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Schulz M, Teissandier A, De La Mata Santaella E, Armand M, Iranzo J, El Marjou F, Gestraud P, Walter M, Kinston S, Göttgens B, Greenberg MVC, Bourc'his D. DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation. Nat Struct Mol Biol 2024; 31:102-114. [PMID: 38177678 DOI: 10.1038/s41594-023-01162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.
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Affiliation(s)
- Mathieu Schulz
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Aurélie Teissandier
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | | | - Mélanie Armand
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Julian Iranzo
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Fatima El Marjou
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Pierre Gestraud
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | | | - Sarah Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Deborah Bourc'his
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France.
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2
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Gentien D, Saberi-Ansari E, Servant N, Jolly A, de la Grange P, Némati F, Liot G, Saule S, Teissandier A, Bourc'his D, Girard E, Wong J, Masliah-Planchon J, Narmanli E, Liu Y, Torun E, Goulancourt R, Rodrigues M, Gaudé LV, Reyes C, Bazire M, Chenegros T, Henry E, Rapinat A, Bohec M, Baulande S, M'kacher R, Jeandidier E, Nicolas A, Ciriello G, Margueron R, Decaudin D, Cassoux N, Piperno-Neumann S, Stern MH, Gibcus JH, Dekker J, Heard E, Roman-Roman S, Waterfall JJ. Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma. Cell Rep 2023; 42:113132. [PMID: 37708024 PMCID: PMC10598242 DOI: 10.1016/j.celrep.2023.113132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Uveal melanoma (UM) is a rare cancer resulting from the transformation of melanocytes in the uveal tract. Integrative analysis has identified four molecular and clinical subsets of UM. To improve our molecular understanding of UM, we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis using Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with the upregulation of PRAME, an independent prognostic biomarker in UM, and a potential therapeutic target. Our findings illustrate how multi-omics approaches can improve our understanding of tumorigenesis and reveal two distinct mechanisms of gene expression dysregulation in UM.
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Affiliation(s)
- David Gentien
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France.
| | - Elnaz Saberi-Ansari
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France
| | | | | | | | - Fariba Némati
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Géraldine Liot
- Institut Curie, PSL Research University, CNRS, INSERM, UMR3347, U1021, Orsay, France
| | - Simon Saule
- Institut Curie, PSL Research University, CNRS, INSERM, UMR3347, U1021, Orsay, France; Université Paris-Saclay Centre National de La Recherche Scientifique, UMR 3347, Unité 1021, Orsay, France
| | - Aurélie Teissandier
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Deborah Bourc'his
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | | | - Jennifer Wong
- Department of Diagnostic and Theranostic Molecular Pathology, Unit of Somatic Genetic, Hospital, Institut Curie, Paris, France
| | - Julien Masliah-Planchon
- Department of Diagnostic and Theranostic Molecular Pathology, Unit of Somatic Genetic, Hospital, Institut Curie, Paris, France
| | - Erkan Narmanli
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France
| | - Yuanlong Liu
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emma Torun
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | | | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laure Villoing Gaudé
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Cécile Reyes
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Matéo Bazire
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Thomas Chenegros
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Emilie Henry
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Audrey Rapinat
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Mylene Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | | | - Eric Jeandidier
- Laboratoire de Génétique, Groupe Hospitalier de la Région de Mulhouse Sud-Alsace, Mulhouse, France
| | - André Nicolas
- Pathex, Institut Curie, PSL Research University, Paris, France
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Raphael Margueron
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Didier Decaudin
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Nathalie Cassoux
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France; Department of Ocular Oncology, Faculty of Medicine, Institut Curie, Université de Paris Descartes, 75005 Paris, France
| | - Sophie Piperno-Neumann
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, 75005 Paris, France
| | - Johan Harmen Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Department of Systems Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Edith Heard
- Director's Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sergio Roman-Roman
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France.
| | - Joshua J Waterfall
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France.
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Ducreux B, Barberet J, Guilleman M, Pérez-Palacios R, Teissandier A, Bourc’his D, Fauque P. Assessing the influence of distinct culture media on human pre-implantation development using single-embryo transcriptomics. Front Cell Dev Biol 2023; 11:1155634. [PMID: 37435029 PMCID: PMC10330962 DOI: 10.3389/fcell.2023.1155634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023] Open
Abstract
The use of assisted reproductive technologies is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. In particular, embryos within their first days of development are highly sensitive to their micro-environment, and it is unknown how their transcriptome adapts to different embryo culture compositions. Here, we determined the impact of culture media composition on gene expression in human pre-implantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of the post-fertilization culture in different commercially available media (Ferticult, Global, and SSM), we revealed medium-specific differences in gene expression changes. Embryos cultured pre-compaction until day 2 in Ferticult or Global media notably displayed 266 differentially expressed genes, which were related to essential developmental pathways. Herein, 19 of them could have a key role in early development, based on their previously described dynamic expression changes across development. When embryos were cultured after day 2 in the same media considered more suitable because of its amino acid enrichment, 18 differentially expressed genes thought to be involved in the transition from early to later embryonic stages were identified. Overall, the differences were reduced at the blastocyst stage, highlighting the ability of embryos conceived in a suboptimal in vitro culture medium to mitigate the transcriptomic profile acquired under different pre-compaction environments.
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Affiliation(s)
- Bastien Ducreux
- Université Bourgogne Franche-Comté—Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France
| | - Julie Barberet
- Université Bourgogne Franche-Comté—Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction—CECOS, Dijon, France
| | - Magali Guilleman
- Université Bourgogne Franche-Comté—Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction—CECOS, Dijon, France
| | - Raquel Pérez-Palacios
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | - Patricia Fauque
- Université Bourgogne Franche-Comté—Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction—CECOS, Dijon, France
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4
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Glaser J, Iranzo J, Borensztein M, Marinucci M, Gualtieri A, Jouhanneau C, Teissandier A, Gaston-Massuet C, Bourc'his D. The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates. eLife 2022; 11:65641. [PMID: 35049495 PMCID: PMC8809892 DOI: 10.7554/elife.65641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.
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Affiliation(s)
- Juliane Glaser
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Julian Iranzo
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Maud Borensztein
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Mattia Marinucci
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Angelica Gualtieri
- Centre for Endocrinology, Queen Mary University of London, London, United Kingdom
| | | | - Aurélie Teissandier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | | | - Deborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
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5
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Chelmicki T, Roger E, Teissandier A, Dura M, Bonneville L, Rucli S, Dossin F, Fouassier C, Lameiras S, Bourc'his D. m 6A RNA methylation regulates the fate of endogenous retroviruses. Nature 2021; 591:312-316. [PMID: 33442060 DOI: 10.1038/s41586-020-03135-1] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
Endogenous retroviruses (ERVs) are abundant and heterogenous groups of integrated retroviral sequences that affect genome regulation and cell physiology throughout their RNA-centred life cycle1. Failure to repress ERVs is associated with cancer, infertility, senescence and neurodegenerative diseases2,3. Here, using an unbiased genome-scale CRISPR knockout screen in mouse embryonic stem cells, we identify m6A RNA methylation as a way to restrict ERVs. Methylation of ERV mRNAs is catalysed by the complex of methyltransferase-like METTL3-METTL144 proteins, and we found that depletion of METTL3-METTL14, along with their accessory subunits WTAP and ZC3H13, led to increased mRNA abundance of intracisternal A-particles (IAPs) and related ERVK elements specifically, by targeting their 5' untranslated region. Using controlled auxin-dependent degradation of the METTL3-METTL14 enzymatic complex, we showed that IAP mRNA and protein abundance is dynamically and inversely correlated with m6A catalysis. By monitoring chromatin states and mRNA stability upon METTL3-METTL14 double depletion, we found that m6A methylation mainly acts by reducing the half-life of IAP mRNA, and this occurs by the recruitment of the YTHDF family of m6A reader proteins5. Together, our results indicate that RNA methylation provides a protective effect in maintaining cellular integrity by clearing reactive ERV-derived RNA species, which may be especially important when transcriptional silencing is less stringent.
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Affiliation(s)
- Tomasz Chelmicki
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France.
| | - Emeline Roger
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Aurélie Teissandier
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Mathilde Dura
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Lorraine Bonneville
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Sofia Rucli
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | | | | | - Sonia Lameiras
- ICGex Next-Generation Sequencing Platform, Institut Curie, PSL Research University, Paris, France
| | - Deborah Bourc'his
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France.
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6
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Abstract
Early preimplantation embryos are precious and scarce samples that contain limited numbers of cells, which can be problematic for quantitative gene expression analyses. Nonetheless, low-input genome-wide techniques coupled with cDNA amplification steps have become a gold standard for RNA profiling of as minimal as a single blastomere. Here, we describe a single-cell/single-embryo RNA sequencing (RNA-seq) method, from embryo collection to sample validation steps prior to DNA library preparation and sequencing. Key quality controls and external Spike-In normalization approaches are also detailed.
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Affiliation(s)
- Raquel Pérez-Palacios
- Institut Curie, INSERM U934, CNRS UMR3215, Paris Sciences Lettres Research University, Paris, France.
| | - Patricia Fauque
- Laboratoire de Biologie de la Reproduction, Hôpital François Mitterrand, Université de Bourgogne, Dijon, France
- INSERM UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aurélie Teissandier
- Institut Curie, INSERM U934, CNRS UMR3215, Paris Sciences Lettres Research University, Paris, France
| | - Déborah Bourc'his
- Institut Curie, INSERM U934, CNRS UMR3215, Paris Sciences Lettres Research University, Paris, France
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7
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Teissandier A, Servant N, Barillot E, Bourc'his D. Tools and best practices for retrotransposon analysis using high-throughput sequencing data. Mob DNA 2019; 10:52. [PMID: 31890048 PMCID: PMC6935493 DOI: 10.1186/s13100-019-0192-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/04/2019] [Indexed: 12/26/2022] Open
Abstract
Background Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome. This problem is exacerbated when dealing with repetitive sequences such as transposable elements that occupy half of the mammalian genome mass. Sequenced reads coming from these regions introduce ambiguities in the mapping step. Therefore, applying dedicated parameters and algorithms has to be taken into consideration when transposable elements regulation is investigated with sequencing datasets. Results Here, we used simulated reads on the mouse and human genomes to define the best parameters for aligning transposable element-derived reads on a reference genome. The efficiency of the most commonly used aligners was compared and we further evaluated how transposable element representation should be estimated using available methods. The mappability of the different transposon families in the mouse and the human genomes was calculated giving an overview into their evolution. Conclusions Based on simulated data, we provided recommendations on the alignment and the quantification steps to be performed when transposon expression or regulation is studied, and identified the limits in detecting specific young transposon families of the mouse and human genomes. These principles may help the community to adopt standard procedures and raise awareness of the difficulties encountered in the study of transposable elements.
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Affiliation(s)
- Aurélie Teissandier
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France.,4INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Nicolas Servant
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France
| | - Emmanuel Barillot
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France
| | - Deborah Bourc'his
- 1Institut Curie, PSL Research University, 75005 Paris, France.,4INSERM U934, CNRS UMR 3215, 75005 Paris, France
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8
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Greenberg M, Teissandier A, Walter M, Noordermeer D, Bourc'his D. Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife 2019; 8:44057. [PMID: 30990414 PMCID: PMC6488298 DOI: 10.7554/elife.44057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/15/2019] [Indexed: 12/29/2022] Open
Abstract
During early mammalian development, the chromatin landscape undergoes profound transitions. The Zdbf2 gene—involved in growth control—provides a valuable model to study this window: upon exit from naïve pluripotency and prior to tissue differentiation, it undergoes a switch from a distal to a proximal promoter usage, accompanied by a switch from polycomb to DNA methylation occupancy. Using a mouse embryonic stem cell (ESC) system to mimic this period, we show here that four enhancers contribute to the Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. In ESCs, the locus is partitioned to facilitate enhancer contacts with the distal Zdbf2 promoter. Relieving the partition enhances proximal Zdbf2 promoter activity, as observed during differentiation or with genetic mutants. Importantly, we show that 3D regulation occurs upstream of the polycomb and DNA methylation pathways. Our study reveals the importance of multi-layered regulatory frameworks to ensure proper spatio-temporal activation of developmentally important genes.
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Affiliation(s)
- Maxim Greenberg
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | | | - Marius Walter
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris Sud, Université Paris-Saclay, CEA, CNRS, Paris, France
| | - Deborah Bourc'his
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
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9
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Tarabay Y, Achour M, Teletin M, Ye T, Teissandier A, Mark M, Bourc'his D, Viville S. Tex19 paralogs are new members of the piRNA pathway controlling retrotransposon suppression. Development 2017. [DOI: 10.1242/dev.153486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Affiliation(s)
- Aurélie Teissandier
- "Epigenetic Decisions and Reproduction" Group, Institut Curie, PSL University, CNRS, INSERM, Paris, France
| | - Déborah Bourc'his
- "Epigenetic Decisions and Reproduction" Group, Institut Curie, PSL University, CNRS, INSERM, Paris, France
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11
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Tarabay Y, Achour M, Teletin M, Ye T, Teissandier A, Mark M, Bourc'his D, Viville S. Tex19 paralogs are new members of the piRNA pathway controlling retrotransposon suppression. J Cell Sci 2017; 130:1463-1474. [PMID: 28254886 DOI: 10.1242/jcs.188763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 02/27/2017] [Indexed: 01/29/2023] Open
Abstract
Tex19 genes are mammalian specific and duplicated to give Tex19.1 and Tex19.2 in some species, such as the mouse and rat. It has been demonstrated that mutant Tex19.1 males display a variable degree of infertility whereas they all upregulate MMERVK10C transposons in their germ line. In order to study the function of both paralogs in the mouse, we generated and studied Tex19 double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in the single Tex19.1KO mice, with small testes and impaired spermatogenesis, defects in meiotic chromosome synapsis, persistence of DNA double-strand breaks during meiosis, lack of post-meiotic germ cells and upregulation of MMERVK10C expression. The phenotypic similarities to mice with knockouts in the Piwi family genes prompted us to check and then demonstrate, by immunoprecipitation and GST pulldown followed by mass spectrometry analyses, that TEX19 paralogs interact with PIWI proteins and the TEX19 VPTEL domain directly binds Piwi-interacting RNAs (piRNAs) in adult testes. We therefore identified two new members of the postnatal piRNA pathway.
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Affiliation(s)
- Yara Tarabay
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Mayada Achour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Marius Teletin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Aurélie Teissandier
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Manuel Mark
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Déborah Bourc'his
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Stéphane Viville
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France .,Centre Hospitalier Universitaire, Strasbourg 67000, France
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12
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Barau J, Teissandier A, Zamudio N, Roy S, Nalesso V, Hérault Y, Guillou F, Bourc’his D. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 2016; 354:909-912. [DOI: 10.1126/science.aah5143] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/19/2016] [Indexed: 12/23/2022]
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13
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Greenberg MVC, Glaser J, Borsos M, Marjou FE, Walter M, Teissandier A, Bourc'his D. Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Nat Genet 2016; 49:110-118. [PMID: 27841881 DOI: 10.1038/ng.3718] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]
Abstract
The potential for early embryonic events to program epigenetic states that influence adult physiology remains an important question in health and development. Using the imprinted Zdbf2 locus as a paradigm for the early programming of phenotypes, we demonstrate here that chromatin changes that occur in the pluripotent embryo can be dispensable for embryogenesis but instead signal essential regulatory information in the adult. The Liz (long isoform of Zdbf2) transcript is transiently expressed in early embryos and embryonic stem cells (ESCs). This transcription locally promotes de novo DNA methylation upstream of the Zdbf2 promoter, which antagonizes Polycomb-mediated repression of Zdbf2. Strikingly, mouse embryos deficient for Liz develop normally but fail to activate Zdbf2 in the postnatal brain and show indelible growth reduction, implying a crucial role for a Liz-dependent epigenetic switch. This work provides evidence that transcription during an early embryonic timeframe can program a stable epigenetic state with later physiological consequences.
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Affiliation(s)
| | - Juliane Glaser
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | - Máté Borsos
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | | | - Marius Walter
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | - Aurélie Teissandier
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France.,École des Mines, Paris, France
| | - Déborah Bourc'his
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
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14
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Walter M, Teissandier A, Pérez-Palacios R, Bourc'his D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. eLife 2016; 5. [PMID: 26814573 PMCID: PMC4769179 DOI: 10.7554/elife.11418] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is extensively remodeled during mammalian gametogenesis and embryogenesis. Most transposons become hypomethylated, raising the question of their regulation in the absence of DNA methylation. To reproduce a rapid and extensive demethylation, we subjected mouse ES cells to chemically defined hypomethylating culture conditions. Surprisingly, we observed two phases of transposon regulation. After an initial burst of de-repression, various transposon families were efficiently re-silenced. This was accompanied by a reconfiguration of the repressive chromatin landscape: while H3K9me3 was stable, H3K9me2 globally disappeared and H3K27me3 accumulated at transposons. Interestingly, we observed that H3K9me3 and H3K27me3 occupy different transposon families or different territories within the same family, defining three functional categories of adaptive chromatin responses to DNA methylation loss. Our work highlights that H3K9me3 and, most importantly, polycomb-mediated H3K27me3 chromatin pathways can secure the control of a large spectrum of transposons in periods of intense DNA methylation change, ensuring longstanding genome stability.
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Affiliation(s)
- Marius Walter
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,Paris Science Lettres Research University, .,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France
| | - Aurélie Teissandier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University, .,Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Paris, France.,Mines Paris Tech, Paris, France.,U900, Inserm, Paris, France
| | - Raquel Pérez-Palacios
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
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15
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Wassef M, Rodilla V, Teissandier A, Zeitouni B, Gruel N, Sadacca B, Irondelle M, Charruel M, Ducos B, Michaud A, Caron M, Marangoni E, Chavrier P, Le Tourneau C, Kamal M, Pasmant E, Vidaud M, Servant N, Reyal F, Meseure D, Vincent-Salomon A, Fre S, Margueron R. Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis. Genes Dev 2015; 29:2547-62. [PMID: 26637281 PMCID: PMC4699384 DOI: 10.1101/gad.269522.115] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023]
Abstract
In this study, Wassef et al. used mouse and human models to show that the high expression of Polycomb protein EZH2 in solid tumors is a consequence, not a cause, of tumorigenesis and that low abundance or deletion of EZH2 relative to proliferation is linked to poor prognosis and transcriptional instability. Alterations of chromatin modifiers are frequent in cancer, but their functional consequences often remain unclear. Focusing on the Polycomb protein EZH2 that deposits the H3K27me3 (trimethylation of Lys27 of histone H3) mark, we showed that its high expression in solid tumors is a consequence, not a cause, of tumorigenesis. In mouse and human models, EZH2 is dispensable for prostate cancer development and restrains breast tumorigenesis. High EZH2 expression in tumors results from a tight coupling to proliferation to ensure H3K27me3 homeostasis. However, this process malfunctions in breast cancer. Low EZH2 expression relative to proliferation and mutations in Polycomb genes actually indicate poor prognosis and occur in metastases. We show that while altered EZH2 activity consistently modulates a subset of its target genes, it promotes a wider transcriptional instability. Importantly, transcriptional changes that are consequences of EZH2 loss are predominantly irreversible. Our study provides an unexpected understanding of EZH2's contribution to solid tumors with important therapeutic implications.
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Affiliation(s)
- Michel Wassef
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Veronica Rodilla
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Aurélie Teissandier
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Bruno Zeitouni
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Nadege Gruel
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Marie Irondelle
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Margaux Charruel
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique Statistique-Ecole Normale Supérieure de Paris, Centre National de la Recherche Scientifique, 75005 Paris, France; UMR 8550, Centre National de la Recherche Scientifique, 75005 Paris, France; Plateforme de PCR Quantitative à Haut Débit Genomic Paris Centre, Institut de Biologie de l'École Normale Supérieure, 75005 Paris, France
| | - Audrey Michaud
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Matthieu Caron
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Elisabetta Marangoni
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Philippe Chavrier
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; EA7285, Université de Versailles, Saint-Quentin-en-Yvelines, 78000 Versailles, France
| | - Maud Kamal
- Department of Medical Oncology, Institut Curie, 75005 Paris, France
| | - Eric Pasmant
- UMR_S745, EA7331, Institut National de la Santé et de la Recherche Médicale, 75006 Paris, France; Facultée des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Michel Vidaud
- UMR_S745, EA7331, Institut National de la Santé et de la Recherche Médicale, 75006 Paris, France; Facultée des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Nicolas Servant
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Fabien Reyal
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Dider Meseure
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; Platform of Investigative Pathology, 75005 Paris, France
| | - Anne Vincent-Salomon
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Silvia Fre
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
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16
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Zamudio N, Barau J, Teissandier A, Walter M, Borsos M, Servant N, Bourc'his D. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev 2015; 29:1256-70. [PMID: 26109049 PMCID: PMC4495397 DOI: 10.1101/gad.257840.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Zamudio et al. demonstrate that DNA methylation restrains transposons from adopting chromatin characteristics amenable to meiotic recombination, which they propose prevents the occurrence of erratic chromosomal events. DNA methylation is essential for protecting the mammalian germline against transposons. When DNA methylation-based transposon control is defective, meiotic chromosome pairing is consistently impaired during spermatogenesis: How and why meiosis is vulnerable to transposon activity is unknown. Using two DNA methylation-deficient backgrounds, the Dnmt3L and Miwi2 mutant mice, we reveal that DNA methylation is largely dispensable for silencing transposons before meiosis onset. After this, it becomes crucial to back up to a developmentally programmed H3K9me2 loss. Massive retrotransposition does not occur following transposon derepression, but the meiotic chromatin landscape is profoundly affected. Indeed, H3K4me3 marks gained over transcriptionally active transposons correlate with formation of SPO11-dependent double-strand breaks and recruitment of the DMC1 repair enzyme in Dnmt3L−/− meiotic cells, whereas these features are normally exclusive to meiotic recombination hot spots. Here, we demonstrate that DNA methylation restrains transposons from adopting chromatin characteristics amenable to meiotic recombination, which we propose prevents the occurrence of erratic chromosomal events.
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Affiliation(s)
- Natasha Zamudio
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Joan Barau
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Aurélie Teissandier
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France; U900, INSERM, Paris 75005, France; Mines ParisTech, Institut Curie, Paris 75005, France
| | - Marius Walter
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Maté Borsos
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Nicolas Servant
- U900, INSERM, Paris 75005, France; Mines ParisTech, Institut Curie, Paris 75005, France
| | - Déborah Bourc'his
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
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17
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Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One 2015; 10:e0124360. [PMID: 25867897 PMCID: PMC4395090 DOI: 10.1371/journal.pone.0124360] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.
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Affiliation(s)
- Eric Dugat-Bony
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Cécile Straub
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Aurélie Teissandier
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Djamila Onésime
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Valentin Loux
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Christophe Monnet
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Marie-Noëlle Leclercq-Perlat
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bento
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | | | - Jean-François Gibrat
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Julie Aubert
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Frédéric Fer
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Eric Guédon
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Sean Kennedy
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bonnarme
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- * E-mail:
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18
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Sanulli S, Justin N, Teissandier A, Ancelin K, Portoso M, Caron M, Michaud A, Lombard B, da Rocha ST, Offer J, Loew D, Servant N, Wassef M, Burlina F, Gamblin SJ, Heard E, Margueron R. Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation. Mol Cell 2015; 57:769-783. [PMID: 25620564 PMCID: PMC4352895 DOI: 10.1016/j.molcel.2014.12.020] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/01/2014] [Accepted: 12/12/2014] [Indexed: 02/06/2023]
Abstract
Polycomb Group (PcG) proteins maintain transcriptional repression throughout development, mostly by regulating chromatin structure. Polycomb Repressive Complex 2 (PRC2), a component of the Polycomb machinery, is responsible for the methylation of histone H3 lysine 27 (H3K27me2/3). Jarid2 was previously identified as a cofactor of PRC2, regulating PRC2 targeting to chromatin and its enzymatic activity. Deletion of Jarid2 leads to impaired orchestration of gene expression during cell lineage commitment. Here, we reveal an unexpected crosstalk between Jarid2 and PRC2, with Jarid2 being methylated by PRC2. This modification is recognized by the Eed core component of PRC2 and triggers an allosteric activation of PRC2’s enzymatic activity. We show that Jarid2 methylation is important to promote PRC2 activity at a locus devoid of H3K27me3 and for the correct deposition of this mark during cell differentiation. Our results uncover a regulation loop where Jarid2 methylation fine-tunes PRC2 activity depending on the chromatin context. PRC2 methylates Jarid2 on K116 Jarid2 methylation promotes PRC2 activity H3K27me3 and Jarid2-K116me3 bind to the aromatic cage of Eed Jarid2 methylation regulates H3K27me3 deposition during ESC differentiation
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Affiliation(s)
- Serena Sanulli
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Neil Justin
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Aurélie Teissandier
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U900, 26 Rue d'Ulm, 75005 Paris, France; Mines ParisTech, 35 Rue Saint Honoré, 77305 Fontainebleau, France
| | - Katia Ancelin
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Manuela Portoso
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Matthieu Caron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Audrey Michaud
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Berangère Lombard
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; Laboratory of Proteomics and Mass Spectrometry, 26 Rue d'Ulm, 75005 Paris, France
| | - Simao T da Rocha
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - John Offer
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Damarys Loew
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; Laboratory of Proteomics and Mass Spectrometry, 26 Rue d'Ulm, 75005 Paris, France
| | - Nicolas Servant
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U900, 26 Rue d'Ulm, 75005 Paris, France; Mines ParisTech, 35 Rue Saint Honoré, 77305 Fontainebleau, France
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Fabienne Burlina
- Sorbonnes Universités, UPMC Univ Paris 06, CNRS, ENS, UMR7203 LBM, 4 Place Jussieu, 75005 Paris, France
| | - Steve J Gamblin
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Edith Heard
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Raphaël Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France.
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