LabMUSE EpiGenMed

Chromatin and DNA replication

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., andRadman-Livaja, M. (2019). The budding yeast heterochromatic SIR complex resets upon exit from stationary phase. bioRxiv, 603613.

Ziane, R., Camasses, A., andRadman-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., andRadman-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 atiScience).

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 EnzymeScience340:195-199, 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 Biology9: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.

mRNA Regulation and Development

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 theDrosophilamodel, an oustanding model forin vivostudies. 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.Nature2010) 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-oncogeneCbl.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 theDrosophilagermline.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 earlyDrosophilaembryo.Nature, 467, 1128-1132

Maintenance of Genome Integrity during DNA Replication

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 2×10¹⁶meters 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* andPasero 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 andPasero P(2018) Mrc1 and Rad9 cooperate to regulate initiation and elongation of DNA replication in response to DNA damage.EMBO J, 37, e99319News & 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* andPasero 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, 2405-2415Recommended 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* andPasero P*(2012). dNTP pools determine fork progression and origin usage under replication stress.EMBO J31, 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 RFC^Ctf18as a key mediator of the replication stress response.Nat Struct Mol Biol17, 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* andPasero P* (2009) Topoisomerase 1 suppresses replication stress and genomic instability by preventing interference between replication and transcription.Nat Cell Biol11, 1315-1324 (* equal contribution)

Epigenetic Chromatin Regulation

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 protozoanTetrahymenaidentifies 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.PNAS116, 14639-14644.

Noto T,Mochizuki K*(2018) Small RNA-mediated trans-nuclear and trans-element communications inTetrahymenaDNA 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 Cell35, 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 inTetrahymenaDNA elimination.Mol Cell59, 229-242.

Woehrer SL, Aronica L, Suhren JH, Busch CJ, Noto T,Mochizuki K*(2015) ATetrahymenaHsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms.EMBO Journal34, 559-577.

Genome Surveillance and Stability

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 earlyXenopusembryos, 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 differentiationin 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 CRL4^Cdt2, 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.

Gene Regulation

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 Kiernanand 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, andR 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 andR Kiernan. 2018. Nuclear RNA surveillance complexes silence HIV-1 transcription. PLoS Pathog. 2018 14(3):e1006950.

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

X Contreras, M Benkirane andR 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 andR Kiernan. 2012. Microprocessor, Setx, Xrn2 and Rrp6 Co-Operate to Induce Premature Termination of Transcription by RNAPII. Cell 150:1147-57.

Nuclear control of cell proliferation

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. andFisher, D.Ki-67 enables tumorigenesis by promoting transcriptome plasticity. Submitted. Posted on bioRxiv 24 July 2019doi:10.1101/712380

Bačević, K.*, Noble, R.*, Soffar, A., Ammar, O.W., Boszonyik, B., Prieto, S., Vincent, C., Hochberg, M.E.^†, Krasinska, L.^†andFisher, D.^†. (2017) Spatial competition constrains resistance to targeted cancer therapyNat Commun8(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., andFisher, 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. andFisher, D.(2017) Cell cycle regulation accounts for variability in Ki-67 expression levels.Cancer Res77, 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. andFisher, D.(2016). The cell proliferation antigen Ki-67 organises heterochromatin.eLife, 5, e13722. doi:10.7554/eLife.13722.

Chromatin and Splicing

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. andLuco 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 Advances2019,5(5), eaav3673 DOI: 10.1126/sciadv.aav3673

Luco RF*
Retrotransposons jump into alternative splicing regulation via a long non-coding RNA.
NatureStructural Molecular Biology2016, 23: 952–954.

Gonzalez I, Munita R, Agirre E, Dittmer TA, Gysling K, Misteli T andLuco RF*
A long non-coding RNA regulates alternative splicing via establishment of a splicing-specific chromatin signature.
Nature Structural Molecular Biology2015, 22(5):370-6.

Luco RF*
The Non-Coding Genome: a universe in expansion for fine-tuning the coding world
Genome Biology2013, 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 Development2011, 21:1-7.

Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T.
Epigenetics in alternative pre-mRNA splicing.
Cell2011, 144 (1): 16-26.

Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith O, Misteli T.
Regulation of alternative splicing by histone modifications.
Science2010, 327(5968):996-1000

Genomic Imprinting and Development

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 mouseDlk1-Dio3andIgf2-H19domains.
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

Meiosis and recombination

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 Cell74, 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 Cell69, 853-865 e856.

Grey C*, Clement JA*, Buard J, Leblanc B, Gut I, Gut M, Duret L andde 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* andde Massy B.* (2016) The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation.Science351, 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 Genet46, 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 Rep5, 13-20.

Baudat F, Imai Y andde Massy B.(2013) Meiotic recombination in mammals: localization and regulation.Nat Rev Genet14, 794-806.

Grey C, Barthes P, Chauveau-Le Friec G, Langa F, Baudat F andde Massy B. (2011) Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination.PLoS Biol9, e1001176.

Kumar R, Bourbon HM andde Massy B. (2010) Functional conservation of Mei4 for meiotic DNA double-strand break formation from yeasts to mice.Genes Dev24, 1266-80.

Baudat F*, Buard J*, Grey C*, Fledel-Alon A, Ober C, Przeworski M, Coop G andde Massy B.(2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice.Science327, 836-40.

Cancer bioinformatics and systems biology

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 andin 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.

Chromatin and Cell Biology

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 inDrosophila. 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 inDrosophila. 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.

Transcription and epigenomics in developing T cells

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 therole 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. 2019May 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. 2018Jan 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. 2017Sep 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 2016May 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. 2016Jan 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 2015Apr 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 2015Jan 23;6:6094.

Molecular Virology

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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RNA Biogenesis and trafficking

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=3300043Chouaib, 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. andBertrand, 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.TIBS2018, 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

Biology of Repetitive Sequences

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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Transcription and Development

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 earlyDrosophilaembryo, 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 andLagha M. MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos” (2019)BioinformaticsOct 3. pii: btz717.
doi: 10.1093/bioinformatics/btz717.

Fernandez C andLagha MLightening up gene activation in living Drosophila embryos (2019) Methods 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 Dec5;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 andLagha M(2018) Remembering the past: Mitotic bookmarking in a developping embryo.Current Opinions in Systems Biology2018 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 CellAug 2;71(3):468-480

Ferraro T, Esposito E, Mancini L, Ng S, Lucas T, Coppey M, Dostatni N, Walczak A, Levine M andLagha M(2016) Transcriptional memory in the Drosophila embryo.Current Biology2016 Jan 25;26(2):212-218. doi: 10.1016/j.cub.2015.11.058

Comment in:

Chubb JR. Gene Regulation: Stable Noise.Current Biology2016;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 Genetics14: 443
Saunders and Ashe (2013) Taking a pause to reflect on morphogenesis,Cell153(5) 941-943.
Recommended byFaculty of 1000.

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

Molecular oncogenesis

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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Replication and Genome Dynamics

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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Mechanisms of DNA Segregation and Remodeling

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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Genetic and phenotypic plasticity of cancer

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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Chromatin Dynamics in Hematopoiesis

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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