Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation

Olivier Finet; Carlo Yague-Sanz; Lara Katharina Krüger; Phong Tran; Valérie Migeot; Max Louski; Alicia Nevers; Mathieu Rougemaille; Jingjing Sun; Felix G M Ernst; Ludivine Wacheul; Maxime Wery; Antonin Morillon; Peter Dedon; Denis L J Lafontaine; Damien Hermand

doi:10.1016/j.molcel.2021.11.003

Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation

Olivier Finet, Carlo Yague-Sanz, Lara Katharina Krüger, Phong Tran, Valérie Migeot, Max Louski, Alicia Nevers, Mathieu Rougemaille, Jingjing Sun, Felix G M Ernst, Ludivine Wacheul, Maxime Wery, Antonin Morillon, Peter Dedon, Denis L J Lafontaine, Damien Hermand

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

Abstract

The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.

Original language	English
Pages (from-to)	404-419.e9
Journal	Molecular Cell
Volume	82
Issue number	2
Early online date	18 Nov 2021
DOIs	https://doi.org/10.1016/j.molcel.2021.11.003
Publication status	Published - 20 Jan 2022

Funding

We are grateful to Eric Phizicky for reagents and Marc Graille for comments on the manuscript. Research in the lab of D.L.J.L. is supported by the Fonds de la Recherche Nationale (F.R.S./FNRS), the Universit\u00E9 Libre de Bruxelles (ULB), the European Joint Programme on Rare Diseases (EJP-RD; RiboEurope and DBAGeneCure), the R\u00E9gion Wallone (RiboCancer), and the International Brachet Stift\u00FCng (IBS). High-throughput sequencing was performed by the NGS platform of Institut Curie, supported by grants from the Agence Nationale de la Recherche (investissements d\u2019avenir; ANR-10-EQPX-03 and ANR10-INBS-09-08 ) and by the Cancerop\u00F4le Ile-de-France . This work was also supported by NIH grants ES031529 and AG063341 (to P.D.) and PDR T.0012.14 , CDR J.0066.16 , and PDR T.0112.21 (to D.H.). O. F. and C.Y.-S. were supported by a FRIA fellowship. D.L.J.L and D.H. are FNRS Directors of Research. We are grateful to Eric Phizicky for reagents and Marc Graille for comments on the manuscript. Research in the lab of D.L.J.L. is supported by the Fonds de la Recherche Nationale (F.R.S./FNRS), the Universit\u00E9 Libre de Bruxelles (ULB), the European Joint Programme on Rare Diseases (EJP-RD; RiboEurope and DBAGeneCure), the R\u00E9gion Wallone (RiboCancer), and the International Brachet Stift\u00FCng (IBS). High-throughput sequencing was performed by the NGS platform of Institut Curie, supported by grants from the Agence Nationale de la Recherche (investissements d'avenir; ANR-10-EQPX-03 and ANR10-INBS-09-08) and by the Cancerop\u00F4le Ile-de-France. This work was also supported by NIH grants ES031529 and AG063341 (to P.D.) and PDR T.0012.14, CDR J.0066.16, and PDR T.0112.21 (to D.H.). O. F. and C.Y.-S. were supported by a FRIA fellowship. D.L.J.L and D.H. are FNRS Directors of Research. O.F. C.Y.-S. L.K.K. M.L. A.N. M.R. J.S. and L.W. designed, performed, and analyzed the experiments. V.M. performed the in vitro translation assays and related experiments. F.G.M.E. and D.L.J.L. designed, performed, and analyzed the HPLC, ribosome profiling, and human CRISPR experiments. P.T. designed the life imaging. P.D. designed and analysed the MS data. M.W. and A.M. contributed to the design and funding of the Rho-seq datasets. D.H. designed the project, acquired funding, supervised the experiments, and wrote the paper with input from all authors. The authors declare no competing interests.

Funders	Funder number
Cancéropôle Ile de France
Fonds de la Recherche Nationale
Waalse Gewest
DBAGeneCure
European Joint Programme on Rare Diseases
Fonds De La Recherche Scientifique - FNRS
Fonds pour la Formation à la Recherche dans l’Industrie et dans l’Agriculture
F.R.S.
Université Libre de Bruxelles
National Institute of Environmental Health Sciences	R01ES031529, R01ES026856
Agence Nationale de la Recherche	ANR-10-EQPX-03, ANR10-INBS-09-08
National Institutes of Health	PDR T.0112.21, PDR T.0012.14, CDR J.0066.16
Fundação para a Ciência e a Tecnologia	PTDC/CCI-BIO/29266/2017
National Institute on Aging	R01AG063341

Keywords

DUS
dihydrouridine
epitranscriptomics
meiosis
yeast

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10.1016/j.molcel.2021.11.003

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Finet, O., Yague-Sanz, C., Krüger, L. K., Tran, P., Migeot, V., Louski, M., Nevers, A., Rougemaille, M., Sun, J., Ernst, F. G. M., Wacheul, L., Wery, M., Morillon, A., Dedon, P., Lafontaine, D. L. J., & Hermand, D. (2022). Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation. Molecular Cell, 82(2), 404-419.e9. https://doi.org/10.1016/j.molcel.2021.11.003

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title = "Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation",

abstract = "The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.",

keywords = "DUS, dihydrouridine, epitranscriptomics, meiosis, yeast",

author = "Olivier Finet and Carlo Yague-Sanz and Kr{\"u}ger, {Lara Katharina} and Phong Tran and Val{\'e}rie Migeot and Max Louski and Alicia Nevers and Mathieu Rougemaille and Jingjing Sun and Ernst, {Felix G M} and Ludivine Wacheul and Maxime Wery and Antonin Morillon and Peter Dedon and Lafontaine, {Denis L J} and Damien Hermand",

note = "Funding Information: We are grateful to Eric Phizicky for reagents and Marc Graille for comments on the manuscript. Research in the lab of D.L.J.L. is supported by the Fonds de la Recherche Nationale (F.R.S./FNRS), the Universit{\'e} Libre de Bruxelles (ULB), the European Joint Programme on Rare Diseases (EJP-RD; RiboEurope and DBAGeneCure), the R{\'e}gion Wallone (RiboCancer), and the International Brachet Stift{\"u}ng (IBS). High-throughput sequencing was performed by the NGS platform of Institut Curie, supported by grants from the Agence Nationale de la Recherche (investissements d{\textquoteright}avenir; ANR-10-EQPX-03 and ANR10-INBS-09-08 ) and by the Cancerop{\^o}le Ile-de-France . This work was also supported by NIH grants ES031529 and AG063341 (to P.D.) and PDR T.0012.14 , CDR J.0066.16 , and PDR T.0112.21 (to D.H.). O. F. and C.Y.-S. were supported by a FRIA fellowship. D.L.J.L and D.H. are FNRS Directors of Research. Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

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doi = "10.1016/j.molcel.2021.11.003",

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Finet, O, Yague-Sanz, C, Krüger, LK, Tran, P, Migeot, V, Louski, M, Nevers, A, Rougemaille, M, Sun, J, Ernst, FGM, Wacheul, L, Wery, M, Morillon, A, Dedon, P, Lafontaine, DLJ & Hermand, D 2022, 'Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation', Molecular Cell, vol. 82, no. 2, pp. 404-419.e9. https://doi.org/10.1016/j.molcel.2021.11.003

TY - JOUR

T1 - Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation

AU - Finet, Olivier

AU - Yague-Sanz, Carlo

AU - Krüger, Lara Katharina

AU - Tran, Phong

AU - Migeot, Valérie

AU - Louski, Max

AU - Nevers, Alicia

AU - Rougemaille, Mathieu

AU - Sun, Jingjing

AU - Ernst, Felix G M

AU - Wacheul, Ludivine

AU - Wery, Maxime

AU - Morillon, Antonin

AU - Dedon, Peter

AU - Lafontaine, Denis L J

AU - Hermand, Damien

N1 - Funding Information: We are grateful to Eric Phizicky for reagents and Marc Graille for comments on the manuscript. Research in the lab of D.L.J.L. is supported by the Fonds de la Recherche Nationale (F.R.S./FNRS), the Université Libre de Bruxelles (ULB), the European Joint Programme on Rare Diseases (EJP-RD; RiboEurope and DBAGeneCure), the Région Wallone (RiboCancer), and the International Brachet Stiftüng (IBS). High-throughput sequencing was performed by the NGS platform of Institut Curie, supported by grants from the Agence Nationale de la Recherche (investissements d’avenir; ANR-10-EQPX-03 and ANR10-INBS-09-08 ) and by the Canceropôle Ile-de-France . This work was also supported by NIH grants ES031529 and AG063341 (to P.D.) and PDR T.0012.14 , CDR J.0066.16 , and PDR T.0112.21 (to D.H.). O. F. and C.Y.-S. were supported by a FRIA fellowship. D.L.J.L and D.H. are FNRS Directors of Research. Publisher Copyright: © 2021 Elsevier Inc.

PY - 2022/1/20

Y1 - 2022/1/20

N2 - The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.

AB - The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.

KW - DUS

KW - dihydrouridine

KW - epitranscriptomics

KW - meiosis

KW - yeast

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U2 - 10.1016/j.molcel.2021.11.003

DO - 10.1016/j.molcel.2021.11.003

M3 - Article

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SN - 1097-2765

VL - 82

SP - 404-419.e9

JO - Molecular Cell

JF - Molecular Cell

IS - 2

ER -

Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation

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Keywords

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