Décisions épigénétiques et reproduction chez les mammifères

Publications

Année de publication : 2017

Aurélie Teissandier, Déborah Bourc'his (2017 Apr 27)

Gene body DNA methylation conspires with H3K36me3 to preclude aberrant transcription.

The EMBO journal : 1471-1473 : DOI : 10.15252/embj.201796812 En savoir plus
Résumé

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Yara Tarabay, Mayada Achour, Marius Teletin, Tao Ye, Aurélie Teissandier, Manuel Mark, Déborah Bourc'his, Stéphane Viville (2017 Mar 4)

Tex19 paralogs are new members of the piRNA pathway controlling retrotransposon suppression.

Journal of cell science : DOI : jcs.188763 En savoir plus
Résumé

Tex19 genes are mammalian specific and duplicated in 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 double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in 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 with Piwi KO mice 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 their VPTEL domain directly binds piRNAs in adult testes. We therefore identified two new members of the postnatal piRNA pathway.

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Maxim V C Greenberg, Juliane Glaser, Máté Borsos, Fatima El Marjou, Marius Walter, Aurélie Teissandier, Déborah Bourc'his (2017 Jan 2)

Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth.

Nature genetics : 110-118 : DOI : 10.1038/ng.3718 En savoir plus
Résumé

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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Année de publication : 2016

Joan Barau, Aurélie Teissandier, Natasha Zamudio, Stéphanie Roy, Valérie Nalesso, Yann Hérault, Florian Guillou, Déborah Bourc'his (2016 Nov 19)

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity.

Science (New York, N.Y.) : 909-912 En savoir plus
Résumé

DNA methylation is prevalent in mammalian genomes and plays a central role in the epigenetic control of development. The mammalian DNA methylation machinery is thought to be composed of three DNA methyltransferase enzymes (DNMT1, DNMT3A, and DNMT3B) and one cofactor (DNMT3L). Here, we describe the discovery of Dnmt3C, a de novo DNA methyltransferase gene that evolved via a duplication of Dnmt3B in rodent genomes and was previously annotated as a pseudogene. We show that DNMT3C is the enzyme responsible for methylating the promoters of evolutionarily young retrotransposons in the male germ line and that this specialized activity is required for mouse fertility. DNMT3C reveals the plasticity of the mammalian DNA methylation system and expands the scope of the mechanisms involved in the epigenetic control of retrotransposons.

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Marius Walter, Aurélie Teissandier, Raquel Pérez-Palacios, Déborah Bourc'his (2016 Jan 27)

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells.

eLife : DOI : 10.7554/eLife.11418 En savoir plus
Résumé

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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Année de publication : 2015

Hung-Fu Liao, Chu-Fan Mo, Shinn-Chih Wu, Dai-Han Cheng, Chih-Yun Yu, Kai-Wei Chang, Tzu-Hao Kao, Chia-Wei Lu, Marina Pinskaya, Antonin Morillon, Shih-Shun Lin, Winston T K Cheng, Déborah Bourc'his, Timothy Bestor, Li-Ying Sung, Shau-Ping Lin (2015 Jul 11)

Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency.

Reproduction (Cambridge, England) : 245-56 : DOI : 10.1530/REP-15-0031 En savoir plus
Résumé

Nuclear transfer (NT) is a technique used to investigate the development and reprogramming potential of a single cell. DNA methyltransferase-3-like, which has been characterized as a repressive transcriptional regulator, is expressed in naturally fertilized egg and morula/blastocyst at pre-implantation stages. In this study, we demonstrate that the use of Dnmt3l-knockout (Dnmt3l-KO) donor cells in combination with Trichostatin A treatment improved the developmental efficiency and quality of the cloned embryos. Compared with the WT group, Dnmt3l-KO donor cell-derived cloned embryos exhibited increased cell numbers as well as restricted OCT4 expression in the inner cell mass (ICM) and silencing of transposable elements at the blastocyst stage. In addition, our results indicate that zygotic Dnmt3l is dispensable for cloned embryo development at pre-implantation stages. In Dnmt3l-KO mouse embryonic fibroblasts, we observed reduced nuclear localization of HDAC1, increased levels of the active histone mark H3K27ac and decreased accumulation of the repressive histone marks H3K27me3 and H3K9me3, suggesting that Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for NT reprogramming.

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Natasha Zamudio, Joan Barau, Aurélie Teissandier, Marius Walter, Maté Borsos, Nicolas Servant, Déborah Bourc'his (2015 Jun 26)

DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination.

Genes & development : 1256-70 : DOI : 10.1101/gad.257840.114 En savoir plus
Résumé

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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Maxim Vc Greenberg, Déborah Bourc'his (2015 May 15)

Cultural relativism: maintenance of genomic imprints in pluripotent stem cell culture systems.

Current opinion in genetics & development : 42-9 : DOI : 10.1016/j.gde.2015.04.005 En savoir plus
Résumé

Pluripotent stem cells (PSCs) in culture have become a widely used model for studying events occurring during mammalian development; they also present an exciting avenue for therapeutics. However, compared to their in vivo counterparts, cultured PSC derivatives have unique properties, and it is well established that their epigenome is sensitive to medium composition. Here we review the specific effects on genomic imprints in various PSC types and culture systems. Imprinted gene regulation is developmentally important, and imprinting defects have been associated with several human diseases. Therefore, imprint abnormalities in PSCs may have considerable consequences for downstream applications.

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Céline Bruno, Virginie Carmignac, Irène Netchine, Cécile Choux, Yannis Duffourd, Laurence Faivre, Christel Thauvin-Robinet, Yves Le Bouc, Paul Sagot, Déborah Bourc'his, Patricia Fauque (2015 Mar 5)

Germline correction of an epimutation related to Silver-Russell syndrome.

Human molecular genetics : 3314-21 : DOI : 10.1093/hmg/ddv079 En savoir plus
Résumé

Like genetic mutations, DNA methylation anomalies or epimutations can disrupt gene expression and lead to human diseases. However, unlike genetic mutations, epimutations can in theory be reverted through developmental epigenetic reprograming, which should limit their transmission across generations. Following the request for a parental project of a patient diagnosed with Silver-Russell syndrome (SRS), and the availability of both somatic and spermatozoa DNA from the proband and his father, we had the exceptional opportunity to evaluate the question of inheritance of an epimutation. We provide here for the first time evidence for efficient reversion of a constitutive epimutation in the spermatozoa of an SRS patient, which has important implication for genetic counseling.

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Année de publication : 2014

William A Pastor, Hume Stroud, Kevin Nee, Wanlu Liu, Dubravka Pezic, Sergei Manakov, Serena A Lee, Guillaume Moissiard, Natasha Zamudio, Déborah Bourc'his, Alexei A Aravin, Amander T Clark, Steven E Jacobsen (2014 Dec 16)

MORC1 represses transposable elements in the mouse male germline.

Nature communications : 5795 : DOI : 10.1038/ncomms6795 En savoir plus
Résumé

The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation.

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Rachel Duffié, Sophie Ajjan, Maxim V Greenberg, Natasha Zamudio, Martin Escamilla del Arenal, Julian Iranzo, Ikuhiro Okamoto, Sandrine Barbaux, Patricia Fauque, Déborah Bourc'his (2014 Mar 5)

The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals.

Genes & development : 463-78 : DOI : 10.1101/gad.232058.113 En savoir plus
Résumé

Many loci maintain parent-of-origin DNA methylation only briefly after fertilization during mammalian development: Whether this form of transient genomic imprinting can impact the early embryonic transcriptome or even have life-long consequences on genome regulation and possibly phenotypes is currently unknown. Here, we report a maternal germline differentially methylated region (DMR) at the mouse Gpr1/Zdbf2 (DBF-type zinc finger-containing protein 2) locus, which controls the paternal-specific expression of long isoforms of Zdbf2 (Liz) in the early embryo. This DMR loses parental specificity by gain of DNA methylation at implantation in the embryo but is maintained in extraembryonic tissues. As a consequence of this transient, tissue-specific maternal imprinting, Liz expression is restricted to the pluripotent embryo, extraembryonic tissues, and pluripotent male germ cells. We found that Liz potentially functions as both Zdbf2-coding RNA and cis-regulatory RNA. Importantly, Liz-mediated events allow a switch from maternal to paternal imprinted DNA methylation and from Liz to canonical Zdbf2 promoter use during embryonic differentiation, which are stably maintained through somatic life and conserved in humans. The Gpr1/Zdbf2 locus lacks classical imprinting histone modifications, but analysis of mutant embryonic stem cells reveals fine-tuned regulation of Zdbf2 dosage through DNA and H3K27 methylation interplay. Together, our work underlines the developmental and evolutionary need to ensure proper Liz/Zdbf2 dosage as a driving force for dynamic genomic imprinting at the Gpr1/Zdbf2 locus.

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Année de publication : 2013

Yara Tarabay, Emmanuelle Kieffer, Marius Teletin, Catherine Celebi, Aafke Van Montfoort, Natasha Zamudio, Mayada Achour, Rosy El Ramy, Emese Gazdag, Philippe Tropel, Manuel Mark, Déborah Bourc'his, Stéphane Viville (2013 May 16)

The mammalian-specific Tex19.1 gene plays an essential role in spermatogenesis and placenta-supported development.

Human reproduction (Oxford, England) : 2201-14 : DOI : 10.1093/humrep/det129 En savoir plus
Résumé

What is the consequence of Tex19.1 gene deletion in mice?

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Rachel Duffié, Déborah Bourc'his (2013 Apr 17)

Parental epigenetic asymmetry in mammals.

Current topics in developmental biology : 293-328 : DOI : 10.1016/B978-0-12-416027-9.00009-7 En savoir plus
Résumé

The early mammalian embryo is marked by genome-wide parental epigenetic asymmetries, which are directly inherited from the sperm and the oocyte, but are also amplified a few hours after fertilization. The yin-yang of these complementary parental programs is essential for proper development, as uniparental embryos are not viable. The majority of these parental asymmetries are erased, as the embryonic genome assumes its own chromatin signature toward pluripotency and then differentiation, reducing the risk for haploinsufficiency. At a few loci, however, parent-of-origin information persists through development, via maintenance and protective complexes. In this review, we discuss the parental asymmetries that are inherited from the gametes, the forces involved in their elimination, reinforcement or protection, and how this influences the embryonic program. We highlight the gradual loss of all parental asymmetries occurring throughout development, except at imprinted loci, which maintain distinct parent-of-origin chromatin and transcriptional characteristics for life. A deeper understanding of the nongenetic contributions of each germline is important to provide insight into the origin of non-Mendelian inheritance of phenotypic traits, as well as the risk of incompatibilities between parental genomes.

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Mounia Guenatri, Rachel Duffié, Julian Iranzo, Patricia Fauque, Déborah Bourc'his (2013 Jan 8)

Plasticity in Dnmt3L-dependent and -independent modes of de novo methylation in the developing mouse embryo.

Development (Cambridge, England) : 562-72 : DOI : 10.1242/dev.089268 En savoir plus
Résumé

A stimulatory DNA methyltransferase co-factor, Dnmt3L, has evolved in mammals to assist the process of de novo methylation, as genetically demonstrated in the germline. The function of Dnmt3L in the early embryo remains unresolved. By combining developmental and genetic approaches, we find that mouse embryos begin development with a maternal store of Dnmt3L, which is rapidly degraded and does not participate in embryonic de novo methylation. A zygotic-specific promoter of Dnmt3l is activated following gametic methylation loss and the potential recruitment of pluripotency factors just before implantation. Importantly, we find that zygotic Dnmt3L deficiency slows down the rate of de novo methylation in the embryo by affecting methylation density at some, but not all, genomic sequences. Dnmt3L is not strictly required, however, as methylation patterns are eventually established in its absence, in the context of increased Dnmt3A protein availability. This study proves that the postimplantation embryo is more plastic than the germline in terms of DNA methylation mechanistic choices and, importantly, that de novo methylation can be achieved in vivo without Dnmt3L.

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Année de publication : 2012

Isabel Iglesias-Platas, Alex Martin-Trujillo, Davide Cirillo, Franck Court, Amy Guillaumet-Adkins, Cristina Camprubi, Deborah Bourc'his, Kenichiro Hata, Robert Feil, Gian Tartaglia, Philippe Arnaud, David Monk (2012 Jun 23)

Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin.

PloS one : e38907 : DOI : 10.1371/journal.pone.0038907 En savoir plus
Résumé

Genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes DNA methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. Genes subject to imprinting are often organised in clusters associated with large non-coding RNAs (ncRNAs), some of which have cis-regulatory functions. Here we have undertaken a detailed allelic expression analysis of an imprinted domain on mouse proximal chromosome 10 comprising the paternally expressed Plagl1 gene. We identified three novel Plagl1 transcripts, only one of which contains protein-coding exons. In addition, we characterised two unspliced ncRNAs, Hymai, the mouse orthologue of HYMAI, and Plagl1it (Plagl1 intronic transcript), a transcript located in intron 5 of Plagl1. Imprinted expression of these novel ncRNAs requires DNMT3L-mediated maternal DNA methylation, which is also indispensable for establishing the correct chromatin profile at the Plagl1 DMR. Significantly, the two ncRNAs are retained in the nucleus, consistent with a potential regulatory function at the imprinted domain. Analysis with catRAPID, a protein-ncRNA association prediction algorithm, suggests that Hymai and Plagl1it RNAs both have potentially high affinity for Trithorax chromatin regulators. The two ncRNAs could therefore help to protect the paternal allele from DNA methylation by attracting Trithorax proteins that mediate H3 lysine-4 methylation.

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