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Accueil > Départements > Biologie des Génomes > Matthieu GERARD : Epigénomique des Mammifères

Publications de l’équipe


  • S. Barral, Y. Morozumi, H. Tanaka, E. Montellier, J. Govin, M. de Dieuleveult, G. Charbonnier, Y. Couté, D. Puthier, T. Buchou, F. Boussouar, T. Urahama, F. Fenaille, S. Curtet, P. Héry, N. Fernandez-Nunez, H. Shiota, M. Gérard, S. Rousseaux, H. Kurumizaka, et S. Khochbin, « Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells », Molecular Cell, vol. 66, nᵒ 1, p. 89-101.e8, 2017.

  • S. Berlivet, I. Hmitou, H. Picaud, et M. Gérard, « Efficient Depletion of Essential Gene Products for Loss-of-Function Studies in Embryonic Stem Cells », Methods in Molecular Biology (Clifton, N.J.), vol. 1622, p. 91-100, 2017.
    Résumé : The development of the CRISPR/Cas9 technology has provided powerful methods to target genetic alterations. However, investigating the function of genes essential for cell survival remains problematic, because genetic ablation of these genes results in cell death. As a consequence, cells recombined at the targeted gene and fully depleted of the gene product cannot be obtained. RNA interference is well suited for the study of essential genes, but this approach often results in a partial depletion of the targeted gene product, which can lead to misinterpretations. We previously developed the pHYPER shRNA vector, a high efficiency RNA interference vector, which is based on a 2.5-kb mouse genomic fragment encompassing the H1 gene. We provide here a pHYPER-based protocol optimized to study the function of essential gene products in mouse embryonic stem cells.
    Mots-clés : DBG, Electroporation, Embryonic stem cell, Essential genes, pHYPER, Puromycin selection, REMOD, RNA Interference, shRNA.


  • M. de Dieuleveult, K. Yen, I. Hmitou, A. Depaux, F. Boussouar, D. Bou Dargham, S. Jounier, H. Humbertclaude, F. Ribierre, C. Baulard, N. P. Farrell, B. Park, C. Keime, L. Carrière, S. Berlivet, M. Gut, I. Gut, M. Werner, J. - F. Deleuze, R. Olaso, J. - C. Aude, S. Chantalat, B. F. Pugh, et M. Gérard, « Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells », Nature, vol. 530, nᵒ 7588, p. 113-116, 2016.
    Résumé : ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription. Surprisingly, large CpG-rich NFRs that extend downstream of annotated transcriptional start sites are nevertheless bound by non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and marked by H3K4me3 and H3K27ac modifications. RNA polymerase II therefore navigates hundreds of base pairs of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3' end of the NFR. Transcriptome analysis after remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers have either positive or negative roles via altering nucleosome stability, at polycomb-enriched bivalent genes the same remodellers act in an opposite manner. These findings indicate that remodellers target specific nucleosomes at the edge of NFRs, where they regulate ES cell transcriptional programs.
    Mots-clés : Animals, Chromatin Assembly and Disassembly, DBG, DNA Helicases, DNA-Binding Proteins, Gene Expression Regulation, Genome, GTR, Histones, Mice, Micrococcal Nuclease, Mouse Embryonic Stem Cells, Nuclear Proteins, Nucleosomes, Promoter Regions, Genetic, REMOD, RNA Polymerase II, Substrate Specificity, Trans-Activators, Transcription Factors, Transcription Initiation Site.

  • Y. Morozumi, F. Boussouar, M. Tan, A. Chaikuad, M. Jamshidikia, G. Colak, H. He, L. Nie, C. Petosa, M. de Dieuleveult, S. Curtet, A. - L. Vitte, C. Rabatel, A. Debernardi, F. - L. Cosset, E. Verhoeyen, A. Emadali, N. Schweifer, D. Gianni, M. Gut, P. Guardiola, S. Rousseaux, M. Gérard, S. Knapp, Y. Zhao, et S. Khochbin, « Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells », Journal of Molecular Cell Biology, vol. 8, nᵒ 4, p. 349-362, 2016.
    Résumé : Although the conserved AAA ATPase and bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics, and RNA-seq experiments in embryonic stem cells where Atad2 is normally highly expressed, we found that Atad2 is an abundant nucleosome-bound protein present on active genes, associated with chromatin remodelling, DNA replication, and DNA repair factors. A structural analysis of its bromodomain and subsequent investigations demonstrate that histone acetylation guides ATAD2 to chromatin, resulting in an overall increase of chromatin accessibility and histone dynamics, which is required for the proper activity of the highly expressed gene fraction of the genome. While in exponentially growing cells Atad2 appears dispensable for cell growth, in differentiating ES cells Atad2 becomes critical in sustaining specific gene expression programmes, controlling proliferation and differentiation. Altogether, this work defines Atad2 as a facilitator of general chromatin-templated activities such as transcription.
    Mots-clés : cancer drug target, DBG, epidrug, FACT, germ cells, histone chaperone, histone turnover, Pax3, REMOD.


  • L. Francelle, L. Galvan, M. - C. Gaillard, M. Guillermier, D. Houitte, G. Bonvento, F. Petit, C. Jan, N. Dufour, P. Hantraye, J. - M. Elalouf, M. De Chaldée, N. Déglon, et E. Brouillet, « Loss of the thyroid hormone-binding protein Crym renders striatal neurons more vulnerable to mutant huntingtin in Huntington's disease », Human Molecular Genetics, vol. 24, nᵒ 6, p. 1563-1573, 2015.
    Résumé : The mechanisms underlying preferential atrophy of the striatum in Huntington's disease (HD) are unknown. One hypothesis is that a set of gene products preferentially expressed in the striatum could determine the particular vulnerability of this brain region to mutant huntingtin (mHtt). Here, we studied the striatal protein µ-crystallin (Crym). Crym is the NADPH-dependent p38 cytosolic T3-binding protein (p38CTBP), a key regulator of thyroid hormone (TH) T3 (3,5,3'-triiodo-l-thyronine) transportation. It has been also recently identified as the enzyme that reduces the sulfur-containing cyclic ketimines, which are potential neurotransmitters. Here, we confirm the preferential expression of the Crym protein in the rodent and macaque striatum. Crym expression was found to be higher in the macaque caudate than in the putamen. Expression of Crym was reduced in the BACHD and Knock-in 140CAG mouse models of HD before onset of striatal atrophy. We show that overexpression of Crym in striatal medium-size spiny neurons using a lentiviral-based strategy in mice is neuroprotective against the neurotoxicity of an N-terminal fragment of mHtt in vivo. Thus, reduction of Crym expression in HD could render striatal neurons more susceptible to mHtt suggesting that Crym may be a key determinant of the vulnerability of the striatum. In addition our work points to Crym as a potential molecular link between striatal degeneration and the THs deregulation reported in HD patients.
    Mots-clés : Animals, Corpus Striatum, Crystallins, DBG, Disease Models, Animal, Down-Regulation, gene expression, Humans, Huntingtin Protein, Huntington Disease, Macaca, Male, Mice, Mice, Transgenic, Mutation, Nerve Tissue Proteins, Rats, REMOD.

  • L. Francelle, L. Galvan, M. - C. Gaillard, F. Petit, B. Bernay, M. Guillermier, G. Bonvento, N. Dufour, J. - M. Elalouf, P. Hantraye, N. Déglon, M. de Chaldée, et E. Brouillet, « Striatal long noncoding RNA Abhd11os is neuroprotective against an N-terminal fragment of mutant huntingtin in vivo », Neurobiology of Aging, vol. 36, nᵒ 3, p. 1601.e7-16, 2015.
    Résumé : A large number of gene products that are enriched in the striatum have ill-defined functions, although they may have key roles in age-dependent neurodegenerative diseases affecting the striatum, especially Huntington disease (HD). In the present study, we focused on Abhd11os, (called ABHD11-AS1 in human) which is a putative long noncoding RNA (lncRNA) whose expression is enriched in the mouse striatum. We confirm that despite the presence of 2 small open reading frames (ORFs) in its sequence, Abhd11os is not translated into a detectable peptide in living cells. We demonstrate that Abhd11os levels are markedly reduced in different mouse models of HD. We performed in vivo experiments in mice using lentiviral vectors encoding either Abhd11os or a small hairpin RNA targeting Abhd11os. Results show that Abhd11os overexpression produces neuroprotection against an N-terminal fragment of mutant huntingtin, whereas Abhd11os knockdown is protoxic. These novel results indicate that the loss lncRNA Abhd11os likely contribute to striatal vulnerability in HD. Our study emphasizes that lncRNA may play crucial roles in neurodegenerative diseases.
    Mots-clés : Animals, Cells, Cultured, Corpus Striatum, DBG, Disease Models, Animal, Down-Regulation, Female, gene expression, Gene Expression Regulation, Gene regulation, Humans, Huntingtin Protein, Huntington Disease, Male, Mice, Inbred C57BL, Mutation, Nerve Tissue Proteins, Neurodegeneration, Neuroprotection, Neuroprotective Agents, Noncoding RNA, Nuclear Proteins, REMOD, Reverse Transcriptase Polymerase Chain Reaction, RNA, Small Interfering, RNA, Untranslated, Serine Proteases, Striatum.
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Principales publications avant 2015

Wu L, Jiang H, Chawsheen HA, Mishra M, Young MR, Gerard M, Toledano MB, Colburn NH, Wei Q. Tumor promoter-induced sulfiredoxin is required for mouse skin tumorigenesis (2014). Carcinogenesis 35:1177-84.

Montellier E, Boussouar F, Rousseaux S, Zhang K, Buchou T, Fenaille F, Shiota H, Debernardi A, Hery P, Curtet S, Jamshidikia M, Barral S, Holota H, Bergon A, Lopez F, Guardiola P, Pernet K, Imbert J, Petosa C, Tan M, Zhao Y, Gerard M, Khochbin S (2013) Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant, TH2B. Genes Dev 27:1680-92

Wei Q, Jiang H, Baker A, Dodge LK, Gerard M, Young MR, Toledano MB, Colburn NH.. Loss of sulfiredoxin renders mice resistant to azoxymethane/dextran sulfate sodium-induced colon carcinogenesis (2013). Carcinogenesis 34:1403-10

Carriere L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude JC, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gerard M, Werner M. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells (2012). Nucleic acids research 40 : 270-283

Galvan L, Lepejova N, Gaillard M C, Malgorn C, Guillermier M, Houitte D, Bonvento G, Petit F, Dufour N, Héry P, Gérard M, Elalouf J M, Deglon N, Brouillet E, de Chaldée M. Capucin does not modify the toxicity of a mutant Huntingtin fragment in vivo (2012). Neurobiol Aging 33 : 1845.e5-6.

Gaucher J, Boussouar F, Montellier E, Curtet S, Buchou T, Bertrand S, Hery P, Jounier S, Depaux A, Vitte AL, Guardiola P, Pernet K, Debernardi A, Lopez F, Holota H, Imbert J, Wolgemuth DJ, Gerard M, Rousseaux S, Khochbin S Bromodomain-dependent stage-specific male genome programming by Brdt (2012). The EMBO journal 31 : 3809-3820

Chantalat S, Depaux A, Hery P, Barral S, Thuret JY, Dimitrov S, Gerard M. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin (2011). Genome research 21 : 1426-1437

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