Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

Schraga Schwartz; Maxwell R. Mumbach; Marko Jovanovic; Tim Wang; Karolina Maciag; G. Guy Bushkin; Philipp Mertins; Dmitry Ter-Ovanesyan; Naomi Habib; Davide Cacchiarelli; Neville E. Sanjana; Elizaveta Freinkman; Michael E. Pacold; Rahul Satija; Tarjei S. Mikkelsen; Nir Hacohen; Feng Zhang; Steven A. Carr; Eric S. Lander; Aviv Regev

doi:10.1016/j.celrep.2014.05.048

Cell Reports (Jul 2014)

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

Schraga Schwartz,
Maxwell R. Mumbach,
Marko Jovanovic,
Tim Wang,
Karolina Maciag,
G. Guy Bushkin,
Philipp Mertins,
Dmitry Ter-Ovanesyan,
Naomi Habib,
Davide Cacchiarelli,
Neville E. Sanjana,
Elizaveta Freinkman,
Michael E. Pacold,
Rahul Satija,
Tarjei S. Mikkelsen,
Nir Hacohen,
Feng Zhang,
Steven A. Carr,
Eric S. Lander,
Aviv Regev

Affiliations

Schraga Schwartz: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Maxwell R. Mumbach: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Marko Jovanovic: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Tim Wang: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Karolina Maciag: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
G. Guy Bushkin: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
Philipp Mertins: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Dmitry Ter-Ovanesyan: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Naomi Habib: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Davide Cacchiarelli: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Neville E. Sanjana: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Elizaveta Freinkman: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
Michael E. Pacold: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
Rahul Satija: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Tarjei S. Mikkelsen: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Nir Hacohen: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Feng Zhang: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Steven A. Carr: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Eric S. Lander: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Aviv Regev: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

DOI: https://doi.org/10.1016/j.celrep.2014.05.048
Journal volume & issue: Vol. 8, no. 1
pp. 284 – 296

Abstract

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N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing “basal” degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.

Published in Cell Reports

ISSN: 2211-1247 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Biology (General)
Website: http://www.cell.com/cell-reports/home

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