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Giacomo Cavalli - Publications
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Selected publications
  • Ciabrelli, F., Comoglio, F., Fellous, S., Bonev, B., Ninova, M., Szabo, Q., Xuereb, A., Klopp, C., Aravin, A., Paro, R., Bantignies, F., and Cavalli, G. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet, doi:10.1038/ng.3848.



- 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, 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).


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

Bonev, B. & Cavalli, G. Organization and function of the 3D genome. Nat Rev Genet 17, 661-678, doi:10.1038/nrg.2016.112 (2016).

- Leblanc, B., Comet, I., Bantignies, F. & Cavalli, G. Chromosome Conformation Capture on Chip (4C): Data Processing. Methods Mol Biol 1480, 243-261, doi:10.1007/978-1-4939-6380-5_21 (2016).

- Cheutin, T. & Cavalli, G. 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 (2016).

- Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins, (2016), Trends Cell Biol. : 26, 7, 511-525

- Sati, S. & Cavalli, G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma, doi:10.1007/s00412-016-0593-6 (2016)


- Herviou, L., Cavalli, G., Cartron, G., Klein, B., and Moreaux, J. EZH2 in normal hematopoiesis and hematological malignancies 2015 Oct 20. Oncotarget doi: 10.18632/oncotarget.6198. [Epub ahead of print] (2015)

- 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 of Ciona intestinalis embryogenesis. Biol. Open, Aug 14. pii: bio.010835. doi: 10.1242/bio.010835. [Epub ahead of print]. (2015) PDF

- 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). PDF

- 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). PDF

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

- Bousquet, J., Anto, J.M., Berkouk, K., Gergen, P., Pinto Antunes, J., Auge, P., Camuzat, T., Bringer, J., Mercier, J., Best, N., et al. (2015). Developmental determinants in non-communicable chronic diseases and ageing. Thorax, Jan 23. pii: thoraxjnl-2014-206304. doi: 10.1136/thoraxjnl-2014-206304. [Epub ahead of print]

- Ciabrelli F, Cavalli G (2015). Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol. 427, 608-625. pii: S0022-2836(14)00512-9. doi: 10.1016/j.jmb.2014.09.013.

- 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. PDF

- 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

- 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 PDF

- Cavalli, G. (2014). A RING to Rule Them All: RING1 as Silencer and Activator. Dev. Cell 28, 1-2.

- Cavalli, G. (2014). Chromosomes : now in 3D. Nat Rev Mol Cell Biol. 2014 Jan;15(1):6. doi: 10.1038/nrm3717. Epub 2013 Nov 27.

- Cheutin T, Cavalli G. Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr Opin Genet Dev. 2014 Jan 13;25C:30-37. doi: 10.1016/j.gde.2013.11.016. [Epub ahead of print].



- Iovino, N., Ciabrelli, F., and Cavalli, G. (2013). PRC2 controls Drosophila oocyte cell fate by repressing cell cycle genes. Dev. Cell 26, 431-439 PDF

- Sexton, T. and Cavalli, G. (2013). The 3D genome shapes up for pluripotency. Cell Stem Cell 13, 3-4

- 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)

B. Schuettengruber, G. Cavalli, Polycomb domain formation depends on short and long distance regulatory cues. PLoS ONE 8, e56531 (2013).  


- Cavalli, G. (2012). Molecular biology. EZH2 goes solo. Science 338, 1430-1431. pdf

- 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
- 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. pdf

- Delest, A., Sexton, T., and Cavalli, G. (2012). Polycomb: a paradigm for genome organization from one to three dimensions. Curr Opin Cell Biol, 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 pdf


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

- 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)

- 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

- Cavalli, G. (2011), From linear genes to epigenetic inheritance of three-dimensional epigenomes. J. Mol. Biol., Mar 15

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

- 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. pdf


- 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.


- Sexton, T., Bantignies, F., and Cavalli, G. (2009). Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation. Semin Cell Dev Biol.

Martinez, A.M. , Schuettengruber, B., Sakr, S., Janic, A., Gonzalez, C., and Cavalli, G. (2009) Polyhomeotic has a tumor suppressor activity mediated by repression of Notch signaling. Nat Genet, doi:10.1038/ng.414

- 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 Embryos. PloS Biol,
7(1): e1000013. doi:10.1371/journal.pbio.100pdf

- 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.


- Mateos-Langerak J, Cavalli G. (2008) Adv. Genet 61, 45-66.

- 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.


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., and Cremer, T. (2007). Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8, 104-115.

- Zuckerkandl, E., and Cavalli, G. (2007). Combinatorial epigenetics, "junk DNA", and the evolution of complex organisms. Gene 390, 232-242.


- 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.
Faculty of 1000

- Grimaud, C., Negre, N., and Cavalli, G. (2006). From genetics to epigenetics: the tale of Polycomb group and trithorax group genes. Chromosome Res 14, 363-375.
- Martinez, A. M., and Cavalli, G. (2006). The role of polycomb group proteins in cell cycle regulation during development. Cell Cycle 5, 1189-1197.pdf

- Bantignies, F., and Cavalli, G. (2006). Cellular memory and dynamic regulation of polycomb group proteins. Curr Opin Cell Biol.
18, 275-83. Epub 2006 May 2

- Cavalli, G. (2006). Chromatin and epigenetics in development: blending cellular memory with cell fate plasticity. Development 133, 2089-2094. pdf

Negre, N., Hennetin, J., Sun, L. V., Lavrov, S., Bellis, M., White, K. P., and Cavalli, G. (2006). Chromosomal Distribution of PcG Proteins during Drosophila Development. PLoS Biol 4, e170;
Faculty of 1000pdf

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. Faculty of 1000 evaluation

- 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. pdf


Akhtar A, Cavalli G (2005) The epigenome network of excellence. PLoS Biol 2(5): e177. 10.1371/journal.pbio.0030177.

- 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 DSP
1. Nature, 434, 533-538 ;doi:10.1038/nature03386. Pdf; Nature link
  Faculty of 1000 evaluation pdf

- 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.


- *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. Faculty of 1000 evaluation

- 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.

Déjardin, J., and Cavalli, G. (2004). Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. EMBO J 23, 857-868.pdf

- 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. Faculty of 1000 evaluation.pdf

- 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). Chromo domain proteins: linking chromatin structure to epigenetic regulation. Curr Opinion Cell Biol 10, 354-360.

- Cavalli, G., and Paro, R. (1998). The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93, 505-518.pdf

- Paro, R., Strutt, H.  and Cavalli, G. (1998). Heritable chromatin states induced by the Polycomb and trithorax group genes. In: Epigenetics. Novartis Found. Symp. 214, 51-66. John Wiley and Sons Ltd Press, Chichester, UK.


- Strutt, H., Cavalli, G. and Paro, R. (1997) Co-localisation of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J 16, 3621-3632.


- 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.

- Thoma, F., Cavalli, G., and Tanaka, S. (1993). Structural and functional organisation of yeast chromatin. The Eukaryotic Genome (eds Broda, Oliver & Sims) Cambridge Univ Press, pp. 43-72.


- 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 Advances in Cellular and Molecular Biology Eds Wegmann, R, J and Wegmann, M, A Peeters Press 6, 245-250.


- Cavalli, G., Casali, E., Spisni, A., and Masotti, L. (1991). Identification of the peroxidation product Hydroxystearic acid in Lewis lung carcinoma cells. Biochem Biophys Res Commun 178, 1260-1265.

Last update: 22/9/2017