Project

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GermMethylation (ERC-2014-CoG)

English title Chromatin and DNA modifications instructed by germline noncoding RNA
Applicant Pillai Ramesh S.
Number 166923
Funding scheme ERC Transferbeiträge
Research institution Département de Biologie Moléculaire Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Biochemistry
Start/End 01.06.2016 - 31.05.2022
Approved amount 1'743'540.00
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All Disciplines (2)

Discipline
Biochemistry
Molecular Biology

Keywords (4)

piRNA; PIWI; Small RNAs; DNA methylation

Lay Summary (French)

Lead
Les petits ARN appelés Piwi-interacting RNAs (piRNAs) sont massivement exprimés en lignée germinale de l'animal et ils sont essentiels pour la fertilité de tous les animaux examinés. Ils sont présentés à fonctionner dans le cytoplasme et le noyau des cellules germinales à faire taire les éléments transposables cibles. Ce projet examine comment piRNAs guident répression des loci génomiques cible par le recrutement de la chromatine ou méthylation de l'ADN dans le noyau.
Lay summary

Contenu et objectifs du travail de recherche

Depuis les année 2006, lorsque piRNAs ont été décrits pour la première chez les mammifères, le domaine a été actif dans la compréhension de la biogenèse des piRNA. Plusieurs études ont également examiné comment piRNAs médiation destruction de ses cibles d'ARN dans le cytoplasme. Cependant, le mécanisme par lequel piRNAs médiation silençage transcriptionnel dans des systèmes de mammifère ne soit pas connue.

En utilisant des modèles de souris, ce projet se propose d'examiner l'effet direct de piRNAs dans le noyau des cellules germinales de mammifères. Initialement, elle examinera les conséquences d'avoir des cibles génomiques pour piRNAs nucléaires en examinant l'ADN et la chromatine modifications sur le locus génomique cible. Par la suite, il permettra d'identifier la composition d'un tel petit complexe de silençage de l'ARN-guidée. Enfin, il va tenter de caractériser la stabilité des marques de silencieux induites au fil des générations et les facteurs qui l'influencent. Notre recherche fera la lumière sur le rôle mal compris de piRNAs en silence transgénérationnelle dans la lignée germinale de l'animal.

Contexte scientifique et social du projet de recherche

Ce projet aidera à comprendre la base moléculaire de l'une des principales voies de défense du génome agissant dans les génomes des animaux. Elle est susceptible d'avoir un impact majeur sur notre compréhension de la fertilité humaine.

Mots-clés

Fertility, piRNAs, Piwi, epigenetics, DNA methylation

Direct link to Lay Summary Last update: 22.02.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m6A recognition
Li Lingyun, Krasnykov Kyrylo, Homolka David, Gos Pascal, Mendel Mateusz, Fish Richard J., Pandey Radha Raman, Pillai Ramesh S. (2022), The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m6A recognition, in Molecular Cell, 82(9), 1678-1690.e12.
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Mendel Mateusz, Delaney Kamila, Pandey Radha Raman, Chen Kuan-Ming, Wenda Joanna M., Vågbø Cathrine Broberg, Steiner Florian A., Homolka David, Pillai Ramesh S. (2021), Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing, in Cell, 184(12), 3125-3142.e25.
The Mammalian Cap-Specific m6Am RNA Methyltransferase PCIF1 Regulates Transcript Levels in Mouse Tissues
Pandey Radha Raman, Delfino Elena, Homolka David, Roithova Adriana, Chen Kuan-Ming, Li Lingyun, Franco Giulia, Vågbø Cathrine Broberg, Taillebourg Emmanuel, Fauvarque Marie-Odile, Pillai Ramesh S. (2020), The Mammalian Cap-Specific m6Am RNA Methyltransferase PCIF1 Regulates Transcript Levels in Mouse Tissues, in Cell Reports, 32(7), 108038-108038.
TEX15 associates with MILI and silences transposable elements in male germ cells
Yang Fang, Lan Yemin, Pandey Radha Raman, Homolka David, Berger Shelley L., Pillai Ramesh S., Bartolomei Marisa S., Wang P. Jeremy (2020), TEX15 associates with MILI and silences transposable elements in male germ cells, in Genes & Development, 34(11-12), 745-750.
Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs
Wu Hao, Li Lingyun, Chen Kuan-Ming, Homolka David, Gos Pascal, Fleury-Olela Fabienne, McCarthy Andrew A., Pillai Ramesh S. (2019), Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs, in Cell Reports, 29(13), 4422-4434.e13.
Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12
Pandey Radha Raman, Homolka David, Olotu Opeyemi, Sachidanandam Ravi, Kotaja Noora, Pillai Ramesh S. (2018), Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12, in Cell Reports, 24(13), 3423-3432.e4.
Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Mendel Mateusz, Chen Kuan-Ming, Homolka David, Gos Pascal, Pandey Radha Raman, McCarthy Andrew A., Pillai Ramesh S. (2018), Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development, in Molecular Cell, 71(6), 986-1000.e11.

Collaboration

Group / person Country
Types of collaboration
Dr. Andrew McCarthy, EMBL, Grenoble Outstation France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Noora Kotaja, University of Turku, Finland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Andre VERDEL, University of Grenoble, IAB France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Tokio Tani, University of Kumamoto Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Marie-Odile Fauvarque, CEA, Grenoble France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Ravi Sachidanandam, Mount Senai, New York United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
RNA Society Meeting 2021, 25.05 - 05.06.2021 (online) Talk given at a conference m6A RNA methylation regulates pre-mRNA splicing by blocking 3′ splice site recognition by the splicing factor U2AF35 25.05.2021 Seattle, United States of America Mendel Mateusz;
15th Microsymposium on Small RNAs, 22 - 23.04.2021, Vienna Biocenter (online) Talk given at a conference m6A RNA methylation regulates pre-mRNA splicing by blocking 3′ splice site recognition by the splicing factor U2AF35 22.04.2021 Vienna, Austria Mendel Mateusz;
Cold Spring Harbor Conference “Eukaryotic mRNA Processing”, 20 – 24 August 2019, Cold Spring Harbor, USA Talk given at a conference The 3’ splice site m6A methylation by METT-10 regulates SAM synthetase pre-mRNA splicing in C. elegans 20.08.2019 New York, United States of America Mendel Mateusz;
Keystone Symposia Noncoding RNAs and RNA-protein interactions, Whistler, Canada, Feb 24-28 Talk given at a conference Noncoding RNAs in gene regulation 24.02.2019 Whistler, Canada Pillai Ramesh S.;
Austrian-Swiss RNA Meeting, January 30 to February 3, 2019, Fuschlsee, Austria Talk given at a conference The evolutionary conserved role of the m6A writer METTL16 30.01.2019 Fuschlsee, Austria Mendel Mateusz;
EMBO-EMBL Symposium: Complex Life of mRNA, Heidelberg, Germany, 3-6 Oct, 2018. Talk given at a conference Small RNAs in germline 03.10.2018 Heidelberg, Germany Pillai Ramesh S.;
EMBO Workshop on piRNAs and PIWI proteins, IGH, Montpellier, France, 12-15 Sept Talk given at a conference piRNA biogenesis 12.09.2018 Montpellier, France Pillai Ramesh S.;
Keystone Symposia: Noncoding RNAs: Form, Function, Physiology, Colorado, USA. Feb25-Mar2, 2018 Talk given at a conference YTHDC2 25.02.2018 Keystone, Colorado, United States of America Pillai Ramesh S.;
Keystone Symposia: Noncoding RNAs: Form, Function, Physiology, Colorado, USA. Feb25-Mar2, 2018 Talk given at a conference Noncoding RNAs 25.02.2018 Colarado, United States of America Pillai Ramesh S.;
Visiting Professor lecture, University of Kumamoto, Japan, 19th-21st Dec, 2017 Individual talk Noncoding genome 19.12.2017 Kumamoto, Japan Pillai Ramesh S.;
Cold Spring Harbour Asia, RNA modifications and Epitranscriptome, 13th-17th Nov, Suzhou Talk given at a conference RNA modifications in germline 14.11.2017 Suzhou, China Pillai Ramesh S.;
Invited talk at Institute of Biochemistry and Cell Biology, CAS, Shanghai, 13th Nov, 2017 Individual talk RNA modifications 13.11.2017 Shanghai, China Pillai Ramesh S.;
Invited talk at ShanghaiTech University, Shanghai, 10th Nov, 2017 Individual talk RNA methylation in germline 10.11.2017 Shanghai, China Pillai Ramesh S.;
EMBO Course on Noncoding RNAs, Heidelberg, 15th Sept, 2017 Talk given at a conference piRNA biogenesis 15.09.2017 Heidelberg, Germany Pillai Ramesh S.;
The Non-Coding Genome - 13 - 16 September 2017 Poster Regulation by the 3→5 RNA helicase YTHDC2 is essential for a successful meiotic program in the mammalian germline. 13.09.2017 Heidelberg, Germany Mendel Mateusz;
FEBS 2017 Meeting, Jerusalem, Israel, 10th-15th Sept, 2017 Talk given at a conference RNA methylation in germline biology 10.09.2017 Jerusalem, Israel Pillai Ramesh S.;
IROAST Symposium, University of Kumamoto, Japan, 22-24th March Talk given at a conference Noncoding RNAs in medicine 22.03.2017 Kumamoto, Japan Pillai Ramesh S.;
Visiting Professor lecture, University of Kumamoto, Japan, 21st March Individual talk piRNA biology 21.03.2017 Kumamoto, Japan Pillai Ramesh S.;
6th International Workshop “Noncoding Genome”, Curie, Paris, 1-3rd March Talk given at a conference piRNA biogenesis 01.03.2017 Paris, France Pillai Ramesh S.;
Visiting Professor lecture, University of Kumamoto, Japan, 19-21st Dec Individual talk piRNA biogenesis 19.12.2016 Kumamoto, Japan Pillai Ramesh S.;
Cell Symposia-Functional RNAs, Guangzhou, China, 6-8th Nov Talk given at a conference piRNA biogenesis 06.11.2016 Guangzhou, China Pillai Ramesh S.;
Invited lecture at State Key Laboratory of Reproductive Medicine, Nanjing Medical University, China, 4th Nov Individual talk piRNA biogenesis 04.11.2016 Nanjing, China Pillai Ramesh S.;
Invited lecture at Institute of Biochemistry and Cell Biology, Shanghai, China, 3rd Nov Individual talk piRNA biogenesis 03.11.2016 Shanghai, China Pillai Ramesh S.;
EMBL PhD Symosium Individual talk piRNA biogenesis 21.10.2016 Heidelberg, Germany Pillai Ramesh S.;
Invited lecture at University of Genoble, France Individual talk piRNA biogenesis 19.09.2016 Grenoble, France Pillai Ramesh S.;
Villars Symposium 2016-Noncoding RNAs: Function and Evolution, Villars sur Ollon, 12-14 Sept Talk given at a conference piRNA biogenesis 12.09.2016 Villars sur Ollon, Switzerland Pillai Ramesh S.;
EMBO Small RNA course, Trento, Italy, 11-16, June Talk given at a conference piRNA biogenesis 11.06.2016 Trento, Italy Pillai Ramesh S.;


Awards

Title Year
Boehringer Ingelheim Fonds PhD Fellowship to Mateusz MENDEL in Sept, 2016 for 2-3 years. 2016

Associated projects

Number Title Start Funding scheme
186266 Cellular determinants of subthalamic nucleus function 01.06.2019 Sinergia

Abstract

Germ cells are entrusted with the task of transmitting the genetic information from one generation to the next. One major threat to germline genome integrity is the mobile genetic elements called transposons. Germline-specific Piwi-interacting RNAs (piRNAs) act as guardians of the genome by silencing transposable elements. The central aims of this proposal are to study how nuclear small RNAs are made and how they function in recruiting DNA methylation to target transposon loci in mammals. Key nucleases involved in piRNA biogenesis are not known. In this proposal, we will characterize the role of two novel nuclease family members in the piRNA biogenesis pathway using biochemical, structural and mouse genetic tools. It will use catalytic-dead mouse mutants of RNA helicases to trap transiently assembled biogenesis and silencing effector machineries in vivo. Since most piRNAs derive from repeat regions, we employ unique artificial piRNA precursors to systematically study piRNA processing steps in insect cell cultures, transgenic fly and mouse models. The use of RNA-crosslinking and deep sequencing strategies will allow us to unambiguously map factor binding sites to these unique reporters. It will aim to biochemically and functionally characterize mammalian piRNA-guided nuclear silencing complexes (RITS). Using artificial reporters and tethering of factors, it will provide direct and unambiguous evidence linking piRNAs to the epigenetic silencing of transposons by DNA methylation in the mammalian genome. Furthermore, it will explore the transgenerational nature of this silencing. Finally, using Cas9 genome editing tools it will examine the role of a set of unique, non-repeat piRNAs whose functions during mouse germ cell development are unknown. Overall, this proposal aims to use interdisciplinary approaches in uncovering the epigenetic role of nuclear germline small RNAs.
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