title: m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome.
abstract: N(6)-Methyladenosine (m(6)A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m(6)A modified ('m(6)A levels') or the relationship of m(6)A modification(s) to alternative RNA isoforms. To deconvolute the m(6)A epitranscriptome, we developed m(6)A-level and isoform-characterization sequencing (m(6)A-LAIC-seq). We found that cells exhibit a broad range of nonstoichiometric m(6)A levels with cell-type specificity. At the level of isoform characterization, we discovered widespread differences in the use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3' untranslated regions, while nonmethylated transcript isoforms tend to use distal APA sites. m(6)A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m(6)A modifications.
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Benoit
authors.identifier: 0000-0002-1246-6890
authors.initials: B
authors.lastname: Molinie
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA.
authors.forename: Jinkai
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Kok Seong
authors.initials: KS
authors.lastname: Lim
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Roman
authors.initials: R
authors.lastname: Hillebrand
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA.
authors.forename: Zhi-Xiang
authors.identifier: 0000-0001-9230-2169
authors.initials: ZX
authors.lastname: Lu
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Van Wittenberghe
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Howard
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Kaveh
authors.identifier: 0000-0002-7863-0489
authors.initials: K
authors.lastname: Daneshvar
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.
authors.forename: Alan C
authors.initials: AC
authors.lastname: Mullen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Dedon
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.|Center for Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Cosmas C
authors.initials: CC
authors.lastname: Giallourakis
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000241:Adenosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000235:genetics; D002478:Cells, Cultured; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D026723:Polyadenylation; D020033:Protein Isoforms; D012333:RNA, Messenger / Q000235:genetics; D013234:Stem Cells / Q000378:metabolism; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D020033:Protein Isoforms; D012333:RNA, Messenger; C010223:N-methyladenosine; D000241:Adenosine