Cooperation between epitranscriptomics and the piRNA pathway in maternal mRNA regulation
Final Report Abstract
Understanding the importance of m6A modifications in the regulation of maternal messenger RNAs and fertility: mRNA regulation involves RNA binding proteins and non-coding RNAs that act in a complex coordinated manner to determine the fate and function of cellular mRNAs. Piwi-interacting RNAs (piRNAs) are a specific class of small non-coding RNAs involved in the repression of transposable elements in the germline. Besides this well-studied function, we have previously described a novel role for piRNAs in controlling maternal mRNA decay during early embryogenesis in the Drosophila model. Recently, mRNA modification, in particular N6-methyladenosine (m6A), has emerged as a novel critical layer of post-transcriptional gene regulation affecting every step of mRNA biogenesis. Yet, it is unknown whether and how the piRNA and m6A pathways may coordinate to ensure efficient maternal mRNA degradation. The objective of the m6ApiRNA project was to decipher the role of m6A RNA modification during the early steps of animal development and its relationships with the piRNA pathway. The project aimed analyze the role of m6A and their readers in maternal mRNA decay in the Drosophila embryo, and to address whether m6A and piRNAs cooperate in this function. Genetic et genomic approaches to analyse the role of m6A modifications during early embryonic development and in the reproductive tract: The main goal of the project was to analyze in detail the role of the mRNA m6A modification pathway in the mechanism of maternal mRNA decay during early embryogenesis in Drosophila. We decided to study all the major players in the m6A pathway, i.e. the components of the methylation complex (Mettl3 and Mettl14: writers) and the effectors that bind to methylated mRNAs (Ythdf and Ythdc1: readers). We therefore used mutants and RNAi of each of these genes and analyzed their phenotypes at different levels: developmental, cellular and genomic. We used RNA-seq approaches to describe the impact of these genes on maternal mRNA decay. In addition, we implemented a novel approach, eTAM-seq, to identify transcriptome-wide maternal m6A mRNAs in the early embryo. We also used the sophisticated genetic tools of the Drosophila model to identify a new function of mRNA m6A methylation in the female genital tract, necessary for fertilization in aging females. Major results of the project: We found that m6A methylation plays an important role in the decay of maternal mRNAs in the early embryo. Moreover, we identified Ythdc1 as the reader of m6A maternal mRNAs. This was surprising as Ythdf is the main reader in oocytes and early embryos in other species. We also found a more prominent role of m6A methylation in aging female from which embryonic lethality increases from 20% in young females to 60% in aging females. We showed that this defect does not depend on the female germline, but on somatic tissues of the reproductive tract. In addition, the Roignant lab identified a new component of the methylation complex and described a new interaction between m6A methylation and the RNA binding protein FMR1. Production scientifique: This project allowed to publish two publications by the German coordinator in Nature Communications and EMBO Journal. Two manuscripts are also currently submitted and posted on the bioRxiv website. Finally, two other manuscripts describing results obtained directly within the framework of this project are currently in progress and should be published later this year. In addition, five invited Reviews or Highlights and a Book Chapter were published as part of this project, including two reviews in Trends in Genetics, one in Bioessays, a comprehensive review on the piRNA pathway in Nature Reviews Molecular Cell Biology and a Perspective in Science.
Publications
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Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends in Genetics, 37(4), 355-372.
Gehring, Niels H. & Roignant, Jean-Yves
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Functional interplay within the epitranscriptome: Reality or fiction?. BioEssays, 44(2).
Worpenberg, Lina; Paolantoni, Chiara & Roignant, Jean‐Yves
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Functions of PIWI Proteins in Gene Regulation: New Arrows Added to the piRNA Quiver. Trends in Genetics, 37(2), 188-200.
Ramat, Anne & Simonelig, Martine
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Hakai is required for stabilization of core components of the m6A mRNA methylation machinery. Nature Communications, 12(1).
Bawankar, Praveen; Lence, Tina; Paolantoni, Chiara; Haussmann, Irmgard U.; Kazlauskiene, Migle; Jacob, Dominik; Heidelberger, Jan B.; Richter, Florian M.; Nallasivan, Mohanakarthik P.; Morin, Violeta; Kreim, Nastasja; Beli, Petra; Helm, Mark; Jinek, Martin; Soller, Matthias & Roignant, Jean-Yves
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Ythdf is a N6‐methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. The EMBO Journal, 40(4).
Worpenberg, Lina; Paolantoni, Chiara; Longhi, Sara; Mulorz, Miriam M.; Lence, Tina; Wessels, Hans‐Hermann; Dassi, Erik; Aiello, Giuseppe; Sutandy, F. X. Reymond; Scheibe, Marion; Edupuganti, Raghu R.; Busch, Anke; Möckel, Martin M.; Vermeulen, Michiel; Butter, Falk; König, Julian; Notarangelo, Michela; Ohler, Uwe; Dieterich, Christoph ... & Roignant, Jean‐Yves
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Activating translation with phase separation. Science, 377(6607), 712-713.
Ramat, Anne & Simonelig, Martine
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Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nature Reviews Molecular Cell Biology, 24(2), 123-141.
Wang, Xin; Ramat, Anne; Simonelig, Martine & Liu, Mo-Fang
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Germ granule higher-order organization coordinates their different functions. openRxiv.
Ramat, Anne; Haidar, Ali; Garret, Céline & Simonelig, Martine
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piRNAs are regulators of metabolic reprogramming in stem cells. openRxiv.
Rojas-Ríos, Patricia; Chartier, Aymeric; Enjolras, Camille; Cremaschi, Julie; Garret, Céline; Boughlita, Adel; Ramat, Anne & Simonelig, Martine
