N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

Radhika A. Varier; Theodora Sideri; Charlotte Capitanchik; Zornitsa Manova; Enrica Calvani; Alice Rossi; Raghu R. Edupuganti; Imke Ensinck; Vincent W.C. Chan; Harshil Patel; Joanna Kirkpatrick; Peter Faull; Ambrosius P. Snijders; Michiel Vermeulen; Markus Ralser; Jernej Ule; Nicholas M. Luscombe; Folkert J. van Werven

doi:10.7554/eLife.84034

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

Radhika A. Varier^*, Theodora Sideri, Charlotte Capitanchik, Zornitsa Manova, Enrica Calvani, Alice Rossi, Raghu R. Edupuganti, Imke Ensinck, Vincent W.C. Chan, Harshil Patel, Joanna Kirkpatrick, Peter Faull, Ambrosius P. Snijders, Michiel Vermeulen, Markus Ralser, Jernej Ule, Nicholas M. Luscombe, Folkert J. van Werven^*

^*Corresponding author for this work

PCE - Proteomics Center of Excellence

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

10 Scopus citations

Abstract

N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contin-gent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

Original language	English (US)
Article number	e84034
Journal	eLife
Volume	11
DOIs	https://doi.org/10.7554/eLife.84034
State	Published - Nov 2022

Funding

We are grateful to the members of the laboratory of Folkert van Werven for fruitful discussions and critical reading of the manuscript. We thank members of Ule and Luscombe labs, specifically Julian Zagalak, Christoph Sadee, Patrick Toolan-Kerr, Igor Ruiz De Los Mozos, Paulo Gameiro, Federica Capraro, Andrew Steele and Flora Lee for sharing ideas, protocols and reagents towards the iCLIP and miCLIP experiments and analysis. We acknowledge Leon Chan, Elçin Ünal, and Martin Pool for sharing reagents and Schraga Schwartz and David Dierks for providing the m6A-seq2 data. We thank the Crick Advanced Sequencing, Proteomics, Metabolomics, Fermentation and Genomics Equipment Park Facilities for experimental support, specifically Phil East for helping with submission to GEO, James MacRae, Christoph Messner and Svend Kjaer for technical support. We also are grateful to the three reviewers for their comments and suggestions.The Vermeulen lab is part of the Oncode institute, which is partly funded by the Dutch Cancer Society (KWF). This research was funded in whole, or in part, by the Wellcome Trust (FC001203, FC010110, FC001134). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. This work was supported by the Francis Crick Institute (FC001203, FC010110, FC001134), which receives its core funding from Cancer Research UK (FC001203, FC010110, FC001134), the UK Medical Research Council (FC001203, FC010110, FC001134), and the Wellcome Trust (FC001203, FC010110, FC001134).Wellcome Trust (FC001203) – Radhika Varier, Theodora Sideri, Zornitsa Manova, Imke Ensinck, Alice Rossi, Folkert van Werven; CRUK (FC001203) - Radhika Varier, Theodora Sideri, Zornitsa Manova, Imke Ensinck, Alice Rossi, Folkert van Werven; Medical research council (FC001203) - Radhika Varier, Theodora Sideri, Zornitsa Manova, Imke Ensinck, Alice Rossi, Folkert van Werven; Wellcome Trust (FC010110) – Charlotte Capi-tanchik and Nicholas Luscombe; CRUK (FC010110) - Charlotte Capitanchik and Nicholas Luscombe; Medical research council (FC010110) - Charlotte Capitanchik and Nicholas Luscombe; Wellcome Trust (FC001134) – Enrica Calvani and Markus Ralser; CRUK (FC001134) - Enrica Calvani and Markus Ralser; Medical research council (FC001134) - Enrica Calvani and Markus Ralser; Dutch Cancer Society (KWF) -Raghu Edupuganti and Michiel Vermeulen.The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. We also are grateful to the three reviewers for their comments and suggestions.

ASJC Scopus subject areas

General Neuroscience
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology

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10.7554/eLife.84034

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Varier, R. A., Sideri, T., Capitanchik, C., Manova, Z., Calvani, E., Rossi, A., Edupuganti, R. R., Ensinck, I., Chan, V. W. C., Patel, H., Kirkpatrick, J., Faull, P., Snijders, A. P., Vermeulen, M., Ralser, M., Ule, J., Luscombe, N. M., & van Werven, F. J. (2022). N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. eLife, 11, Article e84034. https://doi.org/10.7554/eLife.84034

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title = "N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast",

abstract = "N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3{\textquoteright}end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contin-gent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.",

author = "Varier, {Radhika A.} and Theodora Sideri and Charlotte Capitanchik and Zornitsa Manova and Enrica Calvani and Alice Rossi and Edupuganti, {Raghu R.} and Imke Ensinck and Chan, {Vincent W.C.} and Harshil Patel and Joanna Kirkpatrick and Peter Faull and Snijders, {Ambrosius P.} and Michiel Vermeulen and Markus Ralser and Jernej Ule and Luscombe, {Nicholas M.} and {van Werven}, {Folkert J.}",

note = "Publisher Copyright: {\textcopyright} Varier, Sideri, Capitanchik et al.",

year = "2022",

month = nov,

doi = "10.7554/eLife.84034",

language = "English (US)",

volume = "11",

journal = "eLife",

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Varier, RA, Sideri, T, Capitanchik, C, Manova, Z, Calvani, E, Rossi, A, Edupuganti, RR, Ensinck, I, Chan, VWC, Patel, H, Kirkpatrick, J, Faull, P, Snijders, AP, Vermeulen, M, Ralser, M, Ule, J, Luscombe, NM & van Werven, FJ 2022, 'N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast', eLife, vol. 11, e84034. https://doi.org/10.7554/eLife.84034

TY - JOUR

T1 - N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

AU - Varier, Radhika A.

AU - Sideri, Theodora

AU - Capitanchik, Charlotte

AU - Manova, Zornitsa

AU - Calvani, Enrica

AU - Rossi, Alice

AU - Edupuganti, Raghu R.

AU - Ensinck, Imke

AU - Chan, Vincent W.C.

AU - Patel, Harshil

AU - Kirkpatrick, Joanna

AU - Faull, Peter

AU - Snijders, Ambrosius P.

AU - Vermeulen, Michiel

AU - Ralser, Markus

AU - Ule, Jernej

AU - Luscombe, Nicholas M.

AU - van Werven, Folkert J.

PY - 2022/11

Y1 - 2022/11

N2 - N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contin-gent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

AB - N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contin-gent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

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U2 - 10.7554/eLife.84034

DO - 10.7554/eLife.84034

M3 - Article

C2 - 36422864

AN - SCOPUS:85143644530

SN - 2050-084X

VL - 11

JO - eLife

JF - eLife

M1 - e84034

ER -

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

Abstract

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ASJC Scopus subject areas

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