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Nicastro G, Abis G, Klein P, Esteban-Serna S, Gallagher C, Chaves-Arquero B, Cai Y, Figueiredo AM, Martin SR, Patani R, Taylor IA, Ramos A. Direct m6A recognition by IMP1 underlays an alternative model of target selection for non-canonical methyl-readers. Nucleic Acids Res 2023; 51:8774-8786. [PMID: 37377445 PMCID: PMC10484666 DOI: 10.1093/nar/gkad534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
m6A methylation provides an essential layer of regulation in organismal development, and is aberrant in a range of cancers and neuro-pathologies. The information encoded by m6A methylation is integrated into existing RNA regulatory networks by RNA binding proteins that recognise methylated sites, the m6A readers. m6A readers include a well-characterised class of dedicated proteins, the YTH proteins, as well as a broader group of multi-functional regulators where recognition of m6A is only partially understood. Molecular insight in this recognition is essential to build a mechanistic understanding of global m6A regulation. In this study, we show that the reader IMP1 recognises the m6A using a dedicated hydrophobic platform that assembles on the methyl moiety, creating a stable high-affinity interaction. This recognition is conserved across evolution and independent from the underlying sequence context but is layered upon the strong sequence specificity of IMP1 for GGAC RNA. This leads us to propose a concept for m6A regulation where methylation plays a context-dependent role in the recognition of selected IMP1 targets that is dependent on the cellular concentration of available IMP1, differing from that observed for the YTH proteins.
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Affiliation(s)
- Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giancarlo Abis
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Pierre Klein
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sofia Esteban-Serna
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Christopher Gallagher
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Belen Chaves-Arquero
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Yuyang Cai
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Angelo Miguel Figueiredo
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Stephen R Martin
- Structural Biology Technology Platform, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Ramos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
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2
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Song B, Huang D, Zhang Y, Wei Z, Su J, Pedro de Magalhães J, Rigden DJ, Meng J, Chen K. m6A-TSHub: Unveiling the Context-specific m 6A Methylation and m 6A-affecting Mutations in 23 Human Tissues. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:678-694. [PMID: 36096444 PMCID: PMC10787194 DOI: 10.1016/j.gpb.2022.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats.
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Affiliation(s)
- Bowen Song
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daiyun Huang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
| | - Yuxin Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jionglong Su
- School of AI and Advanced Computing, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - João Pedro de Magalhães
- Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jia Meng
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Kunqi Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China.
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3
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Abstract
The epitranscriptome, defined as RNA modifications that do not involve alterations in the nucleotide sequence, is a popular topic in the genomic sciences. Because we need massive computational techniques to identify epitranscriptomes within individual transcripts, many tools have been developed to infer epitranscriptomic sites as well as to process datasets using high-throughput sequencing. In this review, we summarize recent developments in epitranscriptome spatial detection and data analysis and discuss their progression.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
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4
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Abstract
Fibroblasts play an important role in the pathogenic mechanisms of several socially significant diseases, including pulmonary and cardiovascular fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease. The alterations of the epitranscriptome, including more than 170 distinct post-transcriptional RNA modifications or editing events, justified their investigation as an important modulator of fibrosis. Recent development of high-throughput methods allows the identification of RNA modification sites and their mechanistic aspect in the fibrosis development. The most common RNA modification is methylation of N6-adenosine deposited by the m6A methyltransferase complex (METTL3/14/16, WTAP, KIAA1429, and RBM15/15B), erased by demethylases (FTO and ALKBH5), and recognized by binding proteins (e.g., YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, etc.). Adenosine to inosine (A-to-I) RNA editing is another abundant editing event converting adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase (ADAR) proteins. Last, but not least, 5-methylcytosine (m5C) regulates the stability and translation of mRNAs. All those RNA modifications have been observed in mRNA as well as the non-coding regions of pre-mRNA and ncRNAs, and demonstrate to be involved in fibrosis in different cellular and animal models. This Mini-Review focuses on the latest research on epitranscriptomic marks related to fibroblast biology and fibrosis as well as elucidates the future research directions in this context.
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Affiliation(s)
- Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen SV, Denmark
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen SV, Denmark
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Kostyusheva A, Brezgin S, Glebe D, Kostyushev D, Chulanov V. Host-cell interactions in HBV infection and pathogenesis: the emerging role of m6A modification. Emerg Microbes Infect 2021; 10:2264-2275. [PMID: 34767497 PMCID: PMC8648018 DOI: 10.1080/22221751.2021.2006580] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/28/2022]
Abstract
Hepatitis B virus (HBV) is a DNA virus with a complex life cycle that includes a reverse transcription step. HBV is poorly sensed by the immune system and frequently establishes persistent infection that can cause chronic infection, the leading cause of liver cancer and cirrhosis worldwide. Recent mounting evidence has indicated the growing importance of RNA methylation (m6A modification) in viral replication, immune escape, and carcinogenesis. The value of m6A RNA modification for the prediction and clinical management of chronic HBV infection remains to be assessed. However, a number of studies indicate the important role of m6A-marked transcripts and factors of m6A machinery in managing HBV-related pathologies. In this review, we discuss the fundamental and potential clinical impact of m6A modifications on HBV infection and pathogenesis, as well as highlight the important molecular techniques and tools that can be used for studying RNA m6A methylome.
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Affiliation(s)
- Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
| | - Dieter Glebe
- National Reference Center for Hepatitis B Viruses and Hepatitis D Viruses, Institute of Medical Virology, Justus Liebig University of Giessen, Giessen, Germany
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
- Department of Infectious Diseases, Sechenov University, Moscow, Russia
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6
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Gameiro PA, Encheva V, Dos Santos MS, MacRae JI, Ule J. Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling. J Biol Chem 2021; 297:101294. [PMID: 34634303 PMCID: PMC8567201 DOI: 10.1016/j.jbc.2021.101294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023] Open
Abstract
Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. However, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications are poorly understood. Here, we developed a 13C labeling approach, called 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleoside samples and showed the distinct kinetics of the N6-methyladenosine (m6A) versus 7-methylguanosine (m7G) modification in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits distinct turnover in small RNAs and free ribonucleosides when compared to known m62A-modified large rRNAs. Finally, combined measurements of turnover and abundance of these modifications informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of the origin of modified RNAs at steady-state and subsequent dynamics under nonstationary conditions. These results open new directions to probe the presence and biological regulation of modifications in particular RNAs.
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Affiliation(s)
- Paulo A Gameiro
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Vesela Encheva
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | | | - James I MacRae
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | - Jernej Ule
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
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7
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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 2021; 48:2399-2414. [PMID: 33196096 DOI: 10.1042/bst20190492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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The m 6A-epitranscriptome in brain plasticity, learning and memory. Semin Cell Dev Biol 2021; 125:110-121. [PMID: 34053866 DOI: 10.1016/j.semcdb.2021.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
Activity-dependent gene expression and protein translation underlie the ability of neurons to dynamically adjust their synaptic strength in response to sensory experience and during learning. The emerging field of epitranscriptomics (RNA modifications) has rapidly shifted our views on the mechanisms that regulate gene expression. Among hundreds of biochemical modifications on RNA, N6-methyladenosine (m6A) is the most abundant reversible mRNA modification in the brain. Its dynamic nature and ability to regulate all aspects of mRNA processing have positioned m6A as an important and versatile regulator of nervous system functions, including neuronal plasticity, learning and memory. In this review, we summarise recent experimental evidence that supports the role of m6A signalling in learning and memory, as well as providing an overview of the underlying molecular mechanisms in neurons. We also discuss the consequences of perturbed m6A signalling and/or its regulatory networks which are increasingly being linked to various cognitive disorders in humans.
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9
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Song B, Chen K, Tang Y, Wei Z, Su J, de Magalhães JP, Rigden DJ, Meng J. ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. Brief Bioinform 2021; 22:6276017. [PMID: 33993206 DOI: 10.1093/bib/bbab088] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/04/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Motivation N6-methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. Evidence increasingly demonstrates its crucial importance in essential molecular mechanisms and various diseases. With recent advances in sequencing techniques, tens of thousands of m6A sites are identified in a typical high-throughput experiment, posing a key challenge to distinguish the functional m6A sites from the remaining 'passenger' (or 'silent') sites. Results: We performed a comparative conservation analysis of the human and mouse m6A epitranscriptomes at single site resolution. A novel scoring framework, ConsRM, was devised to quantitatively measure the degree of conservation of individual m6A sites. ConsRM integrates multiple information sources and a positive-unlabeled learning framework, which integrated genomic and sequence features to trace subtle hints of epitranscriptome layer conservation. With a series validation experiments in mouse, fly and zebrafish, we showed that ConsRM outperformed well-adopted conservation scores (phastCons and phyloP) in distinguishing the conserved and unconserved m6A sites. Additionally, the m6A sites with a higher ConsRM score are more likely to be functionally important. An online database was developed containing the conservation metrics of 177 998 distinct human m6A sites to support conservation analysis and functional prioritization of individual m6A sites. And it is freely accessible at: https://www.xjtlu.edu.cn/biologicalsciences/con.
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Affiliation(s)
- Bowen Song
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Kunqi Chen
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, School of Basic Medical Science, Fujian Medical University, Fuzhou, China
| | - Yujiao Tang
- Xi'an Jiaotong-Liverpool University, L7 8TX, Liverpool, United Kingdom
| | - Zhen Wei
- Department of Biological Science, Xi'an Jiaotong-Liverpool University, L7 8TX, Liverpool, United Kingdom
| | - Jionglong Su
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, L7 8TX, Liverpool, United Kingdom
| | - João Pedro de Magalhães
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, L7 8TX, Liverpool, United Kingdom
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10
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Wardowska A. m6A RNA Methylation in Systemic Autoimmune Diseases-A New Target for Epigenetic-Based Therapy? Pharmaceuticals (Basel) 2021; 14:ph14030218. [PMID: 33807762 PMCID: PMC8001529 DOI: 10.3390/ph14030218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022] Open
Abstract
The general background of autoimmune diseases is a combination of genetic, epigenetic and environmental factors, that lead to defective immune reactions. This erroneous immune cell activation results in an excessive production of autoantibodies and prolonged inflammation. During recent years epigenetic mechanisms have been extensively studied as potential culprits of autoreactivity. Alike DNA and proteins, also RNA molecules are subjected to an extensive repertoire of chemical modifications. N6-methyladenosine is the most prevalent form of internal mRNA modification in eukaryotic cells and attracts increasing attention due to its contribution to human health and disease. Even though m6A is confirmed as an essential player in immune response, little is known about its role in autoimmunity. Only few data have been published up to date in the field of RNA methylome. Moreover, only selected autoimmune diseases have been studied in respect of m6A role in their pathogenesis. In this review, I attempt to present all available research data regarding m6A alterations in autoimmune disorders and appraise its role as a potential target for epigenetic-based therapies.
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Affiliation(s)
- Anna Wardowska
- Department of Embryology, Medical University of Gdansk, 80-210 Gdansk, Poland
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11
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Chen K, Song B, Tang Y, Wei Z, Xu Q, Su J, de Magalhães JP, Rigden DJ, Meng J. RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. Nucleic Acids Res 2021; 49:D1396-D1404. [PMID: 33010174 PMCID: PMC7778951 DOI: 10.1093/nar/gkaa790] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022] Open
Abstract
Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge. Recent studies suggest that RNA modifications play versatile roles in essential biological mechanisms, and are closely related to the progression of various diseases including multiple cancers. To comprehensively unveil the association between disease-associated variants and their epitranscriptome disturbance, we built RMDisease, a database of genetic variants that can affect RNA modifications. By integrating the prediction results of 18 different RNA modification prediction tools and also 303,426 experimentally-validated RNA modification sites, RMDisease identified a total of 202,307 human SNPs that may affect (add or remove) sites of eight types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G and Nm). These include 4,289 disease-associated variants that may imply disease pathogenesis functioning at the epitranscriptome layer. These SNPs were further annotated with essential information such as post-transcriptional regulations (sites for miRNA binding, interaction with RNA-binding proteins and alternative splicing) revealing putative regulatory circuits. A convenient graphical user interface was constructed to support the query, exploration and download of the relevant information. RMDisease should make a useful resource for studying the epitranscriptome impact of genetic variants via multiple RNA modifications with emphasis on their potential disease relevance. RMDisease is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/rmd.
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Affiliation(s)
- Kunqi Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK
| | - Bowen Song
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK.,Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Yujiao Tang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Qingru Xu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jionglong Su
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | | | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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13
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Wang Y, Zhang Y, Du Y, Zhou M, Hu Y, Zhang S. Emerging roles of N6-methyladenosine (m 6A) modification in breast cancer. Cell Biosci 2020; 10:136. [PMID: 33292526 PMCID: PMC7690038 DOI: 10.1186/s13578-020-00502-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant, dynamic, and reversible epigenetic RNA modification that is found in coding and non-coding RNAs. Emerging studies have shown that m6A and its regulators affect multiple steps in RNA metabolism and play broad roles in various cancers. Worldwide, breast cancer is the most prevalent cancer in female. It is a very heterogeneous disease characterized by genetic and epigenetic variations in tumor cells. Increasing evidence has shown that the dysregulation of m6A-related effectors, as methyltransferases, demethylases, and m6A binding proteins, is pivotal in breast cancer pathogenesis. In this review, we have summarized the most up-to-date research on the biological functions of m6A modification in breast cancer and have discussed the potential clinical applications and future directions of m6A modification as a biomarker as well as a therapeutic target of breast cancer.
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Affiliation(s)
- Yanyan Wang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Meiqi Zhou
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yue Hu
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Suzhan Zhang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
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