Organ Transplantation, School of Allergology and Clinical Immunology, University of Bari Aldo Moro, Policlinico di Bari, 70124 Bari, Italy
| | - Teresa Loverre
- Department of Emergency and Organ Transplantation, School of Allergology and Clinical Immunology, University of Bari Aldo Moro, Policlinico di Bari, 70124 Bari, Italy
| | - Laura Bonzano
- Dermatology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42122 Reggio nell’Emilia, Italy
| | - Eustachio Nettis
- Department of Emergency and Organ Transplantation, School of Allergology and Clinical Immunology, University of Bari Aldo Moro, Policlinico di Bari, 70124 Bari, Italy
| | - Sebastiano Gangemi
- Department of Clinical and Experimental Medicine, School and Division of Allergy and Clinical Immunology, University of Messina, 98125 Messina, Italy
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9
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Ste-Croix DT, Bélanger RR, Mimee B. Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max. RNA Biol 2023; 20:614-628. [PMID: 37599428 PMCID: PMC10443972 DOI: 10.1080/15476286.2023.2244790] [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: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023] Open
Abstract
The soybean cyst nematode (SCN - Heterodera glycines) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of this syncytium. To date, multiple mechanisms have been proposed to regulate the expression of these proteins including through post-transcriptional regulation. MicroRNAs (miRNAs) are a class of small, roughly 22-nucleotide-long, non-coding RNA shown to regulate gene expression through its interaction with the 3' untranslated region of genes. These same small RNAs have also been hypothesized to be able to cross over kingdom barriers and regulate genes in other species in a process called cross-kingdom interactions. In this study, we characterized the miRNome of the SCN via sequencing of small-RNAs isolated from whole nematodes and exosomes representing all developmental stages. We identified 121 miRNA loci encoding 96 distinct miRNA families including multiple lineage- and species-specific candidates. Using a combination of plant- and animal-specific miRNA target predictors, we generated a unique repertoire of miRNA:mRNA interacting partners in the nematode and its host plant leading to the identification of a set of nine probable cross-kingdom miRNA candidates.
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Affiliation(s)
- Dave T. Ste-Croix
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
- Département de Phytologie, Université Laval, Québec, Canada
| | - Richard R. Bélanger
- Département de Phytologie, Université Laval, Québec, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Québec, Canada
| | - Benjamin Mimee
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
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10
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Kuo Y, Falk BW. Artificial microRNA guide strand selection from duplexes with no mismatches shows a purine-rich preference for virus- and non-virus-based expression vectors in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1069-1084. [PMID: 35113475 PMCID: PMC9129084 DOI: 10.1111/pbi.13786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Artificial microRNA (amiRNA) technology has allowed researchers to direct efficient silencing of specific transcripts using as few as 21 nucleotides (nt). However, not all the artificially designed amiRNA constructs result in selection of the intended ~21-nt guide strand amiRNA. Selection of the miRNA guide strand from the mature miRNA duplex has been studied in detail in human and insect systems, but not so much for plants. Here, we compared a nuclear-replicating DNA viral vector (tomato mottle virus, ToMoV, based), a cytoplasmic-replicating RNA viral vector (tobacco mosaic virus, TMV, based), and a non-viral binary vector to express amiRNAs in plants. We then used deep sequencing and mutational analysis and show that when the structural factors caused by base mismatches in the mature amiRNA duplex were excluded, the nucleotide composition of the mature amiRNA region determined the guide strand selection. We found that the strand with excess purines was preferentially selected as the guide strand and the artificial miRNAs that had no mismatches in the amiRNA duplex were predominantly loaded into AGO2 instead of loading into AGO1 like the majority of the plant endogenous miRNAs. By performing assays for target effects, we also showed that only when the intended strand was selected as the guide strand and showed AGO loading, the amiRNA could provide the expected RNAi effects. Thus, by removing mismatches in the mature amiRNA duplex and designing the intended guide strand to contain excess purines provide better control of the guide strand selection of amiRNAs for functional RNAi effects.
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Affiliation(s)
- Yen‐Wen Kuo
- Department of Plant PathologyUniversity of California DavisDavisCAUSA
| | - Bryce W. Falk
- Department of Plant PathologyUniversity of California DavisDavisCAUSA
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Identification of Radiation-Induced miRNA Biomarkers Using the CGL1 Cell Model System. Bioengineering (Basel) 2022; 9:bioengineering9050214. [PMID: 35621492 PMCID: PMC9137836 DOI: 10.3390/bioengineering9050214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as a potential class of biomolecules for diagnostic biomarker applications. miRNAs are small non-coding RNA molecules, produced and released by cells in response to various stimuli, that demonstrate remarkable stability in a wide range of biological fluids, in extreme pH fluctuations, and after multiple freeze–thaw cycles. Given these advantages, identification of miRNA-based biomarkers for radiation exposures can contribute to the development of reliable biological dosimetry methods, especially for low-dose radiation (LDR) exposures. In this study, an miRNAome next-generation sequencing (NGS) approach was utilized to identify novel radiation-induced miRNA gene changes within the CGL1 human cell line. Here, irradiations of 10, 100, and 1000 mGy were performed and the samples were collected 1, 6, and 24 h post-irradiation. Corroboration of the miRNAome results with RT-qPCR verification confirmed the identification of numerous radiation-induced miRNA expression changes at all doses assessed. Further evaluation of select radiation-induced miRNAs, including miR-1228-3p and miR-758-5p, as well as their downstream mRNA targets, Ube2d2, Ppp2r2d, and Id2, demonstrated significantly dysregulated reciprocal expression patterns. Further evaluation is needed to determine whether the candidate miRNA biomarkers identified in this study can serve as suitable targets for radiation biodosimetry applications.
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12
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Matz A, Qu L, Karlinsey K, Zhou B. Impact of microRNA Regulated Macrophage Actions on Adipose Tissue Function in Obesity. Cells 2022; 11:1336. [PMID: 35456015 PMCID: PMC9024513 DOI: 10.3390/cells11081336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Obesity-induced adipose tissue dysfunction is bolstered by chronic, low-grade inflammation and impairs systemic metabolic health. Adipose tissue macrophages (ATMs) perpetuate local inflammation but are crucial to adipose tissue homeostasis, exerting heterogeneous, niche-specific functions. Diversified macrophage actions are shaped through finely regulated factors, including microRNAs, which post-transcriptionally alter macrophage activation. Numerous studies have highlighted microRNAs' importance to immune function and potential as inflammation-modulatory. This review summarizes current knowledge of regulatory networks governed by microRNAs in ATMs in white adipose tissue under obesity stress.
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Affiliation(s)
- Alyssa Matz
- Department of Immunology, School of Medicine, University of Connecticut, Farmington, CT 06030, USA; (A.M.); (L.Q.); (K.K.)
| | - Lili Qu
- Department of Immunology, School of Medicine, University of Connecticut, Farmington, CT 06030, USA; (A.M.); (L.Q.); (K.K.)
| | - Keaton Karlinsey
- Department of Immunology, School of Medicine, University of Connecticut, Farmington, CT 06030, USA; (A.M.); (L.Q.); (K.K.)
| | - Beiyan Zhou
- Department of Immunology, School of Medicine, University of Connecticut, Farmington, CT 06030, USA; (A.M.); (L.Q.); (K.K.)
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
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Bell J, Hendrix DA. Predicting Drosha and Dicer Cleavage Sites with DeepMirCut. Front Mol Biosci 2022; 8:799056. [PMID: 35141278 PMCID: PMC8819831 DOI: 10.3389/fmolb.2021.799056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are a class of small RNAs involved in post-transcriptional gene silencing with roles in disease and development. Many computational tools have been developed to identify novel microRNAs. However, there have been no attempts to predict cleavage sites for Drosha from primary sequence, or to identify cleavage sites using deep neural networks. Here, we present DeepMirCut, a recurrent neural network-based software that predicts both Dicer and Drosha cleavage sites. We built a microRNA primary sequence database including flanking genomic sequences for 34,713 microRNA annotations. We compare models trained on sequence data, sequence and secondary structure data, as well as input data with annotated structures. Our best model is able to predict cuts within closer average proximity than results reported for other methods. We show that a guanine nucleotide before and a uracil nucleotide after Dicer cleavage sites on the 3' arm of the microRNA precursor had a positive effect on predictions while the opposite order (U before, G after) had a negative effect. Our analysis was also able to predict several positions where bulges had either positive or negative effects on the score. We expect that our approach and the data we have curated will enable several future studies.
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Affiliation(s)
- Jimmy Bell
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
| | - David A. Hendrix
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
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14
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Zhao Y, Cui S, Wang Y, Xu R. The Extensive Regulation of MicroRNA in Immune Thrombocytopenia. Clin Appl Thromb Hemost 2022; 28:10760296221093595. [PMID: 35536600 PMCID: PMC9096216 DOI: 10.1177/10760296221093595] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MicroRNA (miRNA) is a small, single-stranded, non-coding RNA molecule that plays
a variety of key roles in different biological processes through
post-transcriptional regulation of gene expression. MiRNA has been proved to be
a variety of cellular processes involved in development, differentiation, signal
transduction, and is an important regulator of immune and autoimmune diseases.
Therefore, it may act as potent modulators of the immune system and play an
important role in the development of several autoimmune diseases. Immune
thrombocytopenia (ITP) is an autoimmune systemic disease characterized by a low
platelet count. Several studies suggest that like other autoimmune disorders,
miRNAs are deeply involved in the pathogenesis of ITP, interacting with the
function of innate and adaptive immune responses. In this review, we discuss
emerging knowledge about the function of miRNAs in ITP and describe miRNAs in
terms of their role in the immune system and autoimmune response. These findings
suggest that miRNA may be a useful therapeutic target for ITP by regulating the
immune system. In the future, we need to have a more comprehensive understanding
of miRNAs and how they regulate the immune system of patients with ITP.
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Affiliation(s)
- Yuerong Zhao
- 74738Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Siyuan Cui
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.,Institute of Hematology, 74738Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruirong Xu
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.,Institute of Hematology, 74738Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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15
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Abstract
MicroRNAs are RNAs of about 18-24 nucleotides in lengths, which are found in the small noncoding RNA class and have a crucial role in the posttranscriptional regulation of gene expression, cellular metabolic pathways, and developmental events. These small but essential molecules are first processed by Drosha and DGCR8 in the nucleus and then released into the cytoplasm, where they cleaved by Dicer to form the miRNA duplex. These duplexes are bound by the Argonaute (AGO) protein to form the RNA-induced silencing complex (RISC) in a process called RISC loading. Transcription of miRNAs, processing with Drosha and DGCR8 in the nucleus, cleavage by Dicer, binding to AGO proteins and forming RISC are the most critical steps in miRNA biogenesis. Additional molecules involved in biogenesis at these stages can enhance or inhibit these processes, which can radically change the fate of the cell. Biogenesis is regulated by many checkpoints at every step, primarily at the transcriptional level, in the nucleus, cytoplasm, with RNA regulation, RISC loading, miRNA strand selection, RNA methylation/uridylation, and turnover rate. Moreover, in recent years, different regulation mechanisms have been discovered in noncanonical Drosha or Dicer-independent pathways. This chapter seeks answers to how miRNA biogenesis and function are regulated through both canonical and non-canonical pathways.
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16
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Shen H, Ye F, Xu D, Fang L, Zhang X, Zhu J. The MYEOV-MYC association promotes oncogenic miR-17/93-5p expression in pancreatic ductal adenocarcinoma. Cell Death Dis 2021; 13:15. [PMID: 34930894 PMCID: PMC8688437 DOI: 10.1038/s41419-021-04387-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy worldwide. As metastasis and malignant progression are primarily responsible for the poor clinical outcomes of PDAC, identifying key genes involved in these processes and the underlying molecular mechanisms of PDAC is vital. In this study, by analyzing TCGA PDAC data and matched GTEx data, we found that MYEOV expression is associated with poor survival in PDAC patients and higher in carcinoma tissues than in healthy tissues. Elevated levels of MYEOV led to enhanced cell proliferation, invasion and migration in vitro and in vivo. Transcriptome analysis results revealed that MYEOV mediates global alterations in gene expression profiles in PDAC cells. MiRNA-seq analysis showed that MYEOV regulates the expression levels of miR-17-5p and miR-93-5p, and its depletion resulted in reduced cell proliferation, invasion and migration, as observed in MYEOV-knockdown PDAC cells. These effects are likely due to the ability of MYEOV to regulate enrichment of the transcription factor MYC at the gene promoter regions of the two miRNAs. Furthermore, we identified a complex containing MYEOV and MYC in the nucleus, providing additional evidence for the association of MYEOV with MYC. Taken together, our results suggest that MYEOV promotes oncogenic miR-17/93-5p expression by associating with MYC, contributing to PDAC progression.
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Affiliation(s)
- Hongzhang Shen
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fuqiang Ye
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Dongchao Xu
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liangliang Fang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaofeng Zhang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Juanjuan Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
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17
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Archacka K, Ciemerych MA, Florkowska A, Romanczuk K. Non-Coding RNAs as Regulators of Myogenesis and Postexercise Muscle Regeneration. Int J Mol Sci 2021; 22:ijms222111568. [PMID: 34768999 PMCID: PMC8583994 DOI: 10.3390/ijms222111568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/21/2022] Open
Abstract
miRNAs and lncRNAs do not encode proteins, but they play an important role in the regulation of gene expression. They differ in length, biogenesis, and mode of action. In this work, we focus on the selected miRNAs and lncRNAs involved in the regulation of myogenesis and muscle regeneration. We present selected miRNAs and lncRNAs that have been shown to control myogenic differentiation and show that manipulation of their levels could be used to improve myogenic differentiation of various types of stem and progenitor cells. Finally, we discuss how physical activity affects miRNA and lncRNA expression and how it affects muscle well-being.
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18
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Simion V, Loussouarn C, Laurent Y, Roncali L, Gosset D, Reverchon F, Rousseau A, Martin F, Midoux P, Pichon C, Garcion E, Baril P. LentiRILES, a miRNA-ON sensor system for monitoring the functionality of miRNA in cancer biology and therapy. RNA Biol 2021; 18:198-214. [PMID: 34570661 DOI: 10.1080/15476286.2021.1978202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A major unresolved challenge in miRNA biology is the capacity to monitor the spatiotemporal activity of miRNAs expressed in animal disease models. We recently reported that the miRNA-ON monitoring system called RILES (RNAi-inducible expression Luciferase system) implanted in lentivirus expression system (LentiRILES) offers unique opportunity to decipher the kinetics of miRNA activity in vitro, in relation with their intracellular trafficking in glioblastoma cells. In this study, we describe in detail the method for the production of LentiRILES stable cell lines and employed it in several applications in the field of miRNA biology and therapy. We show that LentiRILES is a robust, highly specific and sensitive miRNA sensor system that can be used in vitro as a single-cell miRNA monitoring method, cell-based screening platform for miRNA therapeutics and as a tool to analyse the structure-function relationship of the miRNA duplex. Furthermore, we report the kinetics of miRNA activity upon the intracranial delivery of miRNA mimics in an orthotopic animal model of glioblastoma. This information is exploited to evaluate the tumour suppressive function of miRNA-200c as locoregional therapeutic modality to treat glioblastoma. Our data provide evidence that LentiRILES is a robust system, well suited to resolve the activity of endogenous and exogenously expressed miRNAs from basic research to gene and cell therapy.
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Affiliation(s)
- Viorel Simion
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Claire Loussouarn
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Yoan Laurent
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Loris Roncali
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - David Gosset
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Flora Reverchon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Audrey Rousseau
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Francisco Martin
- GENYO, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Patrick Midoux
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Chantal Pichon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Emmanuel Garcion
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Patrick Baril
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
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19
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Belli R, Ferraro E, Molfino A, Carletti R, Tambaro F, Costelli P, Muscaritoli M. Liquid Biopsy for Cancer Cachexia: Focus on Muscle-Derived microRNAs. Int J Mol Sci 2021; 22:ijms22169007. [PMID: 34445710 PMCID: PMC8396502 DOI: 10.3390/ijms22169007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer cachexia displays a complex nature in which systemic inflammation, impaired energy metabolism, loss of muscle and adipose tissues result in unintentional body weight loss. Cachectic patients have a poor prognosis and the presence of cachexia reduces the tolerability of chemo/radio-therapy treatments and it is frequently the primary cause of death in advanced cancer patients. Early detection of this condition could make treatments more effective. However, early diagnostic biomarkers of cachexia are currently lacking. In recent years, although solid biopsy still remains the "gold standard" for diagnosis of cancer, liquid biopsy is gaining increasing interest as a source of easily accessible potential biomarkers. Moreover, the growing interest in circulating microRNAs (miRNAs), has made these molecules attractive for the diagnosis of several diseases, including cancer. Some muscle-derived circulating miRNA might play a pivotal role in the onset/progression of cancer cachexia. This topic is of great interest since circulating miRNAs might be easily detectable by means of liquid biopsies and might allow an early diagnosis of this syndrome. We here summarize the current knowledge on circulating muscular miRNAs involved in muscle atrophy, since they might represent easily accessible and promising biomarkers of cachexia.
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Affiliation(s)
- Roberta Belli
- Department of Translational and Precision Medicine, Sapienza University, 00185 Rome, Italy; (A.M.); (R.C.); (F.T.)
- Correspondence: (R.B.); (M.M.); Tel./Fax: +390-649-972-020 (M.M.)
| | - Elisabetta Ferraro
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, 56126 Pisa, Italy;
| | - Alessio Molfino
- Department of Translational and Precision Medicine, Sapienza University, 00185 Rome, Italy; (A.M.); (R.C.); (F.T.)
| | - Raffaella Carletti
- Department of Translational and Precision Medicine, Sapienza University, 00185 Rome, Italy; (A.M.); (R.C.); (F.T.)
| | - Federica Tambaro
- Department of Translational and Precision Medicine, Sapienza University, 00185 Rome, Italy; (A.M.); (R.C.); (F.T.)
| | - Paola Costelli
- Department of Clinical and Biological Sciences, University of Torino, 10124 Torino, Italy;
| | - Maurizio Muscaritoli
- Department of Translational and Precision Medicine, Sapienza University, 00185 Rome, Italy; (A.M.); (R.C.); (F.T.)
- Correspondence: (R.B.); (M.M.); Tel./Fax: +390-649-972-020 (M.M.)
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20
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Role of SNPs in the Biogenesis of Mature miRNAs. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2403418. [PMID: 34239922 PMCID: PMC8233088 DOI: 10.1155/2021/2403418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functional SNPs and isomiRs. We analyzed the biological characteristics of functional SNPs and isomiRs and studied their distribution in different ethnic groups using whole-genome analysis. Notably, we used individuals from Great Britain (GBR) as examples and identified isomiRs and isomiR-associated SNPs (iso-SNPs). We performed sequence alignments of isomiRs and miRNA sequencing data to verify the identified isomiRs and further revealed GBR ethnographic epigenetic dominant biomarkers. The SNP-pre-miRNA database consisted of 886 pre-miRNAs and 2640 SNPs. We analyzed the effects of SNP type, SNP location, and SNP-mediated free energy change during mature miRNA biogenesis and found that these factors were closely associated to mature miRNA biogenesis. Remarkably, 158 isomiRs were verified in the miRNA sequencing data for the 18 GBR samples. Our results indicated that SNPs affected the mature miRNA processing mechanism and contributed to the production of isomiRs. This mechanism may have important significance for epigenetic changes and diseases.
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21
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Ahmed Z, Mal C. Functional role of hub molecules in miRNA and transcription factor mediated gene regulatory network of colorectal and lung cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Chorley BN, Atabakhsh E, Doran G, Gautier JC, Ellinger-Ziegelbauer H, Jackson D, Sharapova T, Yuen PST, Church RJ, Couttet P, Froetschl R, McDuffie J, Martinez V, Pande P, Peel L, Rafferty C, Simutis FJ, Harrill AH. Methodological considerations for measuring biofluid-based microRNA biomarkers. Crit Rev Toxicol 2021; 51:264-282. [PMID: 34038674 DOI: 10.1080/10408444.2021.1907530] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that regulate the expression of messenger RNA and are implicated in almost all cellular processes. Importantly, miRNAs can be released extracellularly and are stable in these matrices where they may serve as indicators of organ or cell-specific toxicity, disease, and biological status. There has thus been great enthusiasm for developing miRNAs as biomarkers of adverse outcomes for scientific, regulatory, and clinical purposes. Despite advances in measurement capabilities for miRNAs, miRNAs are still not routinely employed as noninvasive biomarkers. This is in part due to the lack of standard approaches for sample preparation and miRNA measurement and uncertainty in their biological interpretation. Members of the microRNA Biomarkers Workgroup within the Health and Environmental Sciences Institute's (HESI) Committee on Emerging Systems Toxicology for the Assessment of Risk (eSTAR) are a consortium of private- and public-sector scientists dedicated to developing miRNAs as applied biomarkers. Here, we explore major impediments to routine acceptance and use of miRNA biomarkers and case examples of successes and deficiencies in development. Finally, we provide insight on miRNA measurement, collection, and analysis tools to provide solid footing for addressing knowledge gaps toward routine biomarker use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | | | | | | | - David Jackson
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rachel J Church
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Lauren Peel
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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23
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Guo S, Huang S, Jiang X, Hu H, Han D, Moreno CS, Fairbrother GL, Hughes DA, Stoneking M, Khaitovich P. Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn. BMC Genomics 2021; 22:286. [PMID: 33879051 PMCID: PMC8059241 DOI: 10.1186/s12864-021-07542-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Analysis of lymphocyte cell lines revealed substantial differences in the expression of mRNA and microRNA (miRNA) among human populations. The extent of such population-associated differences in actual human tissues remains largely unexplored. The placenta is one of the few solid human tissues that can be collected in substantial numbers in a controlled manner, enabling quantitative analysis of transient biomolecules such as RNA transcripts. Here, we analyzed microRNA (miRNA) expression in human placental samples derived from 36 individuals representing four genetically distinct human populations: African Americans, European Americans, South Asians, and East Asians. All samples were collected at the same hospital following a unified protocol, thus minimizing potential biases that might influence the results. RESULTS Sequence analysis of the miRNA fraction yielded 938 annotated and 70 novel miRNA transcripts expressed in the placenta. Of them, 82 (9%) of annotated and 11 (16%) of novel miRNAs displayed quantitative expression differences among populations, generally reflecting reported genetic and mRNA-expression-based distances. Several co-expressed miRNA clusters stood out from the rest of the population-associated differences in terms of miRNA evolutionary age, tissue-specificity, and disease-association characteristics. Among three non-environmental influenced demographic parameters, the second largest contributor to miRNA expression variation after population was the sex of the newborn, with 32 miRNAs (3% of detected) exhibiting significant expression differences depending on whether the newborn was male or female. Male-associated miRNAs were evolutionarily younger and correlated inversely with the expression of target mRNA involved in neuron-related functions. In contrast, both male and female-associated miRNAs appeared to mediate different types of hormonal responses. Demographic factors further affected reported imprinted expression of 66 placental miRNAs: the imprinting strength correlated with the mother's weight, but not height. CONCLUSIONS Our results showed that among 12 assessed demographic variables, population affiliation and fetal sex had a substantial influence on miRNA expression variation among human placental samples. The effect of newborn-sex-associated miRNA differences further led to expression inhibition of the target genes clustering in specific functional pathways. By contrast, population-driven miRNA differences might mainly represent neutral changes with minimal functional impacts.
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Affiliation(s)
- Song Guo
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | - Shuyun Huang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Xi Jiang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Haiyang Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Carlos S Moreno
- Department of Pathology and Laboratory Medicine and Department of Biomedical Informatics, Emory University, Atlanta, GA, 30322, USA
| | - Genevieve L Fairbrother
- Obstetrics and Gynecology of Atlanta, 1100 Johnson Ferry Rd NE Suite 800, Center 2, Atlanta, GA, 30342, USA
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Mark Stoneking
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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24
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Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
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Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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25
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Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima T, Sawada T, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, Saito JI. siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand. RNA (NEW YORK, N.Y.) 2021; 27:163-173. [PMID: 33177188 PMCID: PMC7812868 DOI: 10.1261/rna.073783.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
Small interfering RNAs (siRNAs) can be utilized not only as functional biological research tools but also as therapeutic agents. For the clinical use of siRNA as drugs, various chemical modifications have been used to improve the activity of siRNA drugs, and further chemical modifications are expected to improve the utility of siRNA therapeutics. As the 5' nucleobase of the guide strand affects the interaction between an siRNA and AGO2 and target cleavage activity, structural optimization of this specific position may be a useful strategy for improving siRNA activity. Here, using the in silico model of the complex between human AGO2 MID domain and nucleoside monophosphates, we screened and synthesized an original adenine-derived analog, 6-(3-(2-carboxyethyl)phenyl)purine (6-mCEPh-purine), that fits better than the natural nucleotide bases into the MID domain of AGO2. Introduction of the 6-mCEPh-purine analog at the 5'-end of the siRNA guide strand significantly enhanced target knockdown activity in both cultured cell lines and in vivo animal models. Our findings can help expand strategies for rationally optimizing siRNA activity via chemical modifications of nucleotide bases.
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Affiliation(s)
- Fumikazu Shinohara
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Taiji Oashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Toshimasa Harumoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Tomoyuki Nishikawa
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuki Takayama
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hikaru Miyagi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuichi Takahashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takahiro Nakajima
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takashi Sawada
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yasuo Koda
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Asana Makino
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Atsuko Sato
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kaori Hamaguchi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Michihiko Suzuki
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Junichiro Yamamoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun-Ichi Saito
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
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26
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Huang S, Yoshitake K, Asaduzzaman M, Kinoshita S, Watabe S, Asakawa S. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA Biol 2021; 18:1702-1715. [PMID: 33356816 DOI: 10.1080/15476286.2020.1867798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
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Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Asaduzzaman
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Chen L, Huang K, Yi K, Huang Y, Tian X, Kang C. Premature MicroRNA-Based Therapeutic: A "One-Two Punch" against Cancers. Cancers (Basel) 2020; 12:cancers12123831. [PMID: 33353171 PMCID: PMC7766154 DOI: 10.3390/cancers12123831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The current understanding of miRNA biology is greatly derived from studies on the guide strands and the passenger strands, also called miRNAs*, which are considered as carriers with no sense for long periods. As such, various studies alter the expression of guide strands by manipulating the expression of their primary transcripts or precursors, both of which are premature miRNAs. In this situation, the regulatory miRNA* species may interfere with the phenotypic interpretation against the target miRNA. However, such methods could manipulate the expression of two functionally synergistic miRNAs of the same precursor, leading to therapeutic potential against various diseases, including cancers. Premature miRNAs represent an underappreciated target reservoir and provide molecular targets for “one-two punch” against cancers. Examples of targetable miRNA precursors and available targeting strategies are provided in this review. Abstract Up-to-date knowledge regarding the biogenesis and functioning of microRNAs (miRNAs) has provided a much more comprehensive and concrete view of miRNA biology than anyone ever expected. Diverse genetic origins and biogenesis pathways leading to functional miRNAs converge on the synthesis of ≈21-nucleotide RNA duplex, almost all of which are processed from long premature sequences in a DICER- and/or DROSHA-dependent manner. Formerly, it was assumed that one mature strand of the duplex is preferentially selected for entry into the silencing complex, and the paired passenger strands (miRNA*) are subjected to degradation. However, given the consolidated evidence of substantial regulatory activity of miRNA* species, currently, this preconception has been overturned. Here, we see the caveat and opportunity toward exogenously manipulating the expression of premature miRNA, leading to simultaneous upregulation or downregulation of dual regulatory strands due to altered expressions. The caveat is the overlooked miRNA* interference while manipulating the expression of a target miRNA at the premature stage, wherein lies the opportunity. If the dual strands of a pre-miRNA function synergistically, the overlooked miRNA* interference may inversely optimize the therapeutic performance. Insightfully, targeting the premature miRNAs may serve as the “one-two punch” against diseases, especially cancers, and this has been discussed in detail in this review.
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Affiliation(s)
- Luyue Chen
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, China;
| | - Kaikai Yi
- Laboratory of Neuro-Oncology, Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China;
| | - Yanlin Huang
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
| | - Xinhua Tian
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
- Correspondence: (X.T.); (C.K.); Tel.: +86-0592-229-2941 (X.T.); +86-022-6081-7499 (C.K.)
| | - Chunsheng Kang
- Laboratory of Neuro-Oncology, Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China;
- Correspondence: (X.T.); (C.K.); Tel.: +86-0592-229-2941 (X.T.); +86-022-6081-7499 (C.K.)
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Guo ZZ, Ma ZJ, He YZ, Jiang W, Xia Y, Pan CF, Wei K, Shi YJ, Chen L, Chen YJ. miR-550a-5p Functions as a Tumor Promoter by Targeting LIMD1 in Lung Adenocarcinoma. Front Oncol 2020; 10:570733. [PMID: 33194664 PMCID: PMC7655921 DOI: 10.3389/fonc.2020.570733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
Lung adenocarcinoma accounts for half of all lung cancer cases in most countries. Mounting evidence has demonstrated that microRNAs play important roles in cancer progression, and some of them can be identified as potential biomarkers. This study aimed to explore the role of miR-550a-5p, a lung adenocarcinoma-associated mature microRNA screened out from the TCGA database via R-studio and Perl, with abundant expression in samples and with 5-year survival prognosis difference, as well as having not been studied in lung cancer yet. Potential target genes were predicted by the online database. Gene ontology enrichment, pathway enrichment, protein–protein interaction network, and hub genes–microRNA network were constructed by FunRich, STRING database, and Cytoscape. Then, LIMD1, a known tumor suppressor gene reported by multiple articles, was found to have a negative correlation with miR-550a-5p. The expression of miR-550a-5p was up-regulated in tumor samples and tumor-associated cell lines. Its high expression was also correlated with tumor size. Cell line A549 treated with miR-550a-5p overexpression promoted tumor proliferation, while H1299 treated with miR-550a-5p knockdown showed the opposite result. Mechanically, miR-550a-5p negatively regulated LIMD1 by directly binding to its 3′-UTR validated by dual luciferase assay. In summary, a new potential prognostic and therapeutic biomarker, miR-550a-5p, has been identified by bioinformatics analysis and experimental validation in vitro and in vivo, which promotes lung adenocarcinoma by silencing a known suppressor oncogene LIMD1.
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Affiliation(s)
- Zi-Zhang Guo
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zi-Jian Ma
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao-Zhou He
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Jiang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Xia
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chun-Feng Pan
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ke Wei
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi-Jun Shi
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi-Jiang Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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29
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Medley JC, Panzade G, Zinovyeva AY. microRNA strand selection: Unwinding the rules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1627. [PMID: 32954644 PMCID: PMC8047885 DOI: 10.1002/wrna.1627] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
microRNAs (miRNAs) play a central role in the regulation of gene expression by targeting specific mRNAs for degradation or translational repression. Each miRNA is post‐transcriptionally processed into a duplex comprising two strands. One of the two miRNA strands is selectively loaded into an Argonaute protein to form the miRNA‐Induced Silencing Complex (miRISC) in a process referred to as miRNA strand selection. The other strand is ejected from the complex and is subject to degradation. The target gene specificity of miRISC is determined by sequence complementarity between the Argonaute‐loaded miRNA strand and target mRNA. Each strand of the miRNA duplex has the capacity to be loaded into miRISC and possesses a unique seed sequence. Therefore, miRNA strand selection plays a defining role in dictating the specificity of miRISC toward its targets and provides a mechanism to alter gene expression in a switch‐like fashion. Aberrant strand selection can lead to altered gene regulation by miRISC and is observed in several human diseases including cancer. Previous and emerging data shape the rules governing miRNA strand selection and shed light on how these rules can be circumvented in various physiological and pathological contexts. This article is categorized under:
RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
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Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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30
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Tang S, Jing H, Song F, Huang H, Li W, Xie G, Zhou J. MicroRNAs in the Spinal Microglia Serve Critical Roles in Neuropathic Pain. Mol Neurobiol 2020; 58:132-142. [PMID: 32902792 DOI: 10.1007/s12035-020-02102-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023]
Abstract
Neuropathic pain (NP) can occur after peripheral nerve injury (PNI), and it can be converted into a maladaptive, detrimental phenotype that causes a long-term state of pain hypersensitivity. In the last decade, the discovery that dysfunctional microglia evoke pain, called "microgliopathic pain," has challenged traditional neuronal views of "pain" and has been extensively explored. Recent studies have shown that microRNAs (miRNAs) can act as activators or inhibitors of spinal microglia in NP conditions. We first briefly review spinal microglial activation in NP. We then comprehensively describe miRNA expression changes and their potential mechanisms in the response of microglia to nerve injury. We summarize the roles of the following two representative miRNAs: miR-124, which reverses NP by keeping microglia quiescent, and miR-155, which promotes NP following microglial activation. Finally, we focused on the therapeutic potential of microglial miRNAs in NP. The findings we summarized may be essential tools for basic research and clinical treatment of NP.
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Affiliation(s)
- Simin Tang
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong Province, People's Republic of China
- Sun Yat-sen University, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Huan Jing
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong Province, People's Republic of China
- ZunYi Medical University, ZunYi, 563100, Guizhou Province, People's Republic of China
| | - Fuhu Song
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Haicheng Huang
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Wenjun Li
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Guiling Xie
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Jun Zhou
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510000, Guangdong Province, People's Republic of China.
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31
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Hawkins LJ, Storey KB. MicroRNA expression in the heart of Xenopus laevis facilitates metabolic adaptation to dehydration. Genomics 2020; 112:3525-3536. [DOI: 10.1016/j.ygeno.2020.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/24/2020] [Accepted: 04/02/2020] [Indexed: 12/21/2022]
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32
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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33
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Sala L, Chandrasekhar S, Vidigal JA. AGO unchained: Canonical and non-canonical roles of Argonaute proteins in mammals. Front Biosci (Landmark Ed) 2020; 25:1-42. [PMID: 31585876 DOI: 10.2741/4793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Argonaute (AGO) proteins play key roles in animal physiology by binding to small RNAs and regulating the expression of their targets. In mammals, they do so through two distinct pathways: the miRNA pathway represses genes through a multiprotein complex that promotes both decay and translational repression; the siRNA pathway represses transcripts through direct Ago2-mediated cleavage. Here, we review our current knowledge of mechanistic details and physiological requirements of both these pathways and briefly discuss their implications to human disease.
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Affiliation(s)
- Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Srividya Chandrasekhar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA,
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34
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Hawkins LJ, Storey KB. Advances and applications of environmental stress adaptation research. Comp Biochem Physiol A Mol Integr Physiol 2019; 240:110623. [PMID: 31778815 DOI: 10.1016/j.cbpa.2019.110623] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
Evolution has produced animals that survive extreme fluctuations in environmental conditions including freezing temperatures, anoxia, desiccating conditions, and prolonged periods without food. For example, the wood frog survives whole-body freezing every winter, arresting all gross physiological functions, but recovers functions upon thawing in the spring. Likewise, many small mammals hibernate for months at a time with minimal metabolic activity, organ perfusion, and movement, yet do not suffer significant muscle atrophy upon arousal. These conditions and the biochemical adaptations employed to deal with them can be viewed as Nature's answer to problems that humans wish to answer, particularly in a biomedical context. This review focuses on recent advances in the field of animal environmental stress adaptation, starting with an emphasis on new areas of research such as epigenetics and microRNA. We then examine new and emerging technologies such as genome editing, novel sequencing applications, and single cell analysis and how these can push us closer to a deeper understanding of biochemical adaptation. Next, evaluate the potential contributions of new high-throughput technologies (e.g. next-generation sequencing, mass spectrometry proteomics) to better understanding the adaptations that support these extreme phenotypes. Concluding, we examine some of the human applications that can be gained from understanding the principles of biochemical adaptation including organ preservation and treatments for conditions such as ischemic stroke and muscle disuse atrophy.
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Affiliation(s)
- Liam J Hawkins
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
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35
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Alles J, Fehlmann T, Fischer U, Backes C, Galata V, Minet M, Hart M, Abu-Halima M, Grässer FA, Lenhof HP, Keller A, Meese E. An estimate of the total number of true human miRNAs. Nucleic Acids Res 2019; 47:3353-3364. [PMID: 30820533 PMCID: PMC6468295 DOI: 10.1093/nar/gkz097] [Citation(s) in RCA: 400] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/30/2019] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.
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Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Ulrike Fischer
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Marie Minet
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Masood Abu-Halima
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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36
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Tian S, Terai G, Kobayashi Y, Kimura Y, Abe H, Asai K, Ui-Tei K. A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs. RNA Biol 2019; 17:264-280. [PMID: 31601146 DOI: 10.1080/15476286.2019.1678364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in the regulation of gene function by a mechanism known as RNA silencing. In a previous study, we revealed that miRNA-mediated silencing efficacy is correlated with the combinatorial thermodynamic properties of the miRNA seed-target mRNA duplex and the 5´-terminus of the miRNA duplex, which can be predicted using 'miScore'. In this study, a robust refined-miScore was developed by integrating the thermodynamic properties of various miRNA secondary structures and the latest thermodynamic parameters of wobble base-pairing, including newly established parameters for I:C base pairing. Through repeated random sampling and machine learning, refined-miScore models calculated with either melting temperature (Tm) or free energy change (ΔG) values were successfully built and validated in both wild-type and adenosine-to-inosine edited miRNAs. In addition to the previously reported contribution of the seed-target duplex and 5´-terminus region, the refined-miScore suggests that the central and 3´-terminus regions of the miRNA duplex also play a role in the thermodynamic regulation of miRNA-mediated silencing efficacy.
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Affiliation(s)
- Shen Tian
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba , Japan
| | - Yoshiaki Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba , Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba , Japan
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37
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Trigg NA, Eamens AL, Nixon B. The contribution of epididymosomes to the sperm small RNA profile. Reproduction 2019; 157:R209-R223. [DOI: 10.1530/rep-18-0480] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/18/2019] [Indexed: 12/16/2022]
Abstract
It is now well established that mature spermatozoa harbour a rich and diverse profile of small non-protein-coding regulatory RNAs (sRNAs). There is also growing appreciation that this sRNA profile displays considerable plasticity, being altered in response to paternal exposure to a variety of environmental stressors. Coupled with evidence that upon delivery to the oocyte at the moment of fertilisation, sperm-borne sRNAs are able to influence both early embryonic development and the subsequent health of the offspring, there is now interest in both the timing and degree of change in the composition of the sRNA cargo of sperm. Models in which such epigenetic changes are linked to the spermatogenic cycle are seemingly incompatible with the lack of overt phenotypic changes in the spermatozoa of affected males. Rather, there is mounting consensus that such changes are imposed on sperm during their transit and storage within the epididymis, a protracted developmental window that takes place over several weeks. Notably, since spermatozoa are rendered transcriptionally and translationally silent during their development in the testes, it is most likely that the epididymis-documented alterations to the sperm sRNA profile are driven extrinsically, with a leading candidate being epididymosomes: small membrane enclosed extracellular vesicles that encapsulate a complex macromolecular cargo of proteins and RNAs, including the sRNAs. Here, we review the role of epididymosome–sperm communication in contributing to the establishment of the sperm sRNA profile during their epididymal transit.
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38
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Herrera-Carrillo E, Gao Z, Berkhout B. Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:452-462. [PMID: 31048184 PMCID: PMC6488825 DOI: 10.1016/j.omtn.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
Short hairpin RNAs (shRNAs) can induce gene silencing via the RNA interference (RNAi) mechanism. We designed an alternative shRNA molecule with a relatively short base-paired stem that bypasses Dicer and instead is processed by the Argonaute 2 (Ago2) protein into a single guide RNA strand that effectively induces RNAi. We called these molecules AgoshRNAs. Active anti-HIV AgoshRNAs were developed, but their RNAi activity was generally reduced compared with the matching shRNAs. In an attempt to further optimize the AgoshRNA design, we inserted several self-cleaving ribozymes at the 3′ terminus of the transcribed AgoshRNA and evaluated the impact on AgoshRNA processing and activity. The hepatitis delta virus (HDV) ribozyme is efficiently removed from the transcribed AgoshRNAs and generates a uniform 3′ overhang, which translates into the enhanced antiviral activity of these molecules.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
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39
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Kaadt E, Alsing S, Cecchi CR, Damgaard CK, Corydon TJ, Aagaard L. Efficient Knockdown and Lack of Passenger Strand Activity by Dicer-Independent shRNAs Expressed from Pol II-Driven MicroRNA Scaffolds. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:318-328. [PMID: 30654192 PMCID: PMC6348697 DOI: 10.1016/j.omtn.2018.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
The expression of short hairpin RNAs (shRNAs) may result in unwanted activity from the co-processed passenger strand. Recent studies have shown that shortening the stem of conventional shRNAs abolishes passenger strand release. These Dicer-independent shRNAs, expressed from RNA polymerase III (Pol III) promoters, rely on Ago2 processing in resemblance to miR-451. Using strand-specific reporters, we tested two designs, and our results support the loss of passenger strand activity. We demonstrate that artificial primary microRNA (pri-miRNA) transcripts, expressed from Pol II promoters, can potently silence a gene of choice. Among six different scaffolds tested, miR-324 and miR-451 were readily re-targeted to direct efficient knockdown from either a CMV or a U1 snRNA promoter. Importantly, the miR-shRNAs have no passenger strand activity and remain active in Dicer-knockout cells. Our vectors are straightforward to design, as we replace the pre-miR-324 or -451 sequences with a Dicer-independent shRNA mimicking miR-451 with unpaired A-C nucleotides at the base. The use of Pol II promoters allows for controlled expression, while the inclusion of pri-miRNA sequences likely requires Drosha processing and, as such, mimics microRNA biogenesis. Since this improved and tunable system bypasses the requirement for Dicer activity and abolishes passenger strand activity completely, it will likely prove favorable in both research and therapeutic applications in terms of versatility and enhanced safety.
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Affiliation(s)
- Erik Kaadt
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Sidsel Alsing
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Claudia R Cecchi
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Ophthalmology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
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40
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miRNA arm switching identifies novel tumour biomarkers. EBioMedicine 2018; 38:37-46. [PMID: 30425004 PMCID: PMC6306400 DOI: 10.1016/j.ebiom.2018.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/19/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Background microRNAs have been reported to play critical roles in cancer and to have potential as diagnostic biomarkers. During miRNA biogenesis, one strand of the miRNA hairpin precursor is preferentially selected as a functionally mature miRNA, while the other strand is typically degraded. Arm switching occurs when the strand preference is changed. This preference can be different and can change dynamically depending upon the species, tissue types, or development stages. Due to recent advances in next-generation sequencing methods, arm switching has been observed in a variety of cancers. Methods A tumour miRNA-Seq dataset was collected from The Cancer Genome Atlas (TCGA). The support vector machine (SVM) method combined with 5-fold cross validation was applied to select the best combination of arm-switched miRNA tumour markers. Survival analysis was also applied to identify patient survival associated miRNA markers. Findings We observed 51 arm-switched miRNAs and of these, 7 were associated with patient survival. Twenty-three 1-combination arm switching miRNAs with excellent diagnostic value were identified. Interestingly, ovarian cancer showed a significant difference in arm switching pattern compared with 32 other cancers. Interpretation These results suggest that arm switching miRNAs could be used as potential biomarkers for various cancers. Fund This work was partially supported by the National Natural Science Foundation of China (no. 61472158, 61572227), and University of Macau Faculty of Health Sciences (MYRG2016-00101-FHS).
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41
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Bernier A, Sagan SM. The Diverse Roles of microRNAs at the Host⁻Virus Interface. Viruses 2018; 10:v10080440. [PMID: 30126238 PMCID: PMC6116274 DOI: 10.3390/v10080440] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression at the post-transcriptional level. Through this activity, they are implicated in almost every cellular process investigated to date. Hence, it is not surprising that miRNAs play diverse roles in regulation of viral infections and antiviral responses. Diverse families of DNA and RNA viruses have been shown to take advantage of cellular miRNAs or produce virally encoded miRNAs that alter host or viral gene expression. MiRNA-mediated changes in gene expression have been demonstrated to modulate viral replication, antiviral immune responses, viral latency, and pathogenesis. Interestingly, viruses mediate both canonical and non-canonical interactions with miRNAs to downregulate specific targets or to promote viral genome stability, translation, and/or RNA accumulation. In this review, we focus on recent findings elucidating several key mechanisms employed by diverse virus families, with a focus on miRNAs at the host–virus interface during herpesvirus, polyomavirus, retroviruses, pestivirus, and hepacivirus infections.
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Affiliation(s)
- Annie Bernier
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada.
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada.
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada.
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Liu Z, Zhang C, Skamagki M, Khodadadi-Jamayran A, Zhang W, Kong D, Chang CW, Feng J, Han X, Townes TM, Li H, Kim K, Zhao R. Elevated p53 Activities Restrict Differentiation Potential of MicroRNA-Deficient Pluripotent Stem Cells. Stem Cell Reports 2018; 9:1604-1617. [PMID: 29141234 PMCID: PMC5688240 DOI: 10.1016/j.stemcr.2017.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/21/2022] Open
Abstract
Pluripotent stem cells (PSCs) deficient for microRNAs (miRNAs), such as Dgcr8−/− or Dicer−/– embryonic stem cells (ESCs), contain no mature miRNA and cannot differentiate into somatic cells. How miRNA deficiency causes differentiation defects remains poorly understood. Here, we report that miR-302 is sufficient to enable neural differentiation of differentiation-incompetent Dgcr8−/− ESCs. Our data showed that miR-302 directly suppresses the tumor suppressor p53, which is modestly upregulated in Dgcr8−/− ESCs and serves as a barrier restricting neural differentiation. We demonstrated that direct inactivation of p53 by SV40 large T antigen, a short hairpin RNA against Trp53, or genetic ablation of Trp53 in Dgcr8−/− PSCs enables neural differentiation, while activation of p53 by the MDM2 inhibitor nutlin-3a in wild-type ESCs inhibits neural differentiation. Together, we demonstrate that a major function of miRNAs in neural differentiation is suppression of p53 and that modest activation of p53 blocks neural differentiation of miRNA-deficient PSCs.
miR-302 enables neural differentiation of differentiation-incompetent Dgcr8−/− ESCs miR-302 directly suppresses p53 expression p53 inhibits neural differentiation of Dgcr8−/− and wild-type PSCs p53 may eliminate genetically defective embryos to save maternal resources
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Affiliation(s)
- Zhong Liu
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Maria Skamagki
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Sloan-Kettering Institute, Cell and Developmental Biology Program, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Zhang
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dexin Kong
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chia-Wei Chang
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingyang Feng
- Cook County Health and Hospital System, John H. Stroger Hospital, Chicago, IL 60612, USA
| | - Xiaosi Han
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tim M Townes
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Kitai Kim
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Sloan-Kettering Institute, Cell and Developmental Biology Program, Weill Medical College of Cornell University, New York, NY 10065, USA.
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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The Nefarious Nexus of Noncoding RNAs in Cancer. Int J Mol Sci 2018; 19:ijms19072072. [PMID: 30018188 PMCID: PMC6073630 DOI: 10.3390/ijms19072072] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023] Open
Abstract
The past decade has witnessed enormous progress, and has seen the noncoding RNAs (ncRNAs) turn from the so-called dark matter RNA to critical functional molecules, influencing most physiological processes in development and disease contexts. Many ncRNAs interact with each other and are part of networks that influence the cell transcriptome and proteome and consequently the outcome of biological processes. The regulatory circuits controlled by ncRNAs have become increasingly more relevant in cancer. Further understanding of these complex network interactions and how ncRNAs are regulated, is paving the way for the identification of better therapeutic strategies in cancer.
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Lam IKY, Chow JX, Lau CS, Chan VSF. MicroRNA-mediated immune regulation in rheumatic diseases. Cancer Lett 2018; 431:201-212. [PMID: 29859876 DOI: 10.1016/j.canlet.2018.05.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/11/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are endogenous small, non-coding RNAs that regulate genome expression at the post-transcriptional level. They are involved in a wide range of physiological processes including the maintenance of immune homeostasis and normal function. Accumulating evidence from animal studies show that alterations in pan or specific miRNA expression would break immunological tolerance, leading to autoimmunity. Differential miRNA expressions have also been documented in patients of many autoimmune disorders. In this review, we highlight the evidence that signifies the critical role of miRNAs in autoimmunity, specifically on their regulatory roles in the pathogenesis of several rheumatic diseases including systemic lupus erythematosus, rheumatoid arthritis and spondyloarthritis. The potential of miRNAs as biomarkers and therapeutic targets is also discussed. Manipulation of dysregulated miRNAs in vivo through miRNA delivery or inhibition offers promise for new therapeutic strategies in treating rheumatic diseases.
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Affiliation(s)
- Ian Kar Yin Lam
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jia Xin Chow
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Chak Sing Lau
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Vera Sau Fong Chan
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Trontti K, Väänänen J, Sipilä T, Greco D, Hovatta I. Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression. RNA (NEW YORK, N.Y.) 2018; 24:643-655. [PMID: 29445025 PMCID: PMC5900563 DOI: 10.1261/rna.064881.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism.
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Affiliation(s)
- Kalevi Trontti
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Juho Väänänen
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Tessa Sipilä
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Dario Greco
- Insitute of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
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46
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Herrera-Carrillo E, Harwig A, Berkhout B. Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity. RNA Biol 2017; 14:1559-1569. [PMID: 28569591 PMCID: PMC5785215 DOI: 10.1080/15476286.2017.1328349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
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Affiliation(s)
- Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Alex Harwig
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
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47
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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48
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Herrera-Carrillo E, Gao ZL, Harwig A, Heemskerk MT, Berkhout B. The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site. Nucleic Acids Res 2017; 45:4036-4050. [PMID: 27928054 PMCID: PMC5397164 DOI: 10.1093/nar/gkw1203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
Recent evidence indicates that shRNAs with a relatively short basepaired stem do not require Dicer processing, but instead are processed by the Argonaute 2 protein (Ago2). We named these molecules AgoshRNAs as both their processing and silencing function are mediated by Ago2. This alternative processing yields only a single RNA guide strand, which can avoid off-target effects induced by the passenger strand of regular shRNAs. It is important to understand this alternative processing route in mechanistic detail such that one can design improved RNA reagents. We verified that AgoshRNAs trigger site-specific cleavage of a complementary mRNA. Second, we document the importance of the identity of the 5΄-terminal nucleotide and its basepairing status for AgoshRNA activity. AgoshRNA activity is significantly reduced or even abrogated with C or U at the 5΄-terminal and is enhanced by introduction of a bottom mismatch and 5΄-terminal nucleotide A or G. The 5΄-terminal RNA nucleotide also represents the +1 position of the transcriptional promoter in the DNA, thus further complicating the analysis. Indeed, we report that +1 modification affects the transcriptional efficiency and accuracy of start site selection, with A or G as optimal nucleotide. These combined results allow us to propose general rules for the design and expression of potent AgoshRNA molecules.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zong-Liang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Matthias T Heemskerk
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
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49
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Pawlina K, Gurgul A, Szmatoła T, Koch C, Mählmann K, Witkowski M, Bugno-Poniewierska M. Comprehensive characteristics of microRNA expression profile of equine sarcoids. Biochimie 2017; 137:20-28. [DOI: 10.1016/j.biochi.2017.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
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50
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Herrera-Carrillo E, Harwig A, Berkhout B. Silencing of HIV-1 by AgoshRNA molecules. Gene Ther 2017; 24:453-461. [DOI: 10.1038/gt.2017.44] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022]
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