Format

Send to

Choose Destination
Genes Dev. 2015 Oct 1;29(19):2037-53. doi: 10.1101/gad.269415.115. Epub 2015 Sep 24.

A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation.

Author information

1
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;
2
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;
3
Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
4
Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
5
Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway.
6
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;

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.

KEYWORDS:

alternative polyadenylation; last exon; m6A-CLIP/IP; microRNA

PMID:
26404942
PMCID:
PMC4604345
DOI:
10.1101/gad.269415.115
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center