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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)284-296
Number of pages13
JournalCell Reports
Volume8
Issue number1
DOIs
StatePublished - Jul 10 2014

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Methylation
RNA
Messenger RNA
RNA Stability
Methyltransferases
Life Cycle Stages
Transcriptome
Proteomics
Life cycle
Nucleotides
Tuning
Degradation
Monitoring
Proteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Schwartz, S., Mumbach, M. R., Jovanovic, M., Wang, T., Maciag, K., Bushkin, G. G., ... Regev, A. (2014). Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. Cell Reports, 8(1), 284-296. https://doi.org/10.1016/j.celrep.2014.05.048

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. / Schwartz, Schraga; Mumbach, Maxwell R.; Jovanovic, Marko; Wang, Tim; Maciag, Karolina; Bushkin, G. Guy; Mertins, Philipp; Ter-Ovanesyan, Dmitry; Habib, Naomi; Cacchiarelli, Davide; Sanjana, Neville E.; Freinkman, Elizaveta; Pacold, Michael E.; Satija, Rahul; Mikkelsen, Tarjei S.; Hacohen, Nir; Zhang, Feng; Carr, Steven A.; Lander, Eric S.; Regev, Aviv.

In: Cell Reports, Vol. 8, No. 1, 10.07.2014, p. 284-296.

Research output: Contribution to journalArticle

Schwartz, S, Mumbach, MR, Jovanovic, M, Wang, T, Maciag, K, Bushkin, GG, Mertins, P, Ter-Ovanesyan, D, Habib, N, Cacchiarelli, D, Sanjana, NE, Freinkman, E, Pacold, ME, Satija, R, Mikkelsen, TS, Hacohen, N, Zhang, F, Carr, SA, Lander, ES & Regev, A 2014, 'Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites', Cell Reports, vol. 8, no. 1, pp. 284-296. https://doi.org/10.1016/j.celrep.2014.05.048
Schwartz, Schraga ; Mumbach, Maxwell R. ; Jovanovic, Marko ; Wang, Tim ; Maciag, Karolina ; Bushkin, G. Guy ; Mertins, Philipp ; Ter-Ovanesyan, Dmitry ; Habib, Naomi ; Cacchiarelli, Davide ; Sanjana, Neville E. ; Freinkman, Elizaveta ; Pacold, Michael E. ; Satija, Rahul ; Mikkelsen, Tarjei S. ; Hacohen, Nir ; Zhang, Feng ; Carr, Steven A. ; Lander, Eric S. ; Regev, Aviv. / Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. In: Cell Reports. 2014 ; Vol. 8, No. 1. pp. 284-296.
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