Journal ArticleDOI
Epitranscriptome sequencing technologies: decoding RNA modifications
TLDR
This Review focuses on the major mRNA modifications in the transcriptome of eukaryotic cells: N6-methyladenosine, N6, 2′-O-dimethyladenosines, 5-methylcytidine, 5.hydroxylmethylcyTidine, inosine, pseudouridine and N1-methyl adenosine.Abstract:
In recent years, major breakthroughs in RNA-modification-mediated regulation of gene expression have been made, leading to the emerging field of epitranscriptomics.Our understanding of the distribution, regulation and function of these dynamic RNA modifications is based on sequencing technologies. In this Review, we focus on the major mRNA modifications in the transcriptome of eukaryotic cells: N6-methyladenosine, N6, 2'-O-dimethyladenosine, 5-methylcytidine, 5-hydroxylmethylcytidine, inosine, pseudouridine and N1-methyladenosine. We discuss the sequencing technologies used to profile these epitranscriptomic marks, including scale, resolution, quantitative feature, pre-enrichment capability and the corresponding bioinformatics tools. We also discuss the challenges of epitranscriptome profiling and highlight the prospect of future detection tools. We aim to guide the choice of different detection methods and inspire new ideas in RNA biology.read more
Citations
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Journal ArticleDOI
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
Ki Jun Yoon,Francisca Rojas Ringeling,Caroline Vissers,Fadi Jacob,Michael J. Pokrass,Dennisse Jimenez-Cyrus,Yijing Su,Namshik Kim,Yunhua Zhu,Lily Zheng,Sunghan Kim,Xinyuan Wang,Louis C. Dore,Peng Jin,Sergi Regot,Xiaoxi Zhuang,Stefan Canzar,Chuan He,Guo Li Ming,Hongjun Song +19 more
TL;DR: It is shown that m6A depletion by Mettl14 knockout in embryonic mouse brains prolongs the cell cycle of radial glia cells and extends cortical neurogenesis into postnatal stages and uncovers previously unappreciated transcriptional prepatterning in cortical neural stem cells.
Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA
Schraga Schwartz,Douglas A. Bernstein,Maxwell R. Mumbach,Marko Jovanovic,Rebecca H. Herbst,Brian X. León-Ricardo,Jesse M. Engreitz,Mitchell Guttman,Rahul Satija,Eric S. Lander,Gerald R. Fink,Aviv Regev,Aviv Regev,Aviv Regev +13 more
TL;DR: This work identifies an enhanced, transcriptome-wide scope for pseudouridine and methods to dissect its underlying mechanisms and function and discovers hundreds of unique sites in human and yeast mRNAs and snoRNAs.
Journal ArticleDOI
The role of m6A modification in the biological functions and diseases.
Xiulin Jiang,Xiulin Jiang,Baiyang Liu,Baiyang Liu,Zhi Nie,Zhi Nie,Zhi Nie,Lincan Duan,Qiuxia Xiong,Zhixian Jin,Cui-Ping Yang,Yongbin Chen,Yongbin Chen +12 more
TL;DR: In this paper, the authors discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems.
Journal ArticleDOI
The RNA modification landscape in human disease.
TL;DR: This work summarizes the state of knowledge and provides a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases, expecting that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.
Journal ArticleDOI
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E. Workman,Alison D. Tang,Paul S. Tang,Miten Jain,John R. Tyson,Roham Razaghi,Philip C. Zuzarte,Timothy Gilpatrick,Alexander Payne,Joshua Quick,Norah Sadowski,Nadine Holmes,Jaqueline Goes de Jesus,Karen Jones,Cameron M. Soulette,Terrance P. Snutch,Nicholas J. Loman,Benedict Paten,Matthew Loose,Jared T. Simpson,Jared T. Simpson,Hugh E. Olsen,Angela N. Brooks,Mark Akeson,Winston Timp +24 more
TL;DR: This study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions to identify 33,984 plausible RNA isoforms and describes strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes.
References
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Journal ArticleDOI
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Mamta Tahiliani,Kian Peng Koh,Yinghua Shen,William A. Pastor,Hozefa S. Bandukwala,Yevgeny Brudno,Suneet Agarwal,Lakshminarayan M. Iyer,David R. Liu,L. Aravind,Anjana Rao +10 more
TL;DR: It is shown here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro.
Journal ArticleDOI
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
Dan Dominissini,Sharon Moshitch-Moshkovitz,Schraga Schwartz,Schraga Schwartz,Mali Salmon-Divon,Lior Ungar,Sivan Osenberg,Sivan Osenberg,Karen Cesarkas,Jasmine Jacob-Hirsch,Ninette Amariglio,Martin Kupiec,Rotem Sorek,Gideon Rechavi,Gideon Rechavi +14 more
TL;DR: The findings suggest that RNA decoration by m6A has a fundamental role in regulation of gene expression, and a subset of stimulus-dependent, dynamically modulated sites is identified.
Journal ArticleDOI
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Kate D. Meyer,Yogesh Saletore,Paul Zumbo,Olivier Elemento,Christopher E. Mason,Samie R. Jaffrey +5 more
TL;DR: A method is presented for transcriptome-wide m(6)A localization, which combines m( 6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) and reveals insights into the epigenetic regulation of the mammalian transcriptome.
Journal ArticleDOI
N6-methyladenosine-dependent regulation of messenger RNA stability
Xiao Wang,Zhike Lu,Adrian Gomez,Gary C. Hon,Yanan Yue,Dali Han,Ye Fu,Marc Parisien,Qing Dai,Guifang Jia,Bing Ren,Tao Pan,Chuan He +12 more
TL;DR: It is shown that m6A is selectively recognized by the human YTH domain family 2 (YTHDF2) ‘reader’ protein to regulate mRNA degradation and established the role of YTH DF2 in RNA metabolism, showing that binding of Y THDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies.
Journal ArticleDOI
N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.
Guifang Jia,Ye Fu,Xu Zhao,Xu Zhao,Qing Dai,Guanqun Zheng,Ying Yang,Ying Yang,Chengqi Yi,Tomas Lindahl,Tao Pan,Yun-Gui Yang,Yun-Gui Yang,Chuan He +13 more
TL;DR: FTO exhibits efficient oxidative demethylation activity of abundant N6-methyladenosine (m6A) residues in RNA in vitro, and it is shown that FTO partially colocalizes with nuclear speckles, supporting m6A in nuclear RNA as a physiological substrate of FTO.
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