Evidence map›Paper›PMID 26404942›Full record

ArticleGenes & development2015

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

Shengdong Ke, Endalkachew A Alemu, Claudia Mertens, Emily Conn Gantman, John J Fak, Aldo Mele, Bhagwattie Haripal, Ilana Zucker-Scharff, Michael J Moore, Christopher Y Park and 5 more

Open access · diamondAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes & development, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 530 papers.

0numbers the graph read from it
0cells of the map it votes in
530citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

530 citing papers in PubMed, 822 citations in OpenAlex.

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  18. Probing RNA-protein interactions in the early mouse embryo.bioRxiv : the preprint server for biology · 2026
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470 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 5 institutions in 2 countries.

Shengdong KeLaboratory 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;
Endalkachew A AlemuDepartment 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;
Claudia MertensLaboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
Emily Conn GantmanLaboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
John J FakLaboratory 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;
Aldo MeleLaboratory 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;
Bhagwattie HaripalLaboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
Ilana Zucker-ScharffLaboratory 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;
Michael J MooreLaboratory 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;
Christopher Y ParkLaboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA;
Cathrine Broberg VågbøProteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway.
Anna KusśnierczykProteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway.
Arne KlunglandDepartment 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;
James E DarnellLaboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA;
Robert B DarnellLaboratory 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;
Howard Hughes Medical Institute · USRockefeller University · USNew York Genome Center · USNorwegian University of Science and Technology · NOUniversity of Oslo · NO

Funding

NEUROLOGY AND THE MOLECULAR ROLE OF N-RBPS IN THE BRAINR01NS034389 · NINDS · ROCKEFELLER UNIVERSITY · PI DARNELL, ROBERT B · 1995 to 2016
$6.3M
Mapping the mechanisms of protein synthesis-dependent synaptic plasticityR01NS081706 · NINDS · ROCKEFELLER UNIVERSITY · PI DARNELL, ROBERT B · 2012 to 2016
$5.3M
Neurology and the molecular role of N-RBPs in the brainR56NS034389 · NINDS · ROCKEFELLER UNIVERSITY · PI DARNELL, ROBERT B · 2012 to 2012
$590k
NINDS NIH HHS NS034389NINDS NIH HHS NS081706NINDS NIH HHS R01 NS034389NINDS NIH HHS R01 NS081706NINDS NIH HHS R56 NS034389
6 · The paper itself

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.

Indexed as

Gene Expression Regulation3' Untranslated RegionsAdenosineAnimalsBrainCell LineDNA MethylationExonsGene Knockdown TechniquesHumansLiverMicePolyadenylationRNA, MessengertRNA Methyltransferases3' Untranslated RegionsAdenosineRNA, MessengertRNA Methyltransferasesalternative polyadenylationlast exonm6A-CLIP/IPmicroRNA

Identifiers

PMID26404942
PMCPMC4604345
OpenAlexW2180404227

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.