Epigenetics, Chromatin and Development

Personnel du RDP

François ROUDIER

francois.roudier
(33) 4 72 72 86 04
PU ENS
Publications

Annick DUBOIS

annick.dubois
(33) 4 72 72 14 76
CR1 INRA
Publications

Aurélie VIALETTE

aurelie.vialette
(33) 4 72 72 14 79
AGPR ENS

Alice HUGUES

alice.hugues
Doctorante

Daniel BOUYER

daniel.bouyer
(33) 4 72 72 86 11
CRN CNRS

Jérémy JUST

jeremy.just
(33)4 72 72 86 11
IR2 CNRS
Publications

Julien MACE

julien.mace
(33) 4 72 72 14 70
Doctorant

Marie France GERENTES

marie-france.gerentes
(33) 4 72 72 14 77
AI ENS CDD

Nathalie MATHY-FRANCHET

nathalie.mathy-franchet
(33) 4 72 72 86 11
AI CNRS

Nicolas DALLE

nicolas.dalle
(33) 4 26 73 14 72
Doctorant



Publications HAL du labo/EPI 1001887;772

2021

Journal articles

titre
Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering
auteur
Annick Dubois, François Roudier
article
Epigenomes, MDPI, 2021, 5 (3), pp.17. ⟨10.3390/epigenomes5030017⟩
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titre
A network of transcriptional repressors modulates auxin responses.
auteur
Jekaterina Truskina, Jingyi Han, Elina Chrysanthou, Carlos Galvan-Ampudia, Stéphanie Lainé, Geraldine Brunoud, Julien Macé, Simon Bellows, Jonathan Legrand, Anne-Maarit Bågman, Margot Smit, Ondrej Smetana, Arnaud Stigniani, Silvana Porco, Malcom J. Bennett, Ari Pekka Mähönen, Francois Parcy, Etienne Farcot, François Roudier, Siobhan M Brady, Anthony Bishopp, Teva Vernoux
article
Nature, Nature Publishing Group, 2021, 589 (7840), pp.116-119. ⟨10.1038/s41586-020-2940-2⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-03021204/file/Truskina_%20main_text_all-rev6_CorrLegendFig3_withallFig.pdf BibTex

2020

Journal articles

titre
Mitotic Inheritance of PRC2-Mediated Silencing: Mechanistic Insights and Developmental Perspectives
auteur
Alice Hugues, Chean Sern Jacobs, François Roudier
article
Frontiers in Plant Science, Frontiers, 2020, 11, ⟨10.3389/fpls.2020.00262⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-03142734/file/2020_Hugues_Front_Plant_Sci.pdf BibTex
titre
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
auteur
Noémie Vimont, Fu Xiang Quah, David Guillaume Schöpfer, François Roudier, Elisabeth Dirlewanger, Philip A. Wigge, Bénédicte Wenden, Sandra Cortijo
article
Tree Genetics and Genomes, Springer Verlag, 2020, 16 (1), pp.9. ⟨10.1007/s11295-019-1395-9⟩
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2019

Journal articles

titre
Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis
auteur
Bart Rymen, Ayako Kawamura, Alice Lambolez, Soichi Inagaki, Arika Takebayashi, Akira Iwase, Yuki Sakamoto, Kaori Sako, David Favero, Momoko Ikeuchi, Takamasa Suzuki, Motoaki Seki, Tetsuji Kakutani, François Roudier, Keiko Sugimoto
article
Communications Biology, Nature Publishing Group, 2019, 2, ⟨10.1038/s42003-019-0646-5⟩
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02526385/file/2019_Rymen_Com_Biol.pdf BibTex

Preprints, Working Papers, ...

titre
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
auteur
Noémie Vimont, Fu Xiang Quah, David Guillaume-Schöpfer, François Roudier, Elisabeth Dirlewanger, Philip A. Wigge, Bénédicte Wenden, Sandra Cortijo
article
2019
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02788335/file/2019-Vimont-Bioxriv-Preprint_1.pdf BibTex

2018

Book sections

titre
Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins
auteur
Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
article
Plant Chromatin Dynamics, pp.111-130, 2018, ⟨10.1007/978-1-4939-7318-7_8⟩
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titre
Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis
auteur
Sandra Cortijo, Varodom Charoensawan, François Roudier, Philip A. Wigge
article
Root Development, pp.231-248, 2018, ⟨10.1007/978-1-4939-7747-5_18⟩
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2017

Journal articles

titre
Epigenetic memory and cell fate reprogramming in plants
auteur
Kenneth D. Birnbaum, François Roudier
article
Regeneration, 2017, 4 (1), pp.15-20. ⟨10.1002/reg2.73⟩
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2016

Journal articles

titre
Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation
auteur
Miguel De Lucas, Li Pu, Gina Turco, Allison Gaudinier, Ana Karina Morao, Hirofumi Harashima, Dahae Kim, Mily Ron, Keiko Sugimoto, François Roudier, Siobhan M. Brady
article
The Plant cell, American Society of Plant Biologists (ASPB), 2016, 28 (10), pp.2616-2631. ⟨10.1105/tpc.15.00744⟩
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titre
Emerging concepts in chromatin-level regulation of plant cell differentiation: timing, counting, sensing and maintaining
auteur
Ana Karina Morao, Daniel Bouyer, François Roudier
article
Current Opinion in Plant Biology, Elsevier, 2016, 34, pp.27-34. ⟨10.1016/j.pbi.2016.07.010⟩
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Our research aims at understanding the extent to which chromatin-based mechanisms and epigenetic processes regulate cell fate acquisition, maintenance and reprogramming during plant development.

How cell acquire and maintain their identity during development is indeed a central question in biology. Whereas cell identity is largely dictated by the transcriptional profiles resulting from the activity of specific transcription factors (TFs), the robustness of this state depends on the chromatin context in which these TFs act. Thus, the progression of a cell through successive differentiation stages, from stem cells to end-differentiated cells, is guided by changes in transcriptional programs that are regulated by the bidirectional interplay between TFs and chromatin organization.
In order to understand how epigenome dynamics enable cells to respond selectively to developmental and environmental cues, we develop complementary approaches aimed at characterizing the impact of chromatin-based mechanisms and epigenetic processes on the regulation of cell differentiation within Arabidopsis apical meristems. A particular emphasis is put on the transcriptional repressive pathways associated with proteins of the Polycomb group.

Three research axes, included in a systemic approach that combines genetic, molecular, imaging and genomic approaches at cellular resolution are implemented in order to:

 characterize epigenome dynamics during cell differentiation and reveal the specific role of chromatin regulators in the activity of stem cell niches, cell fate acquisition and identity maintenance.

 determine the impact of chromatin state dynamics on the target repertoire of select transcription factors (and vice-versa) within specific cell populations.

 evaluate how epigenomic variation contributes to shaping developmental programs during evolution.

Team members .
François Roudier Professor ENS (Group leader)
Annick Dubois Senior Researcher INRA
Daniel Bouyer Senior Researcher CNRS
Nathalie Franchet-Mathy Assistant Engineer CNRS
Jérémy Just Ingénieur de Recherche CNRS
Aurélie Vialette Lecturer ENS
Marie France Gérentes Engineer ENS
Julien Macé PhD student bioinformatics ENS (ED bmic)
Nicolas Dalle PhD Student (ED bmic)
Alice Hugues PhD Student (ED bmic)
Alumni
Allan Bernard Biosciences Master2 student
Mohammad Muhieddine Biosciences Master2 student
Julia Buttin Engineer in bioinformatics
Goeffrey Schivre U. Montpellier Master1 student
Alice Hugues Biosciences Master2 student
Chean Sern Jacobs PhD Student (ED bmic)
Marie Biharé Master student M1 U. Lille
Laure Cuby Pre-master student ESTBB Lyon