Research teams
Genome dynamics department
Chromatin and cell biology
The Cavalli lab aims at understanding epigenetic inheritance, namely the information that is contained in our chromosomes and transmitted to daughter cells and to future generations beyond the sequence of DNA . We employ a wide range of molecular and in vivo approaches — single-cell omics, super-resolution microscopy, CRISPR editing, genomics, and physical modeling — to uncover how the 3D epigenome in general, and Polycomb proteins in particular, can establish and maintains transcriptional programs in development and disease.
3D organization and function of the genome:
Frédéric Bantignies, Thierry Cheutin and Marco Di Stefano
The information stored in our genome is intertwined with its function, such that, when cells are submitted to specific sets of conditions, they may pass on to their progeny their functional state. Since DNA has been identified as a critical carrier of genetic information and since the same DNA can correspond to alternative, heritable functional states in certain cases, this transmission of cellular memory has been dubbed epigenetic inheritance. In the most spectacular way, this extends to inheritance of a phenotypic trait into subsequent generation, a phenomenon for which Conrad H. Waddington provided evidence more than seventy years ago and which is well documented in plants. However, to which extent epigenetic inheritance operates in animals is hotly debated. Chromatin and its higher‑order organization are epigenetic components that play an essential role in genome regulation. Both the DNA molecule and the nucleosomal histones can be extensively modified in a way that impinges on gene expression and may be inherited as well as erased upon specific regulatory cues. Furthermore, chromatin fibers can be folded into yet higher‑order structures and chromosomes are confined in discrete “territories”.
We and others have discovered that metazoan chromosomes share a modular organization of their chromatin in structures called “Physical domains” or “Topologically Associating Domains” (TADs). TADs can be defined as linear units of chromatin that fold as discrete three‑dimensional (3D) structures tending to favor internal, rather than external, chromatin interactions. TADs are delimited by boundaries, which contain housekeeping genes and insulator sites. They are detected by methods such as Hi‑C, which allows genome‑wide identification of chromatin contacts, and they correspond to Chromosomal Domains (CDs), previously identified by microscopy. The investigation of chromatin landscapes in metazoa through genome‑wide association studies proved to be a fruitful approach. Theoretically, a huge number of chromatin types based on different combinations of chromatin‑associated marks would be possible but, in fact, every report basically recapitulated the presence of an active chromatin environment, that can be further subdivided because of specific differences between gene promoters, coding regions and distal regulatory elements (enhancers), and of three major types of repressive chromatin: a Polycomb‑repressed environment, a heterochromatic environment and a so-called null environment that is repressed without strong active silencing mechanisms. Strikingly, TADs were found to overlap with linear chromatin domains, indicating that epigenomic labeling of chromosome domains is intimately linked to their 3D folding.
We are trying to understand the principles governing 3D folding of the genome, from establishment of chromatin loops to the generation of chromosome domains, compartments, territories and the establishment of interchromosomal interactions. We use Drosophila , but also mouse and human cells, and state of the art molecular, genomic, computational and imaging approaches, in order to reach an integrated understanding of these different levels of genome organization.
Videos:
https://youtu.be/Pl44JjA–2k
Caption: A documentary-style video on genome organization by the Cavalli lab.
https://youtu.be/JYDrtCuRKVM
Caption: Results described in Bonev et al., Cell, 2017 (PMID: 29053968).
Role of Polycomb Group Proteins in genome regulation
Bernd Schuettengruber
Polycomb group (PcG) and trithorax group (trxG) proteins are key regulators of the expression of major developmental genes. PcG proteins are able to silence gene expression, while trxG proteins counteract gene silencing in the appropriate cells. The current model to explain PcG recruitment in Drosophila, proposes that a sequence-specific DNA binding proteins, the best studied of which is called PHO, bind at so-called Polycomb response elements (PREs). PHO might recruit the PcG complexes PRC1 and PRC2. PRC2 complexes contain the core subunit E(z), a histone methyltransferase that trimethylates histone H3 lysine 27 (H3K27me3), Su(z)12, Esc and Nurf55. H3K27me3 is, in turn, recognized by the chromo domain of the PC subunits of PRC1, which also contains Ph, PSC and Sce/dRing. On the other hand, PRC1 is actually a family with various canonical and variant complexes, that have in common a catalytic activity carried out by the dRing protein, that can ubiquitylate the K119 of histone H2A, a mark that is recognized by a specific subset of the PRC2 complexes. Mammalian PcG components are recruited to DNA unmethylated CpG islands and, once recruited, set up a similar maintenance system. Therefore, this pathway forms a self-sustaining silencing loop, such that once recruited, PcG complexes can propagate silencing through cell division. Genome-wide mapping studies have shown that PcG target genes encode for components controlling major signalling pathways and, importantly, PcG misexpression has also been associated with many cancer types, including breast and prostate cancer.
In addition to their role in cellular memory, PcG proteins participate in dynamic gene regulatory processes. In flies, different cell lines have a partially different set of PcG bound sites and H3K27me3-marked genomic regions change during development. In mammalian embryonic stem cells, many PcG target genes have been reported to bear both repression- and activation-associated marks. Upon differentiation, these “bivalent states” are resolved into fully active or fully repressed. In some instances, PcG components may even activate transcription, although it is unclear how widespread this phenomenon is. Importantly, PcG proteins regulate the organization of their target genes in the three-dimensional space of the nucleus, and this regulatory function is involved in the maintenance of cellular memory.
We would like to understand the molecular mechanisms of action of these factors, the role of regulation of higher order chromatin structure and nuclear organization in gene expression, and the molecular mechanisms at the base of this processes. In particular, our research aims at (1) understanding, on a genome-wide scale, how these proteins are targeted to DNA and what are the consequences of this targeting on chromatin structure; (2) understanding the effect of PcG proteins on cell proliferation, cell differentiation and cell polarity, and dissecting the key components regulated by PcG proteins to modulate these pathways in specific tissues and developmental processes; (3) identifying the rules governing the distribution of their target genes in the cell nucleus and the effect of this organization on gene expression.
The role of Polycomb proteins in development and tumorigenesis
Anne-Marie Martinez and Vincent Loubière
Coordination between cellular proliferation and differentiation ensures proper tissue morphogenesis and maintains homeostasis in multicellular organisms. Appropriate numbers of undifferentiated cells must be generated at specific developmental stages and these cells must exit the cell cycle in a tightly regulated manner to ensure proper cell fate specification and pattern formation.
The prevailing paradigm posits that Polycomb Group (PcG) proteins maintain stem cell identity by repressing differentiation genes. Mutation or misexpression of PcG genes has been associated with several types of human cancer. Polycomb group (PcG) proteins form two main epigenetic transcription repressor complexes, PRC2 and PRC1, highly conserved from fly to humans, which generally coregulate their target genes. They colocalize almost perfectly during embryogenesis, and their embryonic phenotypes are similar, with posterior homeotic transformations due to misexpression of homeotic Hox genes. Later in development, alterations in PcG components induce cancer (Figure 3), suggesting that PcG proteins may be dynamically recruited to new target genes. PcG proteins additionally bind and regulate genes implicated in major signaling pathways and therefore also participate in dynamic gene regulatory processes.
Using as a model the Drosophila larval imaginal eye disc, which shares critical features with mammalian epithelial tissues, we demonstrated that mutations affecting PRC1 subunits, but not PRC2, trigger neoplastic tumours in the larval imaginal discs. PRC1 components act as neoplastic tumor suppressors independently of PRC2 function.
by specifically targeting a thousand of new genes during larval stages of fly development. We named these non-canonical genes, “Neo-PRC1”; they massively outnumber canonical targets, are devoid of the H3K27me3 epigenetic mark and carry instead the active mark H3K27Ac. Remarkably, neo-PRC1 genes are mainly involved in the regulation of cell proliferation, differentiation, signaling and polarity. Alterations in PRC1 components specifically deregulate this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. Together, these results suggest that the mechanism of recruitment of PRC1 on its neo-sites is independent of PRC2 and depends on new molecular mechanisms that remain to be determined. The search for these mechanisms and of their molecular significance in flies and mammals is the basis of our current interest.
Tumor suppressor function for PcG genes. Left: the “+/+” panel shows control clones that do not carry mutations, which are positively labelled by green fluorescent protein. The ph0/ph0 panel shows clones corresponding to a knock out of the ph locus in order to eliminate the PH protein of PRC1. This induces massive overgrowth compared to the +/+ control disc containing neutral clones. The “Control” panel shows a, transplantation from wt GFP tissue into a wt host fly. The black stain in the abdomen shows the scar of the transplanted material. The “ph-/-“ panel shows an F1 generation host in which mutant tissue has been transplanted. The GFP labelled, ph mutant tumor grows in the body and kills the transplanted hosts.
WaddingtonMemory: Deciphering the role of regulatory factors driving epigenetic inheritance of alternative chromatin states
Epigenetics, the study of molecules and mechanisms that perpetuate alternative gene activity states in the context of the same DNA sequence, is an exciting field with important epistemological and biomedical implications, but the molecular mechanisms underlying epigenetic inheritance are still little understood. Polycomb group proteins are pleiotropic chromatin components that have been suggested to be capable of driving epigenetic inheritance and their dysregulation leads to cell fate changes and is associated with cancer. PcG misexpression has also been associated with many cancer types, including breast, prostate and hematological malignancies. The data suggest that the role of Polycomb components vary in different cancer types and there is a great interest in understanding the molecular mechanisms at play.
We and others have shown that mutations affecting PRC1 subunits trigger neoplastic tumours in Drosophila , suggesting that PRC1 components act as neoplastic tumor suppressors in flies. Strikingly, we discovered that a transient decrease in expression of a Polycomb gene can drive the formation of tumors of epigenetic nature, i.e. in the absence of DNA mutations. The goal of the WaddingtonMemory project is to decipher how epigenetic components can lead to stable changes in cell fate.
Aim 1: Identify the molecular steps leading to epigenetic cell fate derailment and to cancer development following transient Polycomb protein depletion in Drosophila. We will perform a time‑course study using bulk and single‑cell multiomic and imaging approaches in order to dissect the dynamics of cell fate transformation.
Aim 2: Identify the Polycomb‑targets leading to cell fate dysregulation and decipher their mechanistic role. We will test candidate factors identified in Aim 1 in order to identify those that drive cell fate derailment and to elucidate their mode of action.
Aim 3: Test the role of epigenetic inheritance in mouse models for cell differentiation, including gastruloids, an in vitro system that reflects cell differentiation events typically found in early embryogenesis.
Together, this groundbreaking project will reveal how epigenetic components drive cell fate derailment and it will establish robust paradigms that can be utilized by the scientific community to discriminate between epigenetic inheritance and DNA sequence‑mediated cell transformation.
The WaddingtonMemory project is an Advanced Investigator Grant funded by the European Research Council
Video: https://youtu.be/82G_T_3kHKk
- Paldi, F., Szalay, M.F., Dufau, S., Di Stefano, M., Reboul, H., Jost, D., Bantignies, F., and Cavalli, G. (2026). Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding. Nat Genet https://doi.org/10.1038/s41588-025-02489-4.
- Paldi, F. and Cavalli, 3D genome folding in epigenetic regulation and cellular memory. Trends Cell Biol, 2026 36:28-41. doi: 10.1016/j.tcb.2025.03.001
- Reboul, H., Normanno, D., Szabo, Q., Jerkovic, I., Cavalli, G., and Bantignies, F. (2025). Oligopaint FISH to Study Chromosomal Architecture and Structural Variations. Methods Mol Biol 2968, 465-484. DOI: 10.1007/978-1-0716-4750-9_28.
- Denaud, S., Sabaris, G., Di Stefano, M., Papadopoulos, G., Schuettengruber, B., and Cavalli, G. Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila. Genome Biol, 2025. 26(1): p. 116. DOI: 10.1186/s13059-025-03587-6.
- Sabaris, G., Schuettengruber, B., Papadopoulos, G. L., Coronado-Zamora, M., Fitz-James, M. H., Gonzalez, J., and Cavalli, G. A mechanistic basis for genetic assimilation in natural fly populations. Proc Natl Acad Sci U S A, 2025. 122(11): p. e2415982122.
- Martinez, A.M. and Cavalli, A possible role for epigenetics in cancer initiation. C R Biol, 2025. 348: p. 43-53.
- Fitz-James, M.H., Sabaris, G., Sarkies, P., Bantignies, F. & Cavalli, G (2024). Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila. Molecular Cell doi: 10.1016/j.molcel.2024.11.021.
- Szalay, M., Majchrzycka, B., Jerkovic, I., Cavalli, G.#, and Ibrahim, D.# (2024). Evolution and function of chromatin domains across the tree of life. Nature Structural & Molecular Biology 31, 1824–1837.
- Denaud, S., Bardou, M., Papadopoulos, G.L., Grob, S., Di Stefano, M., Sabaris, G., Nollmann, M., Schuettengruber, B#., and Cavalli, G#. (2024). A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer promoter communication. Nature Structural & Molecular Biology 31, 1942–1954. DOI: 10.1038/s41594-024-01375-7.
- Rawal, C.C., Loubiere, V., Butova, N.L., Garcia, J., Parreno, V., Merigliano, C., Martinez, A.M#., Cavalli, G#., and Chiolo, I#. (2024). Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. Histochemistry and Cell Biology1007/s00418-024-02302-z.
- Snir, O., Elgart, M., Gnainsky, Y., Goldsmith, M., Ciabrelli, F., Dagan, S., Aviezer, I., Stoops, E., Cavalli, G., and Soen, Y. (2024). Organ transformation by environmental disruption of protein integrity and epigenetic memory in Drosophila. PLoS Biol 22, e3002629. DOI: 1371/journal.pbio.3002629.
- Akilli, N., Cheutin, T., and Cavalli, G. (2024). Phase separation and inheritance of repressive chromatin domains. Curr Opin Genet Dev 86, 102201. DOI: 1016/j.gde.2024.102201.
- Gilbert, G., Renaud, Y., Teste, C., Anglaret, N., Bertrand, R., Hoehn, S., Jurkowski, T.P., Schuettengruber, B., Cavalli, G., Waltzer, L., and Vandel, L. (2024). Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. Sci Adv 10, eadn5861. 10.1126/sciadv.adn5861.
- Parreno, V*., Loubiere, V*., Schuettengruber, B., Fritsch, L., Rawal, C.C., Erokhin, M., Győrffy, B., Normanno, D., Di Stefano, M., Moreaux, J., Butova, N., Chiolo, I, Chetverina, D., Martinez, A-M#, and Cavalli, G.#. (2024). Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 629, 688-696. DOI: 10.1038/s41586-024-07328-w.
- Alaterre, E., Ovejero, S., Bret, C., Dutrieux, L., Sika, D., Fernandez Perez, R., Espeli, M., Fest, T., Cogne, M., Martin-Subero, J.I., Milpied, P., Cavalli, G., and Moreaux, J. (2024). Integrative single-cell chromatin and transcriptome analysis of human plasma cell differentiation. Blood. 144 (5): 496–509. DOI: 1182/blood.2023023237.
- Gurgo, J., Walter, J.C., Fiche, J.B., Houbron, C., Schaeffer, M., Cavalli, G., Bantignies, F., and Nollmann, M. (2024). Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes. Cell Rep 43, 114167. DOI: 1016/j.celrep.2024.114167.
- Sabaris, G., Ortiz, D.M., Laiker, I., Mayansky, I., Naik, S., Cavalli, G., Stern, D.L., Preger-Ben Noon, E., and Frankel, N. (2024). The Density of Regulatory Information Is a Major Determinant of Evolutionary Constraint on Noncoding DNA in Drosophila. Mol Biol Evol 41. DOI: 1093/molbev/msae004.
- Cavalli G, and Dekker J. (2023). Editorial overview: Multiscale regulation of genome folding in space, time, and across the tree of life. Curr Opin Genet Dev. 82:102095. doi: 10.1016/j.gde.2023.102095.
- Chemlal D, Varlet E, Machura A, Ovejero S, Requirand G, Robert N, Cartron G, Alaterre E, Bret C, Vincent L, Herbaux C, Cavalli G, Bruyer A, De Boussac H, Moreaux J. (2023). EZH2 targeting induces CD38 upregulation and response to anti-CD38 immunotherapies in multiple myeloma. Leukemia. 37(9):1925-1928. doi: 10.1038/s41375-023-01983-0.
- Sabaris, G., Fitz-James, M.H., and Cavalli, G. (2023). Epigenetic inheritance in adaptive evolution. Ann N Y Acad Sci. 10.1111/nyas.14992.
- Kahn, T.G., Savitsky, M., Kuong, C., Jacquier, C., Cavalli, G., Chang, J.M., and Schwartz, Y.B. (2023). Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements. Sci Adv 9, eade0090. 10.1126/sciadv.ade0090.
- Di Stefano, M., and Cavalli, G. (2022). Integrative studies of 3D genome organization and chromatin structure. Curr Opin Struct Biol 77, 102493. 10.1016/j.sbi.2022.102493.
- Ringel, A.R., Szabo, Q., Chiariello, A.M., Chudzik, K., Schöpflin, R., Rothe, P., Mattei, A.L., Zehnder, T., Harnett, D., Laupert, V., Bianco, S, Hetzel, S., Glaser, J., Phan, M., Schindler, M., Ibrahim, D., Paliou, C., Esposito, A., Prada-Medina, C. A., Haas, S. A., Giere, P., Vingron, M., Wittler, L., Meissner, A., Nicodemi, M., Cavalli, G., Bantignies, F., Mundlos, S., Robson, M. I. (2022). Promoter repression and 3D-restructuring resolves gene regulation conflicts in evolutionarily rearranged genomes. Cell 185(20):3689-3704.e21. doi: 10.1016/j.cell.2022.09.006.
- Bourbon, H.G., Benetah, M.H., Guillou, E., Mojica-Vazquez, L.H., Baanannou, A., Bernat-Fabre, S., Loubiere, V., Bantignies, F., Cavalli, G., and Boube, M. (2022). A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg. PLoS Genet 18, e1010083.
- Alaterre, E., Ovejero, S., Herviou, L., de Boussac, H., Papadopoulos, G., Kulis, M., Boireau, S., Robert, N., Requirand, G., Bruyer, A., Cartron, G., Vincent, L., Martinez, A.M., Martin-Subero, J.I., Cavalli, G., and Moreaux, J. (2022). Comprehensive characterization of the epigenetic landscape in Multiple Myeloma. Theranostics 12, 1715-1729. DOI: 10.7150/thno.54453.
- Barral, A., Pozo, G., Ducrot, L., Papadopoulos, G.L., Sauzet, S., Oldfield, A.J., Cavalli, G., and Dejardin, J. (2022). SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers. Mol Cell. 10.1016/j.molcel.2021.12.037
- Chang, J.M., Weng, Y.F., Chang, W.T., Lin, F.A., and Cavalli, G. (2022). HiCmapTools: a tool to access HiC contact maps. BMC Bioinformatics 23, 64. 10.1186/s12859-022-04589-y
- Fitz-James, M.H., and Cavalli, G. (2022). Molecular mechanisms of transgenerational epigenetic inheritance. Nat Rev Genet. 10.1038/s41576-021-00438-5
- Parreno, V., Martinez, A.M., and Cavalli, G. (2022). Mechanisms of Polycomb group protein function in cancer. Cell Res. 10.1038/s41422-021-00606-6
- Erokhin, M., Chetverina, O., Győrffy, B., Tatarskiy, V.V., Mogila, V., Shtil, A.A., Roninson, I.B., Moreaux, J., Georgiev, P., Cavalli, G., and Chetverina, D. (2021). Clinical Correlations of Polycomb Repressive Complex 2 in Different Tumor Types. Cancers (Basel) 13. 10.3390/cancers13133155
- Jerkovic, I., and Cavalli, G. (2021). Understanding 3D genome organization by multidisciplinary methods. Nat Rev Mol Cell Biol. doi: 10.1038/s41580-021-00362-w.
- Szabo, Q., Cavalli, G., Bantignies, F. (2021). Higher-Order Chromatin Organization Using 3D DNA Fluorescent In Situ Hybridization. Methods Mol. Biol.; 2157:221-237. doi: 10.1007/978-1-0716-0664-3_13.
- Varlet, E., Ovejero, S., Martinez, A.M., Cavalli, G., and Moreaux, J. (2020). Role of Polycomb Complexes in Normal and Malignant Plasma Cells. Int J Mol Sci 21.
- Rajewsky, N., Almouzni, G., Gorski, S.A., Aerts, S., Amit, I., Bertero, M.G., Bock, C., Bredenoord, A.L., Cavalli, G., et al. (2020). LifeTime and improving European healthcare through cell-based interceptive medicine. Nature, https://doi.org/10.1038/s41586-020-2715-9.
- Bantignies, F., and Cavalli, G. (2020). Le génome est encore plus organisé qu’on ne le pensait. Pour la Science, 19 Octobre, https://www.pourlascience.fr/sd/genetique/le-genome-est-encore-plus-organise-quon-ne-le-pensait-20266.php.
- Szabo, Q., Donjon, A., Jerkovic, I., Papadopoulos, G.L., Cheutin, T., Bonev, B., Nora, E., Bruneau, B.G., Bantignies, F., and Cavalli, G. (2020). Regulation of single-cell genome organization into TADs and chromatin nanodomains. Genet. 52, 1151–1157. https://doi.org/10.1038/s41588-020-00716-8.
- Sati, S., Bonev, , Szabo, Q., Jost, D., Bensadoun, P., Serra, F., Loubiere, V., Papadopoulos, G., Rivera-Mulia, J.C., Fritsch, L., … and Cavalli, G. (2020). 4D genome rewiring during oncogene induced and replicative senescence. Mol Cell 78(3):522-538.e9. doi: 10.1016/j.molcel.2020.03.007. Epub 2020 Mar 26.
- Lee, Y.C.G., Ogiyama, Y., Martins, N.M.C., Beliveau, B.J., Acevedo, D., Wu, C.T., Cavalli, G., and Karpen, G.H. (2020). Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin. PLoS Genet 16(3):e1008673. doi: 10.1371/journal.pgen.1008673. eCollection 2020 Mar.
- Loubière, V., Papadopoulos, G.L., Szabo, Q., Martinez, A-M., Cavalli, G (2020). Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping. Adv. 6, eaax4001, DOI: 10.1126/sciadv.aax4001.
- Pal, K., Forcato, M., Jost, D., Sexton, T., Vaillant, C., Salviato, E., Mazza, E.M.C., Lugli, E., Cavalli, G., and Ferrari, F. (2019). Global chromatin conformation differences in the Drosophila dosage compensated chromosome X. commun. 10, 5355.
- Cheutin, T., and Cavalli, G. (2019). The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol, 54(5):399-417. doi: 10.1080/10409238.2019.1679082. Epub 2019 Nov 7.
- Jerkovic, I., Szabo, Q., Bantignies, F., and Cavalli, G. (2019). Higher-order chromosomal structures mediate genome function. J Mol Biol. 432(3):676-681. doi: 10.1016/j.jmb.2019.10.014. Epub 2019 Nov 2.
- 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
- Cardozo Gizzi, A., Cattoni, D., Fiche, J-B., Espinola, S., M., Gurgo, J., Messina, O., Houbron, C., Ogiyama, Y., Papadopoulos, G., Cavalli, G., Lagha, M., and Nollmann, M. (2019), Microscopy based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. Cell, 74(1):212-222.e5. doi: 10.1016/j.molcel.2019.01.011. Epub 2019 Feb 19
- Szabo, Q., Bantignies, F., and Cavalli, G. (2019). Principles of genome folding into Topologically Associating Domains. Adv., 2019; 5 : eaaw1668, DOI: 10.1126/sciadv.aaw1668
- Loubiere, V., Martinez, A-M, and Cavalli, G. (2019). Cell fate and developmental regulation dynamics by Polycomb proteins and 3D genome architecture. BioEssays, 41(3):e1800222. doi: 10.1002/bies.201800222. Epub 2019 Feb 22
- Herviou, L., Jourdan, M., Martinez, A-M., Cavalli, G., and Moreaux, J. (2019), EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation. Leukemia, Feb 12. doi: 10.1038/s41375-019-0392-1.
- Herviou, L., Kassambara, A., Boireau, S., Robert, N., Requirand, G., Muller-Tidow, C., Vincent, L., Seckinger, A., Goldschmidt, H., Cartron, G., Hose, D., Cavalli, G., and Moreaux, J. (2018). PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs. Clinical Epigenetics 10, 121. DOI: 10.1186/s13148-018-0554-4.
- Marti-Renom, M.A., Almouzni, G., Bickmore, W.A., Bystricky, K., Cavalli, G., Fraser, P., Gasser, S.M., Giorgetti, L., Heard, E., Nicodemi, M., et al. (2018). Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 50, 1352-1358.
- Cheutin, T., and Cavalli, G. (2018). Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis. Nat Commun 9, 3898.
- Herviou, L., Cavalli, G., and Moreaux, J. (2018). [EZH2 is therapeutic target for personalized treatment in multiple myeloma]. Bulletin du cancer.
- Ogiyama, Y., Schuettengruber, B., Papadopoulos, G.L., Chang, J., and Cavalli, G. (2018). Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development. Mol Cell 71, 73-88
- Szabo, Q., Jost, D., Chang, J.M., Cattoni, D.I., Papadopoulos, G.L., Bonev, B., Sexton, T., Gurgo, J., Jacquier, C., Nollmann, M., and Cavalli (2018). TADs are 3D structural units of higher-order chromosome organization in Drosophila. Sci. Adv., 4, eaar8082.
- Grob, S., and Cavalli, G. (2018). Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture. Methods Mol Biol 1675, 233-246.
- Cattoni, D.I., Gizzi, A.M.C., Georgieva, M., Di Stefano, M., Valeri, A., Chamousset, D., Houbron, C., Dejardin, S., Fiche, J.B., Gonzalez, I., Chang, J. M., Sexton, T., Marti-Renom, M. A., Bantignies, F., Cavalli, G., and Nollmann, M. (2017). Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. Nat Commun, 8, 1753.
- 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. DOI: https://doi.org/10.1016/j.cell.2017.08.002
- 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. DOI: https://doi.org/10.1016/j.cell.2017.09.043
- Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E., and Becker, P.B. (2017). Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO Rep. 2017 Aug 9. pii: e201744292. doi: 10.15252/embr.201744292. [Epub ahead of print]
- 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. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila (2017). Nature Genet, 49, 876-886, doi:10.1038/ng.3848.
- Schwartz, Y. B. & Cavalli, G. Three-Dimensional Genome Organization and Function in Drosophila. Genetics 205, 5-24, doi:10.1534/genetics.115.185132 (2017).
- Sati, S. & Cavalli, G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma, 126, 33-44 doi:10.1007/s00412-016-0593-6 (2017).
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- Cheutin, T. & Cavalli, G. (2016). Following the Motion of Polycomb Bodies in Living Drosophila Embryos. Methods Mol Biol 1480, 283-288, doi:10.1007/978-1-4939-6380-5_24.
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- Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins, (2016), Trends Cell Biol. : 26, 7, 511-525
- Herviou, L., Cavalli, G., Cartron, G., Klein, B., and Moreaux, J. EZH2 in normal hematopoiesis and hematological malignancies (2016). Oncotarget : 7, 2284-96. doi:10.18632/oncotarget.6198.
- Cavalli, G. PRC1 proteins orchestrate three-dimensional genome architecture. Nature Genetics, 47(10):1105-6. (2015)
- Le Goff E, Martinand-Mari C, Martin M, Feuillard J, Boublik Y, Godefroy N, Mangeat P, Baghdiguian S, Cavalli G; Enhancer of zeste acts as a major developmental regulator ofCiona intestinalis embryogenesis. Open, Aug 14. pii: bio.010835. doi: 10.1242/bio.010835. [Epub ahead of print]. (2015)
- Yung, P. Y., Stuetzer, A., Fischle, W., Martinez, A. M. & Cavalli, G. Histone H3 Serine 28 Is Essential for Efficient Polycomb-Mediated Gene Repression in Drosophila. Cell reports, Jun 9;11(9):1437-45. doi:10.1016/j.celrep.2015.04.055 (2015).
- Ea, V, Sexton, T., Gostan, T. Herviou, L. Baudement, M. O. Zhang, Y. Berlivet, S. Le Lay-Taha, M. N. Cathala, G. Lesne, A. Victor, J. M. Fan, Y. Cavalli, G., and Forne, T. Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains. BMC genomics 16, 607, doi:10.1186/s12864-015-1786-8 (2015).
- Sexton, T., and Cavalli, G. (2015). The role of chromosome domains in shaping the functional genome. Cell, 160, 1049-1059
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- Gavrilov A, Razin SV, Cavalli G (2015). In vivo formaldehyde cross-linking: it is time for black box analysis. Brief Funct Genomics. Sep 19; 14, 163-165. pii: elu037.
- Schuettengruber, B., Oded Elkayam, N., Sexton, T., Entrevan, M., Stern, S., Thomas, A., Yaffe, E., Parrinello, H., Tanay, A., and Cavalli, G. (2014). Cooperativity, specificity and evolutionary stability of Polycomb targeting in Drosophila. Cell Reports, Oct 9;9(1):219-33. doi: 10.1016/j.celrep.2014.08.072. Epub 2014 Oct 2.
- Bantignies F, Cavalli G (2014). Topological organization of Drosophila Hox genes using DNA fluorescent in situ hybridization. Methods Mol Biol. 2014;1196:103-20. doi: 10.1007/978-1-4939-1242-1_7.
- Jost, D., Carrivain, P., Cavalli, G.* and Vaillant, D* (2014). Modeling epigenome folding: formation and dynamics of topologically-associated chromatin domains. Nucleic Acids Research, Aug 4. pii: gku698. [Epub ahead of print]
- Gonzalez, I., Mateos-Langerak, J., Thomas, A., Cheutin, T., and Cavalli, G. (2014). Identification of new regulators of three dimensional Polycomb organization by a microscopy-based genome-wide RNAi screen. Mol Cell 54, 485-99, pii: S1097-2765(14)00209-3. doi: 10.1016/j.molcel.2014.03.004. [Epub ahead of print].
- Cavalli G (2014) Chromosomes: now in 3D! Nat Rev Mol Cell Biol 15 (1):6. doi:10.1038/nrm3717
- Cheutin T, Cavalli G (2014) Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr Opin Genet Dev 25C:30-37. doi:10.1016/j.gde.2013.11.016
- Cavalli, G. (2014). A RING to Rule Them All: RING1 as Silencer and Activator. Cell 28, 1-2.
- Iovino, N., Ciabrelli, F., and Cavalli, G. (2013). PRC2 controls Drosophila oocyte cell fate by repressing cell cycle genes. Cell 26, 431-439.
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- Tanay, A., and Cavalli, G. (2013). Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization. Curr Opin Genet Dev, 23(2):197-203, doi: 10.1016/j.gde.2012.12.009. Epub 2013 Feb 14.
- Cavalli, G., and Misteli, T. Functional implications of genome topology. Nat Struct Mol Biol 20, 290 (Mar 5, 2013).
- Schuettengruber, G. Cavalli, Polycomb domain formation depends on short and long distance regulatory cues. PLoS ONE 8, e56531 (2013).
- Popkova, A., Bernardoni, R., Diebold, C., Van de Bor, V., Schuettengruber, B., Gonzalez, I., Busturia, A., Cavalli, G., and Giangrande, A. (2012). Polycomb controls gliogenesis by regulating the transient expression of the gcm/glide fate determinant. PLoS Genet 8, e1003159.
- Cavalli, (2012). Molecular biology. EZH2 goes solo. Science 338, 1430-1431.
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- Delest, A., Sexton, T., and Cavalli, G. (2012). Polycomb: a paradigm for genome organization from one to three dimensions. Curr Opin Cell Biol. 24(3):405-14. Epub 2012 Feb 13
- Cheutin, T., and Cavalli, G. (2012). Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion. PLoS Genet 8, e1002465.
- Schuettengruber, B, Martinez, AM, Iovino, N., Cavalli, G. Trithorax group proteins : switching genes on and keeping them active. Nature Reviews Mol Cell Biol. (2011) 12, 799-814.
- Tajbakhsh S, Cavalli G, Richet E. Integrated Gene Regulatory Circuits: Celebrating the 50(th) Anniversary of the Operon Model. Mol Cell. 2011 Aug 19;43(4):505-14.
- Bantignies, F., and Cavalli, G. Polycomb group proteins: repression in 3D. Trends Genet, doi:10.1016/j.tig.2011.06.008 (2011).
- Iovino, N. & Cavalli, G. Rolling ES Cells Down the Waddington Landscape with Oct4 and Sox2. Cell 145, 815-817, doi:10.1016/j.cell.2011.05.027 (2011).
- Cavalli, G. From linear genes to epigenetic inheritance of three-dimensional epigenomes. Mol. Biol. 409, 54-61, doi:10.1016/j.jmb.2011.03.001 (2011).
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- Comet, I., Schuettengruber, B., Sexton, T., and Cavalli, G. (2011) A chromatin insulator driving three-dimensional PRE contacts and Polycomb association with the chromatin fiber. Proc Natl Acad Sci USA, 108(6):2294-9. Epub 2011 Jan 24.
- Hetzer, M., and Cavalli, G. (2011). Eukaryotic cells. Curr Opin Cell Biol Jun;23(3):255-7. Epub 2011 May 16.
- Cheutin, T., Bantignies, F., Leblanc, B., and Cavalli, G. (2010). Chromatin foldings: from linear chromosomes to the 4D nucleus. Cold Spring Harb Symp Quant Biol. 2010;75:461-73. Epub 2011 Mar 29.
- Schuettengruber B, Cavalli, G. (2010). The DUBle life of Polycomb complexes. Dev Cell 18:878-880
- Martinez, A.M., and Cavalli, G. (2010). Uncovering a tumor-suppressor function for Drosophila polycomb group genes. Cell Cycle 9, 215-216.
- Schuettengruber B, Cavalli, G. (2009). Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development. 136:3531-42.
- Martinez, A., 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.
- Sexton, T., Bantignies, F., and Cavalli, G. (2009). Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation. Semin Cell Dev Biol. 20:849-55
- Schuettengruber, B., Ganapathi, M., Leblanc, B., Portoso, M., Jaschek, R., Tolhuis, B., van Lohuizen, M., Tanay, A., and Cavalli, G. (2009). Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila PloS Biol, 7(1): e1000013. doi:10.1371/journal.pbio.1000013
- Reuter G, Cavalli G (2009) Epigenetics and the control of multicellularity. Workshop on chromatin at the nexus of cell division and differentiation. EMBO Rep 10(1): 25-29
- Portoso, M, and Cavalli, G. (2008). The Role of RNAi and Noncoding RNAs in Polycomb Mediated Control of Gene Expression and Genomic Programming. Chapter 3 in: RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Ed. Kevin V. Morris The Scripps Research Institute, La Jolla, USA. Caister Academic Press, UK
- Mateos-Langerak, J., and Cavalli, G. (2008). Polycomb group proteins and long-range gene regulation. Adv Genet 61, 45-66
- Cavalli, G. (2007) Chromosome kissing. Curr Opin Genet Dev, 17:443-450
- Schuettengruber, B., Chourrout, D, Vervoort, M., Leblanc, B., and Cavalli, G. (2007). Genome Regulation by Polycomb and Trithorax Proteins. Cell, 128, 735-745
- Lanctot C, Cheutin T, Cremer M, Cavalli G, Cremer T. (2007). Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions Nat Rev Genet. 8, 104-15
- Zuckerkandl E, Cavalli G. (2007). Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms. Gene. 390, 232-242. Epub 2006 Dec 9
- Negre, N., Lavrov, S., Hennetin, J., Bellis, M., and Cavalli, G. (2006). Mapping the Distribution of Chromatin Proteins by ChIP on Chip. Methods Enzymol 410, 316-341
- Comet, I., Savitskaya, E., Schuettengruber, B., Negre, N., Lavrov, S., Parshikov, A., Juge, F., Gracheva, E., Georgiev, P., and Cavalli, G. (2006). PRE-Mediated Bypass of Two Su(Hw) Insulators Targets PcG Proteins to a Downstream Promoter. Dev Cell 11, 117-124
- Bantignies, F., and Cavalli, G. (2006). Cellular memory and dynamic regulation of polycomb group proteins. Curr Opin Cell Biol 18, 275-283
- Cavalli, G (2006). Chromatin and epigenetics in development: blending cellular memory with Cell Fate plasticity. Development, 133, 2089-94
- Martinez, AM, Cavalli, G (2006) The role of Polycomb Group Proteins in Cell Cycle Regulation During Development Cell Cycle 5, 1189-97. Epub 2006 Jun 1
- Grimaud, C., Nègre, N., and Cavalli, G. (2006) From genetics to epigenetics: the tale of Polycomb group and trithorax group genes Chromosome Res. 14, 363-75
- Nègre N and Cavalli, G. (2006). Polycomb controls the cell fate. Med Sci 22, 1033-1035
- Nègre N, Hennetin J, Sun LV, Lavrov S, Bellis M, White, KP, and Cavalli, G. (2006) Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol 4(6): e170.DOI:10.1371/journal.pbio.0040170.
- Ritter, S., Odenheimer, J., Heermann, DW, Bantignies, F., Grimaud, C., and Cavalli, G. (2006) J. Mod. Phys. C 17, 749-756. doi:10.1142/S0129183106009400
- 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
- Martinez AM, Colomb S, Dejardin J, Bantignies F, Cavalli G (2006) Polycomb group-dependent Cyclin A repression in Drosophila. Genes Dev 20(4): 501-513
- Akhtar A, Cavalli G (2005). The epigenome network of excellence. PLoS Biol 3(5): e177. DOI: 10.1371/journal.pbio.0030177
- Déjardin, J., and Cavalli, G. (2005). Epigenetic inheritance of chromatin states mediated by Polycomb- and trithorax group proteins in Drosophila. Prog Mol Subcell Biol 38, 31-64.
- Dejardin and Cavalli, G. (2005).Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Med Sci 21, 689−691
- 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.
- *Melnikova, L., *Juge, F., Gruzdeva, N., Mazur, A., **Cavalli, G., and **Georgiev, P. (2004). Interaction between GAF and Mod(mdg4) proteins promotes insulator bypass in Drosophila. Proc Natl Acad Sci USA, 101, 14806-14811. Epub 2004 Oct 01. * Co-first authors. ** Corresponding authors.
- Aravin, A. A., Klenov, M. S., Vagin, V. V., Bantignies, F., Cavalli, G., and Gvozdev, V. A. (2004). Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol Cell Biol 24, 6742-6750
- Chanas, G., Lavrov, S., Iral, F., Cavalli, G., and Maschat, F. (2004). Engrailed and polyhomeotic maintain posterior cell identity through cubitus-interruptus regulation. Dev Biol 272, 522-535.
- Nègre, N., Bantignies, F., and Cavalli, G. (2004). Polycomb, trithorax et la mémoire cellulaire. Biofutur 244, 27-31
- Dejardin J,Cavalli G, (2004). Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. EMBO J 23: 857-868
- Lavrov, S., Déjardin, J. and Cavalli, G. (2004) Combined immunostaining and FISH analysis of polytene chromosomes. Methods Mol Biol, 247, 289-303
- Bantignies, F., Grimaud, C., Lavrov, S., Gabut, M., and Cavalli, G. (2003). Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev, 17, 2406-2420.
- Bloyer, S., Cavalli, G., Brock, H. W., and Dura, J. M. (2003). The polyhomeotic PREs and TREs may constitute a new type of DNA element conferring short range quantitative PcG- and trxG-mediated regulation. Dev Biol 261, 426-442
- Sun, L. V., Chen, L., Greil, F., Nègre, N., Li, T. R., Cavalli, G., Zhao, H., Van Steensel, B., and White, K. (2003). Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci USA 100, 9428-9433
- Zraly, C. B., Marenda, D. R., Nanchal, R., Cavalli, G., Muchardt, C., and Dingwall, A. K. (2003). SNR1 is an essential subunit in a subset of Drosophila brm complexes, targeting specific functions during development. Dev Biol 253, 291-308
- Cavalli, G. (2002). Chromatin as a eukaryotic template of genetic information., Curr Opin Cell Biol 14, 269-278
- Grieneberger, A., Sagnier, T., Cavalli, G., Schramke, V., Geli, V., Mariol, M., Berenger, H., Graba, Y., and Pradel, J. (2002). The Drosophila histone acetyltransferase Chameau functions in epigenetic mechanisms of transcriptional repression. Curr Biol 12, 762-766
- Cavalli, G., and Paro, R. (1999). Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 286, 955-958.
- Cavalli, G., Orlando, V., and Paro, R. (1999). Mapping DNA target sites of chromatin-associated proteins by formaldehyde cross-linking in Drosophila embryos. In: Chromosome Structural Analysis: A Practical Approach, pp20-37. Ed. W. A. Bickmore. Oxford University Press. UK
- Cavalli, G., and Paro, R. (1998). The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93, 505-518.
- Cavalli, G. and Paro, R. (1998). Chromo domain proteins: linking chromatin structure to epigenetic regulation. Curr Opin Cell Biol 10, 354-360
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- Cavalli, G., Bachmann, D. and Thoma, F. (1996). Inactivation of topoisomerases affects transcription dependent chromatin transitions in rDNA but not in a gene transcribed by RNA-polymerase II. EMBO J 15, 590-597
- Cavalli, G., and Thoma, F. (1993). Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J 12, 4603-4613
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- Casali, E., Cavalli, G., Spisni, A. and Masotti, L. (1992). Effect of Hydroxystearic acid on proliferation of C108 cells from Lewis lung carcinoma. In: Recent Adv Cell and Mol Biol 6, 245-250. Eds. Wegmann, R., J. and Wegmann, M., A. Peeters Press
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