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

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

838 Scopus citations

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 language	American English
Pages (from-to)	284-296
Number of pages	13
Journal	Cell Reports
Volume	8
Issue number	1
DOIs	https://doi.org/10.1016/j.celrep.2014.05.048
State	Published - 10 Jul 2014
Externally published	Yes

Bibliographical note

Funding Information:
This work was supported by NHGRI CEGS P50 HG006193 (A.R.), U54 HG003067 (E.S.L), and Broad Institute Funds. A.R. was supported by an NIH Pioneer Award and HHMI. S.S. was supported by a European Molecular Biology Organization fellowship, and S.S. and D.C. were supported by Human Frontier Science Program fellowships. M.J. was supported by fellowships of the Swiss National Science Foundation for advanced researchers (SNF) and the Marie Sklodowska-Curie IOF.

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10.1016/j.celrep.2014.05.048

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Schwartz, S., Mumbach, M. R., Jovanovic, M., Wang, T., Maciag, K., Bushkin, G. G., Mertins, P., Ter-Ovanesyan, D., Habib, N., Cacchiarelli, D., Sanjana, N. E., Freinkman, E., Pacold, M. E., Satija, R., Mikkelsen, T. S., Hacohen, N., Zhang, F., Carr, S. A., Lander, E. S., & 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

@article{6012b57fd9414aaba4d99c19dfced91e,

title = "Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites",

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.",

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

note = "Funding Information: This work was supported by NHGRI CEGS P50 HG006193 (A.R.), U54 HG003067 (E.S.L), and Broad Institute Funds. A.R. was supported by an NIH Pioneer Award and HHMI. S.S. was supported by a European Molecular Biology Organization fellowship, and S.S. and D.C. were supported by Human Frontier Science Program fellowships. M.J. was supported by fellowships of the Swiss National Science Foundation for advanced researchers (SNF) and the Marie Sklodowska-Curie IOF. ",

year = "2014",

month = jul,

day = "10",

doi = "10.1016/j.celrep.2014.05.048",

language = "American English",

volume = "8",

pages = "284--296",

journal = "Cell Reports",

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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

TY - JOUR

T1 - Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites

AU - Schwartz, Schraga

AU - Mumbach, Maxwell R.

AU - Jovanovic, Marko

AU - Wang, Tim

AU - Maciag, Karolina

AU - Bushkin, G. Guy

AU - Mertins, Philipp

AU - Ter-Ovanesyan, Dmitry

AU - Habib, Naomi

AU - Cacchiarelli, Davide

AU - Sanjana, Neville E.

AU - Freinkman, Elizaveta

AU - Pacold, Michael E.

AU - Satija, Rahul

AU - Mikkelsen, Tarjei S.

AU - Hacohen, Nir

AU - Zhang, Feng

AU - Carr, Steven A.

AU - Lander, Eric S.

AU - Regev, Aviv

N1 - Funding Information: This work was supported by NHGRI CEGS P50 HG006193 (A.R.), U54 HG003067 (E.S.L), and Broad Institute Funds. A.R. was supported by an NIH Pioneer Award and HHMI. S.S. was supported by a European Molecular Biology Organization fellowship, and S.S. and D.C. were supported by Human Frontier Science Program fellowships. M.J. was supported by fellowships of the Swiss National Science Foundation for advanced researchers (SNF) and the Marie Sklodowska-Curie IOF.

PY - 2014/7/10

Y1 - 2014/7/10

N2 - 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.

AB - 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.

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U2 - 10.1016/j.celrep.2014.05.048

DO - 10.1016/j.celrep.2014.05.048

M3 - Article

C2 - 24981863

AN - SCOPUS:84904035764

SN - 2211-1247

VL - 8

SP - 284

EP - 296

JO - Cell Reports

JF - Cell Reports

IS - 1

ER -

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites

Abstract

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