title: A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation.
abstract: We adapted UV CLIP (cross-linking immunoprecipitation) to accurately locate tens of thousands of m(6)A residues in mammalian mRNA with single-nucleotide resolution. More than 70% of these residues are present in the 3'-most (last) exons, with a very sharp rise (sixfold) within 150-400 nucleotides of the start of the last exon. Two-thirds of last exon m(6)A and >40% of all m(6)A in mRNA are present in 3' untranslated regions (UTRs); contrary to earlier suggestions, there is no preference for location of m(6)A sites around stop codons. Moreover, m(6)A is significantly higher in noncoding last exons than in next-to-last exons harboring stop codons. We found that m(6)A density peaks early in the 3' UTR and that, among transcripts with alternative polyA (APA) usage in both the brain and the liver, brain transcripts preferentially use distal polyA sites, as reported, and also show higher proximal m(6)A density in the last exons. Furthermore, when we reduced m6A methylation by knocking down components of the methylase complex and then examined 661 transcripts with proximal m6A peaks in last exons, we identified a set of 111 transcripts with altered (approximately two-thirds increased proximal) APA use. Taken together, these observations suggest a role of m(6)A modification in regulating proximal alternative polyA choice.
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Shengdong
authors.initials: S
authors.lastname: Ke
authors.affiliation: Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0316 Oslo, Norway;
authors.forename: Endalkachew A
authors.initials: EA
authors.lastname: Alemu
authors.affiliation: Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Claudia
authors.initials: C
authors.lastname: Mertens
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
authors.forename: Emily Conn
authors.initials: EC
authors.lastname: Gantman
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA;
authors.forename: John J
authors.initials: JJ
authors.lastname: Fak
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Aldo
authors.initials: A
authors.lastname: Mele
authors.affiliation: Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Bhagwattie
authors.initials: B
authors.lastname: Haripal
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Ilana
authors.initials: I
authors.lastname: Zucker-Scharff
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA;
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Moore
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
authors.forename: Christopher Y
authors.initials: CY
authors.lastname: Park
authors.affiliation: Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway.
authors.forename: Cathrine Broberg
authors.initials: CB
authors.lastname: Vågbø
authors.affiliation: Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway.
authors.forename: Anna
authors.initials: A
authors.lastname: Kusśnierczyk
authors.affiliation: Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0316 Oslo, Norway;
authors.forename: Arne
authors.initials: A
authors.lastname: Klungland
authors.affiliation: Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
authors.forename: James E
authors.initials: JE
authors.lastname: Darnell
authors.affiliation: Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
authors.forename: Robert B
authors.initials: RB
authors.lastname: Darnell
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000241:Adenosine / Q000378:metabolism*; D000818:Animals; D001921:Brain / Q000166:cytology / Q000378:metabolism; D002460:Cell Line; D019175:DNA Methylation / Q000235:genetics*; D005091:Exons / Q000235:genetics*; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D006801:Humans; D008099:Liver / Q000166:cytology / Q000378:metabolism; D051379:Mice; D026723:Polyadenylation; D012333:RNA, Messenger / Q000737:chemistry*; D012359:tRNA Methyltransferases / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D012333:RNA, Messenger; D012359:tRNA Methyltransferases; D000241:Adenosine
keywords: alternative polyadenylation; last exon; m6A-CLIP/IP; microRNA