EpiGenMed / LabMUSE

EpiGenMed / LabMUSE2020-09-04T10:20:57+02:00

LabMUSE EpiGenMed

The LabMUSE EpiGenMed project is built on the international recognition of Montpellier’s research in epigenetics, (epi)genomics and gene expression, which it aims to consolidate and expand towards other fields. EpiGenMed structures collaborations between basic research, medical research and student training in Montpellier. It is fully integrated into the I-SITE MUSE, and associated to the BioHealth Department, particularly the Genetics-Epigenetics axis.

The scientific scope of LabMUSE concerns epigenetics, epigenomics and gene expression, with the aim to address determination of cell fate, immune defence and metabolism and their links with pathologies. Research in these areas is evolving rapidly and an important aspect will therefore be the development of new technologies, for example single cell-based approaches, and accompanying their transfer to health and industrial benefits.

22 Core teams:

22 leading teams in epigenetics, epigenomics and gene regulation constitute the core of the EpiGenMed LabMUSE, defined for two years initially (2020-2021). These teams are involved in coordinating and managing EpiGenMed, and contribute to the different collaborative research and training activities, that all involve other Montpellier Health Biology groups as well.

LabMUSE EpiGenMed reinforces Montpellier’s Health-Biology research community via the organization of project calls, training actions and scientific events.

News

Director:
Robert Feil

Board:
The Board takes major decisions concerning the strategy and orientation of EpiGenMed, its funding programs and different actions.

Members:
Giacomo Cavalli, IGH, Head (Epi)genetics axis Biohealth Department
Robert Feil, IGMM, Director LabMUSE EpiGenMed
Daniel Fisher, IGMM, Head Master speciality “Cancer” Montpellier University
Jacques Mercier, UM, Vice-President for Research Montpellier University
Pierre-Emmanuel Milhiet, CBS, Director Biohealth Department
Claude Sardet, IRCM, Director IRCM
Martine Simonelig, IGH, Developmental Biology

Scientific Council:
The Scientific Council selects the projects and candidates for the different LabMUSE EpiGenMed project calls. External scientists will be implicated in the decisions for larger funding amounts.

Members:
LabMUSE EpiGenMed Board
4 Core Team members, representing the different scientific orientations present in the LabMUSE EpiGenMed, in a rotation system
Secretary and contact:

Contact

As the LabMUSE EpiGenMed is part of the I-SITE MUSE, its evolution, structure, project calls, research and training actions and its budget are validated and evaluated by the I-SITE MUSE Board

Team leader: Marta RADMAN-LIVAJA

Team’s title: Chromatin and DNA replication

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 67

Email: marta.radman-livaja@igmm.cnrs.fr

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Our group is interested in the mechanisms of chromatin patterns re-establishment after DNA replication and the role of chromatin in the epigenetic transmission of cellular phenotypes. Despite important implications that chromatin reassembly has for our understanding of the role of chromatin in epigenetic phenomena, these processes are just beginning to be explored on a genomic scale. Since the group’s establishment in 2013, we have developed NG Sequencing based methods to map the dynamics of chromatin features on newly replicated DNA. In Vasseur et al. (2016), we have shown that nucleosome positioning maturation in budding yeast depends on transcription after replication and that the kinetics of maturation on sister chromatids are independent of each other and influenced by the direction of transcription relative to replication fork progression. In Ziane et al. (2019) we have demonstrated that RNApol2 enrichment on replicated gene copies in budding yeast shifts from one chromatid to the other after replication, suggesting that replicated gene copies are not equally transcribed. We propose a novel mechanistic framework for asymmetric distribution of maternal nucleosomes on replicated daughter chromatids based on the regulation of local replication fork velocity. We have also demonstrated that the Sir3 subunit of the yeast heterochromatin complex is not inherited after release from stationary phase and is also responsible for gene expression regulation of euchromatic “growth” response genes (Galic et al., 2019). Finally, we have developed a live cell imaging system to follow the inheritance patterns of chromatin proteins after yeast asymmetric cell divisions and uncovered a number of proteins that are preferentially retained in the mother cell (Vasseur et al., 2019).

These findings provide important elements for establishing a mechanistic “’blueprint” of chromatin “inheritance” and shed more light on the role of chromatin structure reestablishment in epigenetic inheritance i.e. the transmission of transcription states from one cell generation to the next.

Keywords: Chromatin, epigenetic inheritance, genomics, budding yeast, bioinformatics

Recent publications

PRE-PRINTS:

Galic, H., Vasseur, P., and Radman-Livaja, M. (2019). The budding yeast heterochromatic SIR complex resets upon exit from stationary phase. bioRxiv, 603613.

Ziane, R., Camasses, A., and Radman-Livaja, M. (2019). Mechanics of DNA Replication and Transcription Guide the Asymmetric Distribution of RNAPol2 and New Nucleosomes on Replicated Daughter Genomes. bioRxiv, 553669.

Vasseur, P., Tonazzini, S., Rubert Castro, F., Sucec, I., El Koulali, K., Urbach, S., and Radman-Livaja, M. (2019). Inheritance of Chromatin Proteins in Budding Yeast: metabolic gene regulators TUP1, FPR4 and Rpd3L are retained in the mother cell. bioRxiv, 644138. (in review at iScience).

Peer-reviewed Publications:

Topal, S., Vasseur, P., Radman-Livaja, M., Peterson, C.L. Distinct Transcriptional Roles For Histone H3-K56 Acetylation During The Cell Cycle In Yeast. Nat Commun 10, 4372., 2019

Vasseur P., Tonazzini S., Ziane R., Camasses A., Rando O.J., Radman-Livaja M. Dynamics of nucleosome positioning maturation following genomic replication. Cell Reports, 16(10): 2651-2665, 2016.

Soares L, Radman-Livaja M, Lin SG, Rando OJ, Buratowski S. Feedback Control of Set1 Protein Levels Is Important for Proper H3K4 Methylation Patterns. Cell Reports. 6(6):961-72, 2014.

Watanabe S, Radman-Livaja M, Rando OJ, Peterson CL. A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme Science 340:195-199, 2013

Radman-Livaja M, Quan T K, Valenzuela L, Armstrong J A, van Welsem T, Kim T, Lee L J, Buratowski S, van Leeuwen F, Rando O J, Hartzog GA. A key role for chd1 in histone h3 dynamics at the 3′ ends of long genes in yeast. PLoS Genet. 8: e1002811, 2012

Radman-Livaja M, Verzijlbergen K, Weiner A, van Welsem T, Friedman N, Rando OJ, van Leeuwen F. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biology 9: e1001075, 2011.

Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, and Rando OJ. Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. EMBO J. 30: 1012-1026, 2011.

Team leader: Martine SIMONELIG

Team’s title: mRNA Regulation and Development

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 59

Email: Martine.Simonelig@igh.cnrs.fr

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Gene regulation at the post-transcriptional level is of crucial importance in a wide number of biological processes. The main focus of our lab is to understand mRNA regulation in developmental and pathological processes. We are using the Drosophila model, an oustanding model for in vivo studies. We have recently identified the role of a specific class of small non-coding RNAs, called Piwi-interacting RNAs (piRNAs) in the regulation of maternal mRNAs during early embryogenesis. piRNAs have been discovered in the last decade in germ cells of animal species. They are loaded into specific Argonaute proteins, the PIWI proteins and their function is to repress transposable elements in the germline. piRNAs are mostly produced from transposable element sequences. In the last years, we pioneered the discovery of a new function of piRNAs and PIWI proteins in gene regulation. Specifically, piRNAs produced from transposable elements target and repress maternal mRNAs that encode protein essential for embryonic patterning. These data allowed us to propose the new concept of gene regulation by piRNAs. Furthermore, we revealed a developmental function of transposable elements, a component of the genome whose function has not been clarified. Our first publication on this topic (Rouget et al. Nature 2010) opened up a new field in piRNA biology and many studies have confirmed that this function of piRNAs in gene regulation is conserved through evolution. Therefore, gene regulation by piRNAs should have a major impact in many biological processes, including diseases.

Our projects aim at understanding the molecular mechanisms of gene regulation by the piRNA pathway during developmental processes, including embryonic and germline development, stem cell biology, as well as in pathologies.

We have started a series of biennial EMBO Workshops on piRNAs and PIWI proteins in Montpellier, placing Montpellier University in a leader position in the field (http://events.embo.org/16-piRNA/; http://meetings.embo.org/event/18-pirna).

Keywords: germline; mRNA regulation; PIWI; small non-coding RNAs; stem cells

Recent publications

Rojas-Rios P, Simonelig M (2018). piRNAs and PIWI proteins: regulators of gene expression in development and stem cells. Development, 145, dev161786.

Dufourt J, Bontonou G, Chartier A, Jahan C, Meunier A-C, Pierson S, Harrison PF, Papin C, Beilharz TH, Simonelig M (2017). piRNAs and Aubergine cooperate with Wispy poly(A) polymerase to stabilize mRNAs in the germ plasm. Nature Communications, 8, 1305.

Rojas-Rios P, Chartier A, Pierson S, Simonelig M (2017). Aubergine and piRNAs promote germline stem cell self-renewal by repressing the proto-oncogene Cbl. EMBO Journal, 36, 3194-3211.

Rojas-Ríos P*, Chartier A*, Pierson S, Séverac D, Dantec C, Busseau I, Simonelig M (2015). Translational control of autophagy by Orb in the Drosophila germline. Developmental Cell, 35, 622-631.

Barckmann B*, Pierson S*, Dufourt J*, Papin C, Armenise C, Port F, Grentzinger T, Chambeyron S, Baronian G, Desvignes JP, Curk T, Simonelig M (2015). Aubergine iCLIP reveals piRNA-dependent decay of mRNAs involved in germ cell development in the early embryo. Cell Reports,12, 1205-16.

Chartier A*, Klein P*, Pierson S, Barbezier N, Gidaro T, Casas F, Carberry S, Dowling P, Maynadier L, Bellec M, Oloko M, Jardel C, Bodo M, Dickson G, Mouly V, Ohlendieck K, Butler-Browne G, Trollet C#, Simonelig M# (2015). Mitochondrial dysfunction reveals the role of mRNA poly(A) tail regulation in oculopharyngeal muscular dystrophy pathogenesis. PLoS Genetics,11(3):e1005092.

Joly Willy, Chartier Aymeric, Rojas-Rios Patricia, Busseau Isabelle, Simonelig Martine (2013). The CCR4 deadenylase acts with Nanos and Pumilio in the fine-tuning of Mei-P26 expression to promote germline stem cell self-renewal. Stem Cell Reports, 1, 411-424.

Rouget Christel, Papin Catherine, Boureux Anthony, Meunier Anne-Cécile, Franco Bénédicte, Robine Nicolas, Lai Eric C., Pélisson Alain, Simonelig Martine (2010). Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature, 467, 1128-1132

Team leader: Philippe PASERO

Team’s title: Maintenance of Genome Integrity during DNA Replication

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 29

Email: philippe.pasero@igh.cnrs.fr

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Our body synthesizes more than 2×1016 meters of DNA in a life time, which represents 130,000 times the distance from Earth to the sun. This daunting task is executed by micro-machines called replisomes that act at DNA structures called replication forks. As they progress along the chromosomes, forks encounter obstacles leading to replication pausing. Stalled forks are fragile structures that can give rise to chromosome breaks and trigger genomic instability, a driving force of tumorigenesis. Understanding how cells respond to replication stress represents therefore a major challenge in cancer biology. Our group investigates the cellular responses to replication stress in budding yeast and in human cell lines. Owing to the small size of its genome and the power of molecular genetics, budding yeast is an invaluable model organism to study the RS response and to characterize novel mechanisms that are relevant to cancer. This is achieved through the use of powerful technologies to monitor the progression, arrest and recovery of replication forks. These methods include single-molecule approaches such as DNA combing and DNA fiber spreading and NGS-based assays such as ChIP-seq, BrdU-IP-seq, DRIP-seq and BLESS. These methods provide a comprehensive view of the replication stress response, from individual DNA molecules to whole genomes. To further characterize the links between replication stress and cancer, we have recently teamed up with the group of Jérôme Moreaux (Hematology Department of the University Hospital of Montpellier) who is an expert of the pathophysiology of malignant plasma cells, including lymphoma and multiple myeloma.

Keywords: Replication stress, Checkpoints, Fork processing, R-loops, Chromatin

Recent publications

Delamarre A, Barthe A, de la Roche Saint‐André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V*, Pasero P* and Lengronne A* (2019) MRX increases chromatin accessibility at stalled replication forks to promote nascent DNA resection and cohesin loading. Mol Cell, in press

Bianco JN, Bergoglio V, Lin Y-L, Pillaire M-J, Schmitz A-L, Gilhodes J, Lusque A, Mazières J, Lacroix-Triki M, Roumeliotis TI, Choudhary J, Moreaux J, Hoffmann JS, Tourrière H* and Pasero P* (2019) Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner. Nat Commun, 10, 910-923.

Bacal J#, Moriel-Carretero M#, Pardo B, Barthe A, Sharma S, Chabes A, Lengronne A and Pasero P (2018) Mrc1 and Rad9 cooperate to regulate initiation and elongation of DNA replication in response to DNA damage. EMBO J, 37, e99319 News & Views in EMBO J, Recommended by F1000

Coquel F#, Silva M-J#, Técher H#, Zadorozhny K, Sushma S, Nieminuszczy J, Mettling C, Dardillac E, Barthe A, Schmitz A-L, Promonet A, Cribier A, Sarrazin A, Niedzwiedz W, Lopez B, Costanzo V, Krejci L, Chabes A, Benkirane M, Lin YL* and Pasero P* (2018) SAMHD1 acts at stalled replication forks to prevent induction of interferon. Nature, 557, 57-61. Comments in Nature, Nature Reviews Immunology, Cancer Discovery, F1000

Fang D#, Lengronne A#, Shi D#, Forey R, Skrzypczak M, Ginalski K, Yan C, Wang X, Cao Q, Pasero P* and Lou H* (2017) Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing. Gene Dev, 31, 2405-2415 Recommended by F1000

Yoshida K, Bacal J, Desmarais D, Padioleau I, Tsaponina O, Chabes A, Pantesco V, Dubois E, Parrinello H, Skrzypczak M, Ginalski K, Lengronne A, Pasero P (2014) HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors. Mol Cell, 54, 691-697

Tittel-Elmer M#, Lengronne A#, Davidson MB, Bacal J, François P, Hohl M, Petrini J, Pasero P* and Cobb JA* (2012) Cohesin association to replication sites depends on Rad50 and promotes fork restart. Mol Cell, 48, 98-108. (*corresponding authors) Recommended by F1000

Poli J, Tsaponina O, Crabbe L, Keszthelyi A, Pantesco V, Chabes A, Lengronne A* and Pasero P* (2012). dNTP pools determine fork progression and origin usage under replication stress. EMBO J 31, 883-894 (*corresponding authors)

Crabbé L, Thomas A, Pantesco V, De Vos J, Pasero P* and Lengronne A* (2010) Genomic analysis of replication profiles identifies RFCCtf18 as a key mediator of the replication stress response. Nat Struct Mol Biol 17, 1391-1397 (* equal contribution)

Tuduri S, Crabbé L, Conti C, Tourrière H, Holtgreve-Grez H, Jauch A, Pantesco V, de Vos J, Theillet C, Thomas A, Pommier Y, Tazi J, Coquelle A* and Pasero P* (2009) Topoisomerase 1 suppresses replication stress and genomic instability by preventing interference between replication and transcription. Nat Cell Biol 11, 1315-1324 (* equal contribution)

Team leader: Kazufumi MOCHIZUKI

Team’s title: Epigenetic Chromatin Regulation

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 18

Email: kazufumi.mochizuki@igh.cnrs.fr

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Small RNA-mediated transcriptional gene silencing is a fundamental process that has been observed in many different eukaryotes including fungi, plants, flies, worms and mammals. One of its main tasks is to neutralize the activity of transposable elements (TEs), which otherwise destabilize our genome and potentially cause diseases. Small RNAs use their base complementarities to TEs to specifically silence them. However, how cells ensure TE-silencing without disturbing expressions of normal genes is not fully understood.

The ciliated protozoan Tetrahymena identifies TE-derived sequences by a germline-some genome comparison mechanism using small RNAs during programmed DNA elimination, which provides fascinating examples of epigenetic genome regulations and important insights into the interaction between TEs and host genomes. Because programmed DNA elimination can be synchronously induced in laboratory in a large scale, it serves as a useful laboratory model for genetically and biochemically investigating small RNA-mediated chromatin regulation.

The goal of our study is to understand: how cells accumulate small RNAs specifically from TE-related sequences; how cells use those small RNAs to identify TE-related sequences; and how a small RNA pathway establishes heterochromatin on TE-related sequences. We believe that our study of DNA elimination in the tiny-hairy eukaryotic model will provide important and general insights about epigenetic regulation of chromatin activities by small RNAs.

Keywords: Small RNA, epigenetics, heterochromatin, genome rearrangement, Tetrahymena

Recent publications

Mutazono M, Noto T, Mochizuki K* (2019) Diversification of small RNA amplification mechanisms for targeting transposon-related sequences in ciliates. PNAS 116, 14639-14644.

Noto T, Mochizuki K* (2018) Small RNA-mediated trans-nuclear and trans-element communications in Tetrahymena DNA Elimination. Curr Biol, 28, 1938-1949.

Suhren, J. H., Noto, T., Kataoka, K., Gao, S., Liu, Y., and Mochizuki, K.* (2017) Negative regulators of an RNAi-heterochromatin positive feedback loop safeguard somatic genome integrity in Tetrahymena. Cell Reports, 18, 2494-2507.

Kataoka, K.*, Noto, T., and Mochizuki, K.* (2016) Phosphorylation of an HP1-like protein is a prerequisite for heterochromatin body formation in Tetrahymena DNA elimination. PNAS 113, 9027-32.

Kataoka K, Mochizuki K* (2015) Phosphorylation of an HP1-like protein regulates RNA-bridged heterochromatin body assembly for DNA elimination. Dev Cell 35, 775-788.

Noto T, Kataoka K, Suhren JH, Hayashi A, Woolcock KJ, Gorovsky MA, Mochizuki K* (2015) Small RNA-mediated genome-wide trans-recognition network in Tetrahymena DNA elimination. Mol Cell 59, 229-242.

Woehrer SL, Aronica L, Suhren JH, Busch CJ, Noto T, Mochizuki K* (2015) A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms. EMBO Journal 34, 559-577.

Team leader: Domenico MAIORANO

Team’s title: Genome Surveillance and Stability

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 46

Email: domenico.maiorano@igh.cnrs.fr

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Our Team is interested in studying the regulation of the DNA damage response, in particular during embryonic development and in cancer recurrence. Inactivation of the DNA damage response is a feature of cancer cells, and surprisingly also of early embryos, playing an important role in facilitating cellular reprogramming. We have recently identified a major repressor of the DNA damage response in early Xenopus embryos, the Rad18 ubiquitin ligase, a master regulator of DNA damage tolerance, whose expression is abundant in early embryos and declines at later stages of development. We have observed that Rad18 is overexpressed in glioblastoma cancer stem cells and provided evidence that its high expression is relevant to therapy resistance for this cancer. We are currently investigating the specific involvement of Rad18 in cancer stem cells survival and adaptation to therapy. We have also identified an important regulator of the DNA damage response in mouse embryonic stem cells, the Dub3 ubiquitin hydrolase. We have shown that expression of Dub3 is controlled by the Esrrb pluripotency factor and that Dub3 expression declines very rapidly upon differentiation in vitro, more rapidly than that of the Oct4 pluripotency factor, making of Dub3 a very early marker of commitment to differentiation. We have also shown that Dub3 downregulation induces spontaneous heterogenous differentiation of mouse embryonic stem cells. We are currently exploring the possibility to manipulate the DNA damage response of pluripotent cells to improve their genomic instability, a hurdle that undermines their use in regenerative medicine.

Keywords: cancer stem cells; embryonic stem cells; DNA damage; chromatin; translesion DNA synthesis

Recent publications

Kermi C, Aze A, Maiorano D. Preserving Genome Integrity During the Early Embryonic DNA Replication Cycles. Genes (Basel). 2019 May 24;10(5). pii: E398. doi: 10.3390/genes10050398. Review. PubMed PMID: 31137726; PubMed Central PMCID: PMC6563053.

Hodroj D, Recolin B, Serhal K, Martinez S, Tsanov N, Abou Merhi R, Maiorano D. An ATR-dependent function for the Ddx19 RNA helicase in nuclear R-loop metabolism. EMBO J. 2017 May 2;36(9):1182-1198. doi: 10.15252/embj.201695131. Epub 2017 Mar 17. PubMed PMID: 28314779; PubMed Central PMCID: PMC5412905.

Benkafadar N, Menardo J, Bourien J, Nouvian R, François F, Decaudin D, Maiorano D, Puel JL, Wang J. Reversible p53 inhibition prevents cisplatin ototoxicity without blocking chemotherapeutic efficacy. EMBO Mol Med. 2017 Jan;9(1):7-26. doi: 10.15252/emmm.201606230. PubMed PMID: 27794029; PubMed Central PMCID: PMC5210089.

Kermi C, Prieto S, van der Laan S, Tsanov N, Recolin B, Uro-Coste E, Delisle MB, Maiorano D. RAD18 Is a Maternal Limiting Factor Silencing the UV-Dependent DNA Damage Checkpoint in Xenopus Embryos. Developmental Cell. 2015 Aug 10;34(3):364-72.doi: 0.1016/j.devcel.2015.06.002. Epub 2015 Jul 23. PubMed PMID: 26212134.

van der Laan S, Golfetto E, Vanacker JM, Maiorano D. Cell cycle-dependent expression of Dub3, Nanog and the p160 family of nuclear receptor coactivators (NCoAs) in mouse embryonic stem cells. PLoS One. 2014 Apr 2;9(4):e93663. doi: 10.1371/journal.pone.0093663. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e105649. PubMed PMID: 24695638; PubMed Central PMCID: PMC3973558.

Tsanov N, Kermi C, Coulombe P, Van der Laan S, Hodroj D, Maiorano D. PIP degron proteins, substrates of CRL4Cdt2, and not PIP boxes, interfere with DNA polymerase η and κ focus formation on UV damage. Nucleic Acids Res. 2014 Apr;42(6):3692-706. doi: 10.1093/nar/gkt1400. Epub 2014 Jan 14. PubMed PMID: 24423875; PubMed Central PMCID: PMC3973308.

van der Laan S, Tsanov N, Crozet C, Maiorano D. High Dub3 expression in mouse ESCs couples the G1/S checkpoint to pluripotency. Molecular Cell. 2013 Nov 7;52(3):366-79. doi: 10.1016/j.molcel.2013.10.003. PubMed PMID: 24207026.

Team leader: Rosemary Kiernan

Team’s title: Gene Regulation

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 74

Email: Rosemary.Kiernan@igh.cnrs.fr

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All organisms must regulate the expression of their genes to achieve the silencing of certain genes, and the activation of others during development and homeostasis. Disregulation of gene expression frequently has dire consequences, and can lead to pathologies such as cancer. The regulation of gene expression occurs at different levels, all of which depend on a multitude of factors. Chromatin is a primary regulator of gene expression. Studies performed over recent years have revealed the enormous complexity involved in modifying chromatin to regulate gene expression. Using proteomic and genomic approaches, our lab is interested in identifying novel factors implicated in human gene expression and understanding their mechanism of action.

Keywords: transcription, gene expression, chromatin, RNA processing, biochemistry

Recent publications

K Salifou, R Kiernan and X Contreras. 2019. Nuclear RNA Surveillance complexes control HIV-1 transcription. (French) Med Sci (Paris). 35:113-115. doi: 10.1051/medsci/2019018.

J Barbier, X Chen, G Sanchez, M Cai, M Helsmoortel, T Higuchi, P Giraud, X Contreras, G Yuan, Z Feng, R Nait-Saidi, O Deas, L Bluy, JG Judde, S Rouquier, W Ritchie, S Sakamoto, D Xie, and R Kiernan. 2018. An NF90/NF110-mediated feedback amplification loop regulates dicer expression and controls ovarian carcinoma progression. Cell Res. 28: 556-571.

X Contreras, K Salifou, G Sanchez, M Helsmoortel, E Beyne, L Bluy, S Pelletier, E Rousset, S Rouquier and R Kiernan. 2018. Nuclear RNA surveillance complexes silence HIV-1 transcription. PLoS Pathog. 2018 14(3):e1006950.

D Latreille, L Bluy, M Benkirane and R Kiernan. 2014. Identification of Histone 3 variant 2 interacting partners. Nuc Acids Res. 42: 3542-50

X Contreras, M Benkirane and R Kiernan. 2013. Premature termination of transcription by RNAP II: the beginning of the end. Transcription. 2013 4:72-6

A Wagschal, E Rousset, P Basavarajaiah, X Contreras, A. Harwig, S Laurent-Chabalier, M Nakamura, X Chen, K Zhang, O Meziane, F Boyer, H Parrinello, B Berkhout, C Terzian, M Benkirane and R Kiernan. 2012. Microprocessor, Setx, Xrn2 and Rrp6 Co-Operate to Induce Premature Termination of Transcription by RNAPII. Cell 150:1147-57.

Team leader: Daniel FISHER

Team’s title: Nuclear control of cell proliferation

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 94

Email: daniel.fisher@igmm.cnrs.fr

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Our group, specialist of nuclear cyclin dependent kinases, has contributed to determining the principles by which CDKs control cell proliferation, and the importance of this in cancer biology and therapy. Our results suggest that CDK-mediated phosphorylation is less specific than originally thought and generally controls the properties of structural molecules involved in nuclear sub-compartments. Recently, we demonstrated that nuclear actin is dynamically regulated during the cell cycle and is required in concert with CDK activity for DNA replication (Parisis, Krasinska et al., 2017). From phosphoproteomics experiments we discovered a novel phosphorylation of histone H3 mediated by the CDK-opposing checkpoint kinase CHK1 and demonstrated its involvement in responses to replication stress (Parisis et al., in revision). Analysing functions of CDK substrates, we have found that the synthesis and degradation of the cell proliferation antigen Ki-67 is regulated by the cell cycle machinery, accounting for variation in its expression levels (Sobecki, Mrouj et al., 2017), but it is not required for cell proliferation and knockout mice are viable; instead, Ki-67 is required for heterochromatin organisation (Sobecki et al., 2016). Recently, we found that Ki-67 ensures gene expression programmes required for all steps of tumourigenesis (Mrouj et al., 2019) and are currently working on the molecular mechanisms.

Keywords: CDK, cell cycle, DNA replication stress, heterochromatin, Ki-67

Recent publications

Mrouj, K., Singh, P., Sobecki, M., Dubra, G., Al Ghoul, E., Aznar, A., Prieto, S., Vincent, C., Pirot, N., Bernex, F., Bordignon, B., Hassen-Khodja, C., Pouzolles, M., Zimmerman, V., Dardalhon, V., Villalba, M., Krasinska, L. and Fisher, D. Ki-67 enables tumorigenesis by promoting transcriptome plasticity. Submitted. Posted on bioRxiv 24 July 2019 doi:10.1101/712380

Bačević, K.*, Noble, R.*, Soffar, A., Ammar, O.W., Boszonyik, B., Prieto, S., Vincent, C., Hochberg, M.E. , Krasinska, L. and Fisher, D.. (2017) Spatial competition constrains resistance to targeted cancer therapy Nat Commun 8(1):1995. doi: 10.1038/s41467-017-01516-1. co-senior authors.

Parisis, N.*, Krasinska, L.*, Harker, B., Urbach, S., Rossignol, M., Camasses, A., Dewar, J., Morin, N., and Fisher, D. (2017) Initiation of DNA replication requires actin dynamics and formin activity. EMBO J. 36, 3212-3231. doi: 10.15252/embj.201796585.

Sobecki, M. and Mrouj, K. , Colinge, J., Gerbe, F., Jay, P., Krasinska, L., Dulic, V. and Fisher, D. (2017) Cell cycle regulation accounts for variability in Ki-67 expression levels. Cancer Res 77, 2722–2734. doi: 10.1158/0008-5472.CAN-16-0707. co-first authors. PMID: 28283655

Sobecki, M., Mrouj, K., Camasses, A., Parisis, N., Nicolas, E., Llères, D., Gerbe, F., Prieto, S., Krasinska, L., David, A., Eguren, M., Birling, M.-C., Urbach, S., Hem, S., Déjardin, J., Malumbres, M., Jay, P., Dulic, V., Lafontaine, D.L.J., Feil, R. and Fisher, D. (2016). The cell proliferation antigen Ki-67 organises heterochromatin. eLife, 5, e13722. doi:10.7554/eLife.13722.

Team leader: Reini FERNANDEZ DE LUCO

Team’s title: Chromatin and Splicing

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 12

Email: reini.luco@igh.cnrs.fr

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The team looks for novel mechanisms of alternative splicing regulation amongst chromatin and long non-coding RNAs. Alternative splicing is a highly regulated process that allows to generate protein diversity in different cell-types. Its misregulation can lead to various diseases, including cancer. Traditionally, alternative splicing has been thought to be regulated at the RNA level by combinatorial recruitment of splicing factors to specific RNA-binding sites. However, epigenetic modifications, such as DNA methylation or histone modifications, chromatin conformation, and non-coding RNAs have recently been shown to play a role in alternative splicing regulation. We hypothesize that epigenetic mechanisms may play a critical role in the establishment and maintenance of cell-specific alternative splicing programs. By using a well established inducible human cell reprogramming system, based on the epithelial-to-mesenchymal transition (EMT), which has been intimately involved in early development and cancer metastasis, we aim at understanding which is the dynamic interplay between chromatin, 3D chromatin conformation and lncRNAs in regulating cell-specific splicing, with the final goal of impairing EMT. By using state-of-the-art epigenomics, transcriptomics, chromosome conformation capture (Hi-C, 4C-seq) and CRISPR editing tools during the EMT, we are understanding how, when and which marks play a role in establishing a novel cell-specific splicing program essential for the EMT and tumor progression. With these studies, we will better understand the multilayer role of chromatin in gene expression and will learn how to take advantage of these novel regulatory layers to revert more efficiently the EMT to reduce tumor metastasis and cancer progression.

Keywords: alternative splicing, chromatin, epithelial-to-mesenchymal transition, lncRNAs, 3D conformation

Recent publications

Agirre E., Oldfield A., Bellora N. and Luco R.F.*
Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition
In revision at Nature Communications

Sahu S, Agirre E, Diken M, Strand S, Luco RF, Tiwari VK
ZNF827-dependent splicing dynamics governs epithelial to mesenchymal transition
Submitted to Nature Communications

Gauchier M, Kan S, Barral A, Sauzet S, Agirre E, Bonnell E, Saksouk N, Barth TK, Ide S, Urbach S, Wellinger RJ, Luco RF, Imhof A and Déjardin J
SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres
Science Advances 2019, 5(5), eaav3673 DOI: 10.1126/sciadv.aav3673

Luco RF*
Retrotransposons jump into alternative splicing regulation via a long non-coding RNA.
Nature Structural Molecular Biology 2016, 23: 952–954.

Gonzalez I, Munita R, Agirre E, Dittmer TA, Gysling K, Misteli T and Luco RF*
A long non-coding RNA regulates alternative splicing via establishment of a splicing-specific chromatin signature.
Nature Structural Molecular Biology 2015, 22(5):370-6.

Luco RF*
The Non-Coding Genome: a universe in expansion for fine-tuning the coding world
Genome Biology 2013, 14(11):314.

Luco RF* and Misteli T.
More than a splicing code: Integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation.
Current Opinion in Genetics and Development 2011, 21:1-7.

Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T.
Epigenetics in alternative pre-mRNA splicing.
Cell 2011, 144 (1): 16-26.

Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith O, Misteli T.
Regulation of alternative splicing by histone modifications.
Science 2010, 327(5968):996-1000

Team leader: Robert FEIL

Team’s title: Genomic Imprinting and Development

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 63

Email: robert.feil@igmm.cnrs.fr

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Our lab explores epigenetic regulation in mammals and we are particularly interested in genomic imprinting. Imprinted genes are organised in large chromosomal domains and play important roles in development and disease. They are expressed in a mono-allelic manner, depending entirely on whether the gene is inherited from the mother or from the father. This remarkable expression pattern is controlled by allelic DNA methylation ‘imprints’ put onto key regulatory sequences called ‘imprinting control regions’ (ICRs). We have explored how these methylation imprints are established in germ cells, and how after fertilization, they are maintained throughout development. We discovered that the latter process is linked to a repressive chromatin signature that is similar to that found at endogenous retroviruses. Another question is how allelic DNA methylation imprints mediate imprinted gene expression during embryogenesis, often in a tissue-specific manner. Here, we have pinpointed critical roles of histone lysine methylation and of nuclear long non-coding RNAs. Another recent theme concerns the higher-order structuration of imprinted chromosomal domains. Using fluorescence microscopy and ‘chromosome conformation capture’ technologies, our recent collaborative studies on disease-associated imprinted domains have revealed that these domains are structured differently on the maternal versus the paternal chromosome, and we are currently unravelling the functional consequences. In parallel, our laboratory has developed an advanced fluorescence microscopy technology that enables us to monitor nanoscale chromatin compaction in living stem and differentiated cells. Combined, these strategic studies enhance our understanding of chromatin structuration and imprinted gene expression and their contributions to human disease.

Keywords: DNA methylation, chromatin structure, advanced fluorescence microscopy, genomic imprinting, non-coding RNA

Recent publications

CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains.
Llères D, Moindrot B, Pathak R, Piras V, Matelot M, Pignard B, Marchand A, Poncelet M, Perrin A, Tellier V, Feil R*, Noordermeer D*
Genome Biology, in the press.

Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses.
Pathak R, Feil R.
Curr Opin Chem Biol. 2018 Aug;45:139-147

Meg3 Non-coding RNA Expression Controls Imprinting by Preventing Transcriptional Upregulation in cis.
Sanli I, Lalevée S, Cammisa M, Perrin A, Rage F, Llères D, Riccio A, Bertrand E, Feil R.
Cell Rep. 2018 Apr 10;23(2):337-348.

Parallels between Mammalian Mechanisms of Monoallelic Gene Expression.
Khamlichi AA, Feil R.
Trends Genet. 2018 Dec;34(12):954-971.

Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes.
Llères D, Bailly AP, Perrin A, Norman DG, Xirodimas DP, Feil R.
Cell Rep. 2017 Feb 14;18(7):1791-1803.

The placental imprinted DLK1-DIO3 domain: a new link to prenatal and postnatal growth in humans.
Prats-Puig A, Carreras-Badosa G, Bassols J, Cavelier P, Magret A, Sabench C, de Zegher F, Ibáñez L, Feil R*, López-Bermejo A*.
Am J Obstet Gynecol. 2017 Sep;217(3):350.e1-350.e13.

Regulatory links between imprinted genes: evolutionary predictions and consequences.
Patten MM, Cowley M, Oakey RJ, Feil R.
Proc Biol Sci. 2016 Feb 10;283(1824).

Insertion of an imprinted insulator into the IgH locus reveals developmentally regulated, transcription-dependent control of V(D)J recombination.
Puget N, Hirasawa R, Hu NS, Laviolette-Malirat N, Feil R*, Khamlichi AA*.
Mol Cell Biol. 2015 Feb;35(3):529-43.

ICR noncoding RNA expression controls imprinting and DNA replication at the Dlk1-Dio3 domain.
Kota SK, Llères D, Bouschet T, Hirasawa R, Marchand A, Begon-Pescia C, Sanli I, Arnaud P, Journot L, Girardot M, Feil R.
Dev Cell. 2014 Oct 13;31(1):19-33.

PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome.
Girardot M, Hirasawa R, Kacem S, Fritsch L, Pontis J, Kota SK, Filipponi D, Fabbrizio E, Sardet C, Lohmann F, Kadam S, Ait-Si-Ali S, Feil R.
Nucleic Acids Res. 2014

Team leader: Bernard DE MASSY

Team’s title: Meiosis and recombination

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 92

Email: bernard.de-massy@igh.cnrs.fr

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Our team is investigating several aspects of the mechanism and regulation of meiotic recombination and its evolutionary implication using the mouse as a model system. Meiotic recombination events are initiated by the formation of DNA double-strand breaks (DSBs, several hundred per nucleus in mice). Proper control of DSB formation is critical for an error-free repair and thus to maintain genome stability. In addition, DNA exchanges promoted by meiotic recombination contribute to genetic diversity and genome evolution. We aim to understand the molecular mechanisms that control the localization, the frequency and the timing of meiotic DSB formation. These controls are thought to involve several layers of regulations at the DNA level, at the chromatin and epigenetic levels and at chromosome organisation level.

Keywords: Meiosis, recombination, reproduction, genome stability, chromosome organization

Recent publications

Papanikos F*, Clément JAJ*, Testa E, Ravindranathan R, Grey C, Dereli I, Bondarieva A, Valerio-Cabrera S, Stanzione M, Schleiffer A, Jansa P, Lustyk D, Jifeng F, Adams IR, Forejt J, Barchi M, de Massy B*, Toth A*. (2019) ANKRD31 regulates spatiotemporal patterning of meiotic recombination initiation and ensures recombination between heterologous sex chromosomes in mice. Mol Cell 74, 1069-1085 e1011,

Diagouraga, B. *., Clement, J.A.J. *., Duret, L., Kadlec, J., de Massy, B.*., and Baudat, F. *. (2018) PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites. Mol Cell 69, 853-865 e856.

Grey C*, Clement JA*, Buard J, Leblanc B, Gut I, Gut M, Duret L and de Massy B. (2017) In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites. Genome Res. 27, 580-590.

Robert T, Nore A, Brun C, Maffre C, Crimi B, Guichard V, Bourbon HM* and de Massy B.* (2016) The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation. Science 351, 943-9.

Cole F*, Baudat F*, Grey C, Keeney S*, de Massy B* and Jasin M. * (2014) Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet 46, 1072-80.

Wu H, Mathioudakis N, Diagouraga B, Dong A, Dombrovski L, Baudat F, Cusack S, de Massy B* and Kadlec J.* (2013) Molecular Basis for the Regulation of the H3K4 Methyltransferase Activity of PRDM9. Cell Rep 5, 13-20.

Baudat F, Imai Y and de Massy B. (2013) Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14, 794-806.

Grey C, Barthes P, Chauveau-Le Friec G, Langa F, Baudat F and de Massy B. (2011) Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination. PLoS Biol 9, e1001176.

Kumar R, Bourbon HM and de Massy B. (2010) Functional conservation of Mei4 for meiotic DNA double-strand break formation from yeasts to mice. Genes Dev 24, 1266-80.

Baudat F*, Buard J*, Grey C*, Fledel-Alon A, Ober C, Przeworski M, Coop G and de Massy B. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327, 836-40.

Team leader: Jacques COLINGE

Team’s title: Cancer bioinformatics and systems biology

Institute: Institut of Cancer Research Montpellier – IRCM

Phone: 00 33 4 67 61 23 92

Email: jacques.colinge@inserm.fr

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Our main field of research is the development of methods to analyze and integrate large genomic data sets. Morst of the projects entail collaboration with biologists and/or clinicians and are based on patient material. The techniques employed are bioinformatics, computational statistics, network science, and numerical analysis.

Current research falls into two axes. Firstly, we infer large, qualitative biological networks utilizing multi-omics data integration to discover active modules, resistance mechanisms, and potential new therapeutic targets. This work covers both intra- (signaling, transcription) and inter-cellular (tumor microenvironment) interactions. In case we are interested in smaller, targeted biological networks, we also develop mathematical modeling techniques aimed at inferring their topology, coupling and to predict their behavior. Secondly, we work on computational proteomics and some of its advanced applications. At the moment, our main interest is the development (with clinical partners) of an innovative experimental/computational framework to determine protein turnover parameters in biological fluids in patients and in vivo. We have obtained very promising results in the cerebrospinal fluid and plasma. With those tools, we want to explore new classes of biomarkers related to abnormal clearance rates or passage across biological barriers in disease. A farther goal is to work on the impact of active molecules on tumor proteome dynamics.

Keywords: genomics, systems biology, networks, tumor microenvironment, computational proteomics

Recent publications

Melissa Alame, Emmanuel Cornillot, Valère Cacheux, Guillaume Tosato, Marion Four, Laura De Oliveira, Stéphanie Gofflot, Philippe Delvenne, Evgenia Turtoi, Simon Cabello-Aguilar, Hidero Obinata, Masahiko Nishiyama, Andreï Turtoi*, Valérie Costes-Martineau*, Jacques Colinge* (submitted). The molecular landscape and microenvironment of salivary duct carcinoma reveals new therapeutic opportunities. *Co-senior authors. Available from bioXiv.

Sylvain Lehmann*, Christophe Hirtz, Jérôme Vialaret, Maxence Ory, Guillaume Gras Combes, Marine Le Corre, Stéphanie Badiou, Jean-Paul Cristol, Olivier Hanon, Emmanuel Cornillot, Luc Bauchet, Audrey Gabelle, Jacques Colinge* (2019). In vivo large scale mapping of protein turnover in the human cerebrospinal fluid. Anal Chem. *Co-senior authors.

Sobecki, M., Mrouj, K., Colinge, J., Gerbe, F., Jay, P., Krasinska, L., Dulic, V. and Fisher, D. (2017) Cell-Cycle Regulation Accounts for Variability in Ki-67 Expression Levels. Cancer Res, 77, 2722–2734.

Granier, C., Dariane, C., Combe, P., Verkarre, V., Urien, S., Badoual, C., Roussel, H., Mandavit, M., Ravel, P., Sibony, M., Biard, L., Radulescu, C., Vinatier, E., Benhamouda, N., Peyromaure, M., Oudard, S., Mejean, A., Timsit, M.-O., Gey, A. and Tartour, E. (2017) Tim-3 Expression on Tumor-Infiltrating PD-1(+)CD8(+) T Cells Correlates with Poor Clinical Outcome in Renal Cell Carcinoma. Cancer Res, 77, 1075–1082.

Mazouzi, A., Stukalov, A., Muller, A.C., Chen, D., Wiedner, M., Prochazkova, J., Chiang, S.-C., Schuster, M., Breitwieser, F.P., Pichlmair, A., El-Khamisy, S.F., Bock, C., Kralovics, R., Colinge, J., Bennett, K.L. and Loizou, J.I. (2016) A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN. Cell Rep, 15, 893–908.

Blomen, V.A.#, Majek, P.#, Jae, L.T., Bigenzahn, J.W., Nieuwenhuis, J., Staring, J., Sacco, R., van Diemen, F.R., Olk, N., Stukalov, A., Marceau, C., Janssen, H., Carette, J.E., Bennett, K.L., Colinge, J.*, Superti-Furga, G.* and Brummelkamp, T.R.* (2015) Gene essentiality and synthetic lethality in haploid human cells. Science, 350, 1092–1096. * Co-senior authors, #co-first authors.

Huber, K.V.M., Olek, K.M., Muller, A.C., Tan, C.S.H., Bennett, K.L., Colinge, J.* and Superti-Furga, G.* (2015) Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nat Methods, 12, 1055–1057. * Co-senior authors.

Muellner, M.K., Mair, B., Ibrahim, Y., Kerzendorfer, C., Lechtermann, H., Trefzer, C., Klepsch, F., Muller, A.C., Leitner, E., Macho-Maschler, S., Superti-Furga, G., Bennett, K.L., Baselga, J., Rix, U., Kubicek, S., Colinge, J., Serra, V. and Nijman, S.M. (2015) Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol, 11, 789.

Huber, K.V., Salah, E., Radic, B., Gridling, M., Elkins, J.M., Stukalov, A., Jemth, A.S., Gokturk, C., Sanjiv, K., Stromberg, K., Pham, T., Berglund, U.W., Colinge, J., Bennett, K.L., Loizou, J.I., Helleday, T., Knapp, S. and Superti-Furga, G. (2014) Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy. Nature, 508, 222–7.

Team leader: Giacomo CAVALLI

Team’s title: Chromatin and Cell Biology

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 70

Email: Giacomo.Cavalli@igh.cnrs.fr

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The genome is organized into a hierarchy of higher-order structures. Strings of genes organize in chromosomal domains, either active or repressed. In the 3D space, each of the elements in one domain makes frequent contacts with other elements in the same domain. These entities have been called physical- or topologically associated- domains (TADs). Individual TADs form contacts with other TADs, preferentially of the same type, in order to build chromosome territories. Finally, different chromosomes organize non randomly in the nuclear space. This sophisticated organization can be transmitted or modulated during the life of cells and organisms and involves thousands of different players – DNA sequences, RNAs and proteins – but rather than combining in infinite numbers of ways, these components organize a relatively limited number of types of chromatin. In particular, two main groups of genome regulatory components are proteins of the Polycomb Group (PcG) and of the trithorax Group (trxG). PcG proteins maintain the memory of silent states of gene expression through cell physiology and multiple cell divisions, while trxG members maintain active chromatin states. These proteins are able to recognize regulatory states of their target genes and to maintain these states even after disappearance of the primary transcriptional regulators that have induced them in the first place. Remarkably, these states can also be transmitted to a fraction of the progeny over multiple generations. In our lab, we aim at understanding the principle governing 3D genome organization, its functional implications, and the molecular mechanisms by which PcG and trxG proteins regulate their target genes, convey inheritance of chromatin states and orchestrate development. To reach this goal, we employ a variety of complementary approaches and techniques in the areas of molecular, cellular and developmental biology, genomics and bioinformatics.

Keywords: Epigenetics, 3D Genome, Polycomb, Trithorax, development and differentiation

Recent publications

Cavalli, G.* and Heard, E.* (2019) 21st Century Epigenetics linking Genetics to the Environment and Health. Nature, 571, 489_499 doi: 10.1038/s41586-019-1411-0.

Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., and Cavalli, G. (2017). Multi-scale 3D genome rewiring during mouse neural development. Cell 171, 557-572.e24.

Schuettengruber, B., Bourbon, H., Di Croce, L., and Cavalli, G. (2017). Genome Regulation by Polycomb and Trithorax: 70 years and counting. Cell 171, 34-57.

Ciabrelli, F., Comoglio, F. Fellous, S., Bonev, B., Ninova, M., Szabo, Q., Xuéreb, A., Klopp, C., Aravin, A. Paro, R., Bantignies, F., and Cavalli, G (2017). Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nature Genet, 49, 876-886, doi:10.1038/ng.3848

Loubiere, V., Delest, A., Thoma, A., Bonev, B., Schuettengruber, B., Sati, S., Martinez, AM., and Cavalli, G. (2016) Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nature Genet, 48, 1436-1442, doi:10.1038/ng.3671

Sexton, T., and Cavalli, G. (2015). The role of chromosome domains in shaping the functional genome. Cell, 160, 1049-1059

Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., and Cavalli, G. (2012). Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472

Bantignies, F., Roure, V., Comet, I., Leblanc, B., Schuettengruber, B., Bonnet, J., Tixier, V., Mas, A., and Cavalli, G. (2011). Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214-26.

Martinez, AM., Schuettengruber, B., Sakr, S., Janic, A., Gonzalez, C., and Cavalli, G. (2009). Polyhomeotic has a tumor suppressor activity mediated by repression of Notch signaling. Nature Genet. 41:1076-82.

Grimaud, C., Bantignies, F., Pal-Bhadra, M., Ghana, P., Bhadra, U., and Cavalli, G. (2006). RNAi Components Are Required for Nuclear Clustering of Polycomb Group Response Elements. Cell 124, 957-971

Déjardin, J., Rappailles, A., Cuvier, O., Grimaud, C., Decoville, M., Locker, D., and Cavalli, G. (2005). Recruitment of Drosophila Polycomb Group proteins to chromatin by DSP1. Nature, 434, 533-538; doi:10.1038/nature03386.

Team leader: Jean-Christophe ANDRAU

Team’s title: Transcription and epigenomics in developing T cells

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 52

Email: jean-christophe.andrau@igmm.cnrs.fr

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Our team is interested in the process of transcription and epigenetic control of mammalian cells with a focus on T cell differentiation. An important aspect of our research relies to understanding the role of the Carboxy-Terminal Domain (CTD) of RNA Polymerase II (Pol II) in transcriptional regulation (axis 1). In the recent years we focused our investigations in Tyr residues of the CTD and showed that they are essential for the control of termination of transcription. We are currently studying the properties of mutants having lost their ablity to terminate transcription that are able to transcription over several TAD borders to interrogate whether pervasive transcription is likely to disrupt chromatin structure.

During differentiation, important epigenetic and transcriptional changes allow stem cells to modulate their original genetic program, resulting in dramatic transitions in cellular functions and properties. Enhancers and promoters of both coding and noncoding genes are major genomic modules, crucial for regulating this process (axes 2 and 3). Deciphering their mechanism of action represents therefore an essential task for the future years and is also a common theme in our 3 research topics. More specifically, we are tesing the hypotheses that enhancers play a role in the control of isoform expression (2) and that G-quadruplexes are essential for promoter opening prior transcription activation in mammalian cells (3).

Keywords: Transcription, Enhancers, Promoters, G-quadruplexes, RNA polymerase II

Recent publications

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection. Sultana T, van Essen D, Siol O, Bailly-Bechet M, Philippe C, Zine El Aabidine A, Pioger L, Nigumann P, Saccani S, Andrau JC, Gilbert N, Cristofari G. Mol Cell. 2019 May 2;74(3):555-570.

Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals. Shah N, Maqbool MA, Yahia Y, El Aabidine AZ, Esnault C, Forné I, Decker TM, Martin D, Schüller R, Krebs S, Blum H, Imhof A, Eick D*, Andrau JC*. Mol Cell. 2018 Jan 4;69(1):48-61.

ARS2 is a general suppressor of pervasive transcription. Iasillo C, Schmid M, Yahia Y, Maqbool MA, Descostes N, Karadoulama E, Bertrand E, Andrau JC*, Jensen TH*. Nucleic Acids Res. 2017 Sep 29;45(17):10229-10241.

Dynamic recruitment of Ets1 to both nucleosome -occupied and -depleted enhancer regions mediates transcriptional program switch during early T-cell differentiation. Cauchy P, Maqbool MA, Zacarías-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S*, Andrau JC*. Nucleic Acid Research 2016 May 5;44(8):3567-85.

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells. Soucie EL, Weng Z, Geirsdóttir L, Molawi K, Maurizio J, Fenouil R, Mossadegh-Keller N, Gimenez G, VanHille L, Beniazza M, Favret J, Berruyer C, Perrin P, Hacohen N, Andrau JC, Ferrier P, Dubreuil P, Sidow A, Sieweke MH. Science. 2016 Jan 21. pii: aad5510.

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals Vanhille L, Griffon A, Maqbool MA, Zacarías-Cabeza J, Lan. T.M. Dao, Fernandez N, Ballester B, Andrau JC, Spicuglia S. Nature Communications 2015 Apr 15; 6:6905.

Site- and allele-specific polycomb dysregulation in T-cell leukaemia. Navarro JM, Touzart A, Pradel LC, Loosveld M, Koubi M, Fenouil R, Le Noir S, Maqbool MA, Morgado E, Gregoire C, Jaeger S, Mamessier E, Pignon C, Hacien-Bey-Abina S, Malissen B, Gut M, Gut I, Hevré D, Macintyre EA, Howe SJ, Gaspar HB, Trasher AJ, Ifrah N, Payet-Bornet D, Duprez E**, Andrau JC**, Asnafi V**, Nadel B.** Nature Communications 2015 Jan 23;6:6094.

Team leader: Monsef BENKIRANE

Team’s title: Molecular Virology

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 96

Email: monsef.benkirane@igh.cnrs.fr

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Team leader: Edouard BERTRAND

Team’s title: RNA Biogenesis and trafficking

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 47

Email: edouard.bertrand@igmm.cnrs.fr

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Our group has strong interests in gene expression mechanisms, from transcription to translation. While we are interested in the regulation of these processes and their functional consequences, the big question that moves us is to understand how they occur in the context of a living cell.

Indeed, cells are not only the individual units where gene regulation takes place, they are also incredible objects: if we consider RNA and proteins, a typical cell contains several hundreds of thousands of different molecular species, with some present in millions of copies per cell while others in only few. In order to function with such a high molecular complexity, cells have evolved a fascinating spatial organization, which is not only  pushed to an amazing degree, but is also remarkably plastic and with a high molecular mobility. It is to get insights into these very fundamental questions that we first developed tools to image single mRNAs in live cells (Bertrand et al., 1998; Fusco et al., 2003). With these tools in hands and others that we developed later on (for instance see Pichon et al, 2016; Tantale et al. 2016), we aim at imaging the basic mechanisms of gene expression directly in living cells. We hope to provide a renewed vision of these fundamental processes.

Our strategy is to invest in technological developments to access and image new facets of gene expression. Over the years, we have been able to contribute to the resolution of important issues in the area of gene expression, including transcription, splicing and translation. We currently have four research themes: (i) imaging transcription to characterize the origins and consequences of transcriptional noise; (ii) spatio-temporal regulation of RNA localization and translation; (iii) assembly of macromolecular complexes by the HSP90/R2TP chaperone; (iv) computational identification of non-coding genomic elements.

Keywords: RNA biology, single molecule imaging, transcription, translation, RNP assembly

Recent publications:

A localization screen reveals translation factories and widespread co-translational protein targeting. Preprint available at https://ssrn.com/abstract=3300043 Chouaib, R., Safieddine, A., Pichon, X., Kwon, OS., Samacoits, A., Traboulsi, AM., Tsanov, N., Robert, MC., Poser, I., Zimmer, C., Hyman, A. A., Le Hir, H., Zibara, K., Peter, M., Mueller, F.*, and Walter, T.*, Bertrand, E.*
* co-corresponding authors.

A computational framework to study sub-cellular mRNA localization. Nat Comm, 2018, 9:4584. Samacoits, A., Chouaib, R., Safieddine, S., Traboulsi, A., Ouyang, W., Zimmer, C., Peter, M., Bertrand, E.*, Walter, T.*, Mueller, F.*
* co-corresponding authors.

A growing toolbox to image gene expression in single cells: sensitive approaches for demanding challenges. Mol. Cell, 2018, 71:468-480. Pichon, X., Lagha, M., Mueller, F. and Bertrand, E.
Invited review for the 20th anniversary of the journal; featured article of the issue

The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones. Nat Comm, 2018, 9:2093. Maurizy, C., Quinternet, M., Abel, Y., Verheggen, C., Santo, P. E., Bourguet, M., Paiva, A. C. F., Bragantini, B., Chagot, ME., Robert, MC., Abeza, C. Fabra, P., Fort, P., Vandermoere, F., Sousa, P., Rain, JC., Charpentier, B., Cianférani, S., Bandeiras, T. M., Pradet-Balade, B., Manival, X., Bertrand, E.
Comment in Nature Comm, 2018.

The PAQosome, an R2TP-based chaperone for quaternary structure formation. TIBS 2018, 43:4-9. Houry, W.A.*, Bertrand, E.*, and Coulombe, B.*
*co-corresponding authors.

Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J. Cell Biol., 2017, 21:1579-1596. Malinová, A., Cvačková, Z., Matějů, D., Hořejší, Z., Abéza, C., Vandermoere, F., Bertrand, E.*, Staněk, D.*, Verheggen, C.*
*co-corresponding authors.

Mutually exclusive CBC-containing complexes contribute to RNA fate. Cell Reports, 2017, 18:2635-2650. Giacometti, S., Benbahouche, N. H., Domanski, M., Robert, M-C., Meola, N., Lubas, M., Bukenborg, J., Andersen, J. S., Schultze, W. M., Verheggen, C., Kudla, G.*, Jensen, T. H.*, Bertrand, E.*
*co-corresponding authors

Visualization of single polysomes reveals translation dynamics of endogenous mRNAs in living human cells, J. Cell Biol., 2016, 214:769-81. Pichon X., Bastide A., Safieddine A., Chouaib R., Samacoits A., Basyuk E., Peter M., Mueller F., Bertrand E.
Spotlight article, see commentary in doi:10.1083/jcb.201608075, selected by F1000

SmiFISH and FISH-quant –  a flexible single mRNA detection approach with super-resolution capability. Nucleic Acids Res, 2016, pii:gwk784, Tsanov, N., Samacoits, A., Chouaib, R., Traboulsi, A.M., Gostan, T., Weber, C., Zimmer, C., Zibara, K., Walter, T., Peter, M.*, Bertrand, E.*, Mueller, F*
*co-corresponding authors.

A real-time, single molecule view of transcription reveals convoys of RNA polymerases and multiscale bursting. Nat. Comm., 2016, 7:12248. Tantale, K., Müller, F., Kozulic-Pirher, A., Lesne, A., Victor, JL., Robert, MC., Capozi, S., Bäcker, V., Mateos-Langerak, J., Darzacq, X., Zimmer, C., Basyuk, E., Bertrand, E.
Selected by F1000

Team leader: Jérôme DEJARDIN

Team’s title: Biology of Repetitive Sequences

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 45

Email: jerome.dejardin@igh.cnrs.fr

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Team leader: Mounia LAGHA

Team’s title: Transcription and Development

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 50

Email: mounia.lagha@igmm.cnrs.fr

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www.laghalab.com

Gene expression is precisely controlled in time and space during the development of Metazoan organisms. While numerous studies have established how spatial information is integrated by gene regulatory regions, called enhancers, little is known about the temporal aspects of transcription. Most of our insights into gene regulation stem from the use of fixed preparations where timing is artificially reconstituted from different snapshots. Our goal is to integrate the dynamic aspects of gene regulation to understand how coordination is achieved and whether it is required during development. Transcriptional coordination refers to the inter-nuclear temporal coordination in gene activation (synchrony) and homogeneity in mRNA distribution across a field of coordinately developing cells. We characterize the mechanisms of transcriptional coordination in the early Drosophila embryo, a model system which allows quantitative imaging and genetic manipulations.

Specifically our team employs live imaging techniques to address fundamental questions about transcriptional dynamics in a multicellular developing embryo, with three main objectives:

1-examine the effects of promoter sequence and enhancer priming on transcriptional coordination.
2-analyse the inheritance of transcriptional states from mother to daughter cells and identify the bookmarking mechanisms responsible for this memory.
3-explore the interplay between transcription and translation for precise cell fate decisions.

5 Keywords: transcription, quantitative imaging, development, systems biology, dynamics

Recent publications:

Trullo A, Dufourt J and Lagha M. MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos” (2019) Bioinformatics Oct 3. pii: btz717.
doi: 10.1093/bioinformatics/btz717.

Fernandez C and Lagha M Lightening up gene activation in living Drosophila embryos (2019Methods Mol Biol, 2019;2038:63-74. doi: 10.1007/978-1-4939-9674-2_5.

Dufourt J, Trullo A, Hunter J, Fernandez C, Lazaro J, Dejean M, Morales L, Nait-Amer S, Schulz KN, Harrison MM, Favard C, Radulescu O, Lagha M (2018) Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs. Nat Commun. 2018 Dec 5;9(1):5194. doi: 10.1038/s41467-018-07613-z.

Comment in:
* Preprint highlights, by preLights (The Company of Biologists)
* Nature Communications Editor’s Highlight
* CNRS_INSB journal

Bellec M, Radulescu O and Lagha M (2018) Remembering the past: Mitotic bookmarking in a developping embryo. Current Opinions in Systems Biology 2018 Oct;11:41-49. doi: 10.1016/j.coisb.2018.08.003.11:41–49

Pichon X, Lagha M, Mueller F and Bertrand E (2018) A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges. Molecular Cell Aug 2;71(3):468-480

Ferraro T, Esposito E, Mancini L, Ng S, Lucas T, Coppey M, Dostatni N, Walczak A, Levine M and Lagha M (2016) Transcriptional memory in the Drosophila embryo. Current Biology 2016 Jan 25;26(2):212-218. doi: 10.1016/j.cub.2015.11.058

Comment in:

Chubb JR. Gene Regulation: Stable Noise. Current Biology 2016;26:R61–4. doi:10.1016/j.cub.2015.12.002.

Lagha M, Bothma J, Esposito E, Samuel Ng, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour D, Zeitlinger J and Levine M. (2013) Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell; 153(5) 976-87.

Comment in:

Burgess.D, (2013) Time flies thanks to Pol II pausing. Nature Review Genetics 14: 443
Saunders and Ashe (2013) Taking a pause to reflect on morphogenesis, Cell 153(5) 941-943.
Recommended by Faculty of 1000.

Lagha M, Bothma J and Levine M (2012) Mechanisms of transcriptional precision in development. Trends in Genetics; (8)409-16.

Team leader: Laurent LE CAM

Team’s title: Molecular oncogenesis

Institute: Institut of Cancer Research Montpellier – IRCM

Phone: 00 33 4 67 61 23 49

Email: laurent.lecam@inserm.fr

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Team leader: Marcel MECHALI

Team’s title: Replication and Genome Dynamics

Institute: Institute of Human Genetics – IGH

Phone: 00 33 4 34 35 99 17

Email: marcel.mechali@igh.cnrs.fr

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Team leader: Marcelo NOLLMANN

Team’s title: Mechanisms of DNA Segregation and Remodeling

Institute: Centre of Structural Biochemistry – CBS

Phone: 00 33 4 67 41 79 12

Email: nollmann@cbs.cnrs.fr

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Team leader: Claude SARDET & Charles THEILLET
Team’s title: Genetic and phenotypic plasticity of cancer

Institute: Institut of Cancer Research Montpellier – IRCM

Phone: 00 33 4 67 61 30 84 & 00 33 4 67 61 37 66

Email: claude.sardet@inserm.fr & Charles.theillet@inserm.fr

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Team leader: Eric SOLER
Team’s title: Chromatin Dynamics in Hematopoiesis

Institute: Institute of Molecular Genetics of Montpellier – IGMM

Phone: 00 33 4 34 35 96 55

Email: eric.soler@igmm.cnrs.fr

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LabMUSE EpiGenMed – International Collaborative PhD Training networks 2020

The international LabMUSE EpiGenMed PhD program is currently accepting applications for 3-year PhD positions in collaborative PhD training networks starting October 1st, 2020 at Montpellier University.

LabMUSE EpiGenMed collaborative PhD Training networks

The aim of the LabMUSE EpiGenMed collaborative PhD program is to constitute networks of 3-4 Montpellier research groups for the joint training of 3-4 PhD students. The teams integrated in a PhD training network together establish a training plan over three years. Each research group hosts one PhD student for three years who will benefit from training in the team, in the other teams and from common training actions set up by the network.

The PhD salaries are funded by the I-SITE MUSE – Montpellier University of Excellence.

PhD Training networks proposing PhD positions starting on October 1st, 2020

Network “Transcriptional noise in development and disease”

Edouard Bertrand (Institute of Molecular Genetics of Montpellier – IGMM) & Ovidiu Radulescu (Laboratory of Pathogen Host Interactions – LPHI)
Mounia Lagha (Institute of Molecular Genetics of Montpellier – IGMM)
Séverine Chambeyron (Institute of Human Genetics – IGH)

A fundamental question in biology is how cellular processes are so reproducible despite the inherent stochasticity of biochemical reactions. For transcription in particular, imaging has revealed that genes function in an intermittent fashion, with periods of activity followed by periods of inactivity. This transcriptional noise has two sources: intrinsic noise arises from the stochasticity of reactions leading to transcription initiation, while extrinsic noise comes from environmental or global changes affecting the entire cell. While transcriptional fluctuations need to be dampened during embryonic development, they can also generate diversity. Thus, they can be both useful and detrimental.

In this training network, we will decipher the mechanisms and functions of transcriptional noise during development and disease. In particular, we will disentangle extrinsic and intrinsic noise and therefore determine how transcription is affected by the cell’s life. We will use two biological models: Drosophila embryos where noise buffering is important, and HIV-1 latency where stochasticity is beneficial. We will directly image transcription in live cells and combine quantitative imaging data with mathematical modelling.

The network will train 3 PhD Students by 4 teams located in Montpellier (E. Bertrand, S. Chambeyron, M. Lagha, O. Radulescu). It will provide common activities, interdisciplinary training and an environment uniting biologists and mathematicians.

Keywords: Transcription Regulation, Quantitative Imaging and Systems Biology,

Developmental Biology, HIV-1

Mathematical modelling of HIV-1 transcription: contribution of extrinsic and intrinsic noise to latency exit

Latent cells infected with HIV-1 virus prevent patients from being cured. In these cells, viral transcription is brief and rare, rather than totally non-existent. Because of this residual activity, latent viruses can remain at undetectable levels for years and yet rapidly provoke viral rebounds after stopping antiviral treatments. Several mechanisms have been proposed to trigger latency exit. Spontaneous activation of the viral promoter can occur because of the stochastic nature of transcription initiation (intrinsic noise). External events affecting the entire cell can also activate viral transcription (extrinsic noise). In this project, the PhD student will use single-molecule methods to image the transcriptional activity of HIV-1 in live single cells. He/she will then develop mathematical models to extract the contribution of extrinsic versus intrinsic factors to HIV-1 transcriptional bursts. Applicants should be skilled in statistics and scripting, and should aim at being trained in both wet and dry biological sciences.

Learn more (Bertrand)

Learn more (Radulescu)

Impact of paused polymerase on transcriptional noise during development

Live cell imaging of transcription has revealed that transcription is discontinuous and occurs in bursts. These have a great potential for generating cell-to-cell variability but, in the context of a developing organism, must be regulated to ensure reproducible outcomes. In this project, the PhD student will decipher the impact of paused polymerase on transcriptional noise in Drosophila embryos. Indeed, during early development, there is a switch in transcriptional regulation whereby developmental promoters acquire paused polymerases as a major regulatory checkpoint. The effects of pausing on transcriptional noise have not yet been characterized and could in principle either buffer or increase noise.

The student will employ quantitative live imaging of transcription combined with mathematical approaches, to detect each polymerase initiation events for each nucleus in vivo and to model extrinsic and intrinsic noise. Candidates should be cell/developmental biologists with an interest in gene expression and quantitative biology. Prior experience in Drosophila genetics and coding would be a plus.

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Impact of chromatin compaction on transcription noise

Transcription is a discontinuous process leading to fluctuations of RNA levels even between isogenic cells. One mechanism generating transcriptional noise is a stochastic switching of promoters between active and inactive states. The inactive state is presumably controlled by chromatin compaction. However, as gene models were only imaged in euchromatin, there is a surprising lack of knowledge on how transcription fluctuates in a repressive heterochromatin environment. By imaging the transcription of heterochromatic regions in live Drosophila embryos, this project will decipher the impact of local chromatin states on transcriptional noise. Further analysis of extrinsic versus intrinsic noise will determine how heterochromatinization is regulated by the local cell environment. The student will monitor nascent transcription of loci located in heterochromatin in live embryos. To demonstrate a role of chromatin marks in transcription fluctuations, he/she will deplete chromatin modifying enzymes using optogenetic tools. Candidates should have an interest in Drosophila genetics and programing knowledge would be appreciated.

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Network “Role of phase separation mechanisms in higher-order chromatin organization during development”

Marcelo Nollmann (Centre of Structural Biochemistry – CBS)
Giacomo Cavalli (Institute of Human Genetics – IGH)
Andrea Parmeggiani (Laboratoire Charles Coulomb – L2C) & Marie Schaeffer (Institute of Functional Genomics – IGF)

Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during development in both Drosophila and mammals, and they do so by mediating the formation of H3K27me3 chromatin domains. PcG proteins compact chromatin and form higher-order hubs inside the cell nucleus, but the molecular mechanisms at the basis of PcG-dependent 3D chromatin folding are poorly understood. The cell nucleus is a highly organized yet dynamic organelle. Besides chromosomes, it contains a variety of membrane-less compartments, including nuclear bodies (i.e. nucleolus, P-bodies, etc) assembling through liquid-liquid Phase Separation (LLPS). LLPS is the process by which macromolecules separate, or demix, from the surrounding nucleoplasm to form distinct, coexisting liquid phases with different molecular compositions and material properties. Critically, condensation and higher-order folding of H3K27me3 chromatin domains in the nucleus need to be modulated between tissues in concordance with specific transcriptional programs. Recent models have suggested that phase separation may play a role in these processes. This PhD Training network will investigate the biological and physical mechanisms involved in the establishment and regulation of H3K27me3 domains and their relation with the process of phase separation. Students will get a highly interdisciplinary training in imaging-based genomics, epigenetics, advanced microscopies, and physical modeling. Their training will be enhanced by frequent rotations between labs, and participation in weekly, monthly, and annual network meetings to discuss results, exchange ideas, and improve presentation skills.

Keywords: 3D Genome Architecture, Single Cell Epigenetics, Imaging-based Genomics, Physical Modeling.

Multi-scale organization of H3K27me3 domains in single cells with spatial resolution

Dissection of single-cell heterogeneity in the condensation and higher-order organization of H3K27me3 domains and maintenance of spatial information are critical to understand and model the mechanisms of formation of H3K27me3 domains. Up until now, the lack of appropriate technologies impeded these measurements. We have recently developed a novel imaging technique called Hi-M, based on the sequential hybridization, imaging and bleaching of Oligopaint FISH and RNA probes. This new technology enables: (1) the simultaneous detection of tens (25-100) of DNA loci in each single cell; (2) the reconstruction of chromatin architecture in single cells in whole-mount embryos while maintaining spatial information; (3) single-cell multi-omics, as it simultaneously measures 3D chromatin architecture and transcriptional status. We will use Hi-M to understand and characterize tissue specific and single cell variability in the higher-order folding organization of H3K27me3 domains. For this, we will further develop different technological aspects of HiM. These experiments will directly feed modelling efforts from the Parmeggiani Lab, and predictions from their models will be tested using our experimental methods. Hi-M experiments in Polycomb group mutants will be performed to understand the mechanism of folding of H3K27me3 domains, while Hi-C experiments in the Cavalli Lab will be done to get genome-wide information.

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Functional dissection of mechanisms involved in the formation of H3K27me3 domains

Our goal is to show whether PcG proteins undergo liquid-liquid phase transitions and, if yes, identify the mechanism and consequences. To test this hypothesis, we will compare the nuclear distribution of different PcG proteins by observing immuno-labelling in confocal and super-resolution microscopy. We will perform co-localization experiments with the two histone marks H3K27me3 and H2A118Ub. The effect of PcG proteins on targeted genes will be monitored during embryogenesis by performing RNA FISH in both WT and mutant embryos. ChIP experiments will identify the genomic localization of PcG proteins during Drosophila embryogenesis and, we will analyze the effect of mutations on the genomic distribution of other PcG proteins and histone marks. We will use STED microscopy and Hi-M to analyze high-resolution chromosome folding to test the LLPS hypothesis. Wild type or mutated forms of PcG proteins will be overexpressed and their consequence on chromosome architecture and gene expression analyzed. These results will be used to feed modelling approaches from the Parmeggiani Lab. We will work with the Nollmann Lab to perform Hi-M analysis (see Project 1) in different genomic regions with genes either active or silenced by PcG proteins.

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Modelling the multi-scale organization of H3K27me3 domains

Our team is specialized in theoretical physics modeling of complex systems and non-linear phenomena, in particular those inspired by biological systems, such as DNA and chromatin structures, membranes and complex biological transport phenomena such as cytoskeletal based intracellular transport and ribosome collective dynamics on RNA. Numerical and analytical methods are developed using non-linear physics, statistical mechanics, polymer physics and advanced methods in mathematical physics, which can be used for analytical modeling of protein dynamics and in silico experiments. The multi-scale organization of H3K27me3 domains and its regulation is key to understand epigenetic mechanisms and provides an excellent model-system to advance our knowledge of phase separation phenomena combining modeling with experimental data from single-cell microscopy and high-throughput analysis such as ChIP, HiM and Hi-C experiments. Our aim in this project is to provide a general theoretical view of the multi-scale organization and maintenance of H3K27me3 domains in close collaboration with the Nollmann and Cavalli Labs. The PhD student will work in our Lab on analytical and numerical models issued from polymer physics and the statistical mechanics of lattice gases in polymeric networks.

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Application for a PhD position

Candidates must have achieved academic excellence and be highly motivated to pursue a PhD research project in the above-mentioned PhD networks. They should have obtained a Master-2 level diploma or equivalent by Summer 2020.

Successful candidates will be enrolled at Montpellier University’s Doctoral School of biological and chemical sciences related to health (CBS2). The University of Montpellier is a major interdisciplinary campus (49.000 students) in the South of France, with state-of-the-art facilities for biomedical research.

Applications in English can be uploaded until May 31st, 2020 and have to include:

  • Detailed Curriculum vitae
  • Letter of motivation
  • Copies of university diplomas (Bachelor/Licence, Master, others)
  • Transcripts/Grades of University results
  • List of attended University courses and their content (only those which are the most representative of the university career and supporting the application)
  • 2 Reference letters from former supervisors in French or in English (signed and on headed paper)

All documents need to be gathered in one PDF. Please name the PDF as follows: NAME_FirstName

Applications should be uploaded via the upload button below. Please first register and then upload your application file.

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