Décisions épigénétiques et reproduction chez les mammifères

Publications

Année de publication : 2014

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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Charlotte Proudhon, Rachel Duffié, Sophie Ajjan, Michael Cowley, Julian Iranzo, Guillermo Carbajosa, Heba Saadeh, Michelle L Holland, Rebecca J Oakey, Vardhman K Rakyan, Reiner Schulz, Déborah Bourc'his (2012 Feb 20)

Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes.

Molecular cell : 909-20 : DOI : 10.1016/j.molcel.2012.07.010 En savoir plus
Résumé

Identifying loci with parental differences in DNA methylation is key to unraveling parent-of-origin phenotypes. By conducting a MeDIP-Seq screen in maternal-methylation free postimplantation mouse embryos (Dnmt3L-/+), we demonstrate that maternal-specific methylation exists very scarcely at midgestation. We reveal two forms of oocyte-specific methylation inheritance: limited to preimplantation, or with longer duration, i.e. maternally imprinted loci. Transient and imprinted maternal germline DMRs (gDMRs) are indistinguishable in gametes and preimplantation embryos, however, de novo methylation of paternal alleles at implantation delineates their fates and acts as a major leveling factor of parent-inherited differences. We characterize two new imprinted gDMRs, at the Cdh15 and AK008011 loci, with tissue-specific imprinting loss, again by paternal methylation gain. Protection against demethylation after fertilization has been emphasized as instrumental in maintaining parent-of-origin methylation inherited from the gametes. Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life.

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Année de publication : 2011

David Monk, Philippe Arnaud, Jennifer M Frost, Andrew J Wood, Michael Cowley, Alejandro Martin-Trujillo, Amy Guillaumet-Adkins, Isabel Iglesias Platas, Cristina Camprubi, Deborah Bourc'his, Robert Feil, Gudrun E Moore, Rebecca J Oakey (2011 Feb 9)

Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes.

Nucleic acids research : 4577-86 : DOI : 10.1093/nar/gkq1230 En savoir plus
Résumé

Imprinted retrotransposed genes share a common genomic organization including a promoter-associated differentially methylated region (DMR) and a position within the intron of a multi-exonic ‘host’ gene. In the mouse, at least one transcript of the host gene is also subject to genomic imprinting. Human retrogene orthologues are imprinted and we reveal that human host genes are not imprinted. This coincides with genomic rearrangements that occurred during primate evolution, which increase the separation between the retrogene DMRs and the host genes. To address the mechanisms governing imprinted retrogene expression, histone modifications were assayed at the DMRs. For the mouse retrogenes, the active mark H3K4me2 was associated with the unmethylated paternal allele, while the methylated maternal allele was enriched in repressive marks including H3K9me3 and H4K20me3. Two human retrogenes showed monoallelic enrichment of active, but not of repressive marks suggesting a partial uncoupling of the relationship between DNA methylation and repressive histone methylation, possibly due to the smaller size and lower CpG density of these DMRs. Finally, we show that the genes immediately flanking the host genes in mouse and human are biallelically expressed in a range of tissues, suggesting that these loci are distinct from large imprinted clusters.

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Année de publication : 2010

Reiner Schulz, Charlotte Proudhon, Timothy H Bestor, Kathryn Woodfine, Chyuan-Sheng Lin, Shau-Ping Lin, Marine Prissette, Rebecca J Oakey, Déborah Bourc'his (2010 Dec 3)

The parental non-equivalence of imprinting control regions during mammalian development and evolution.

PLoS genetics : e1001214 : DOI : 10.1371/journal.pgen.1001214 En savoir plus
Résumé

In mammals, imprinted gene expression results from the sex-specific methylation of imprinted control regions (ICRs) in the parental germlines. Imprinting is linked to therian reproduction, that is, the placenta and imprinting emerged at roughly the same time and potentially co-evolved. We assessed the transcriptome-wide and ontology effect of maternally versus paternally methylated ICRs at the developmental stage of setting of the chorioallantoic placenta in the mouse (8.5dpc), using two models of imprinting deficiency including completely imprint-free embryos. Paternal and maternal imprints have a similar quantitative impact on the embryonic transcriptome. However, transcriptional effects of maternal ICRs are qualitatively focused on the fetal-maternal interface, while paternal ICRs weakly affect non-convergent biological processes, with little consequence for viability at 8.5dpc. Moreover, genes regulated by maternal ICRs indirectly influence genes regulated by paternal ICRs, while the reverse is not observed. The functional dominance of maternal imprints over early embryonic development is potentially linked to selection pressures favoring methylation-dependent control of maternal over paternal ICRs. We previously hypothesized that the different methylation histories of ICRs in the maternal versus the paternal germlines may have put paternal ICRs under higher mutational pressure to lose CpGs by deamination. Using comparative genomics of 17 extant mammalian species, we show here that, while ICRs in general have been constrained to maintain more CpGs than non-imprinted sequences, the rate of CpG loss at paternal ICRs has indeed been higher than at maternal ICRs during evolution. In fact, maternal ICRs, which have the characteristics of CpG-rich promoters, have gained CpGs compared to non-imprinted CpG-rich promoters. Thus, the numerical and, during early embryonic development, functional dominance of maternal ICRs can be explained as the consequence of two orthogonal evolutionary forces: pressure to tightly regulate genes affecting the fetal-maternal interface and pressure to avoid the mutagenic environment of the paternal germline.

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Déborah Bourc'his, Olivier Voinnet (2010 Oct 30)

A small-RNA perspective on gametogenesis, fertilization, and early zygotic development.

Science (New York, N.Y.) : 617-22 : DOI : 10.1126/science.1194776 En savoir plus
Résumé

Transient populations of cis- and trans-acting small RNAs have recently emerged as key regulators of extensive epigenetic changes taking place during periconception, which encompasses gametogenesis, fertilization, and early zygotic development. These small RNAs are not only important to maintain genome integrity in the gametes and zygote, but they also actively contribute to assessing the compatibility of parental genomes at fertilization and to promoting long-term memory of the zygotic epigenetic landscape by affecting chromatin. Striking parallels exist in the biogenesis and modus operandi of these molecules among diverse taxa, unraveling universal themes of small-RNA-mediated epigenetic reprogramming during sexual reproduction.

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Charlotte Proudhon, Déborah Bourc'his (2010 Sep 11)

Identification and resolution of artifacts in the interpretation of imprinted gene expression.

Briefings in functional genomics : 374-84 : DOI : 10.1093/bfgp/elq020 En savoir plus
Résumé

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression.

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Charlotte Proudhon, Déborah Bourc'his (2010 Jun 1)

[Evolution of genomic imprinting in mammals: what a zoo!].

Médecine sciences : M/S : 497-503 : DOI : 10.1051/medsci/2010265497 En savoir plus
Résumé

Genomic imprinting imposes an obligate mode of biparental reproduction in mammals. This phenomenon results from the monoparental expression of a subset of genes. This specific gene regulation mechanism affects viviparous mammals, especially eutherians, but also marsupials to a lesser extent. Oviparous mammals, or monotremes, do not seem to demonstrate monoparental allele expression. This phylogenic confinement suggests that the evolution of the placenta imposed a selective pressure for the emergence of genomic imprinting. This physiological argument is now complemented by recent genomic evidence facilitated by the sequencing of the platypus genome, a rare modern day case of a monotreme. Analysis of the platypus genome in comparison to eutherian genomes shows a chronological and functional coincidence between the appearance of genomic imprinting and transposable element accumulation. The systematic comparative analyses of genomic sequences in different species is essential for the further understanding of genomic imprinting emergence and divergent evolution along mammalian speciation.

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N Zamudio, D Bourc'his (2010 May 6)

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

Heredity : 92-104 : DOI : 10.1038/hdy.2010.53 En savoir plus
Résumé

Retrotransposable elements comprise around 50% of the mammalian genome. Their activity represents a constant threat to the host and has prompted the development of adaptive control mechanisms to protect genome architecture and function. To ensure their propagation, retrotransposons have to mobilize in cells destined for the next generation. Accordingly, these elements are particularly well suited to transcriptional networks associated with pluripotent and germinal states in mammals. The relaxation of epigenetic control that occurs in the early developing germline constitutes a dangerous window in which retrotransposons can escape from host restraint and massively expand. What could be observed as risky behavior may turn out to be an insidious strategy developed by germ cells to sense retrotransposons and hold them back in check. Herein, we review recent insights that have provided a detailed picture of the defense mechanisms that concur toward retrotransposon silencing in mammalian genomes, and in particular in the germline. In this lineage, retrotransposons are hit at multiple stages of their life cycle, through transcriptional repression, RNA degradation and translational control. An organized cross-talk between PIWI-interacting small RNAs (piRNAs) and various nuclear and cytoplasmic accessories provides this potent and multi-layered response to retrotransposon unleashing in early germ cells.

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Année de publication : 2008

Alexei A Aravin, Ravi Sachidanandam, Deborah Bourc'his, Christopher Schaefer, Dubravka Pezic, Katalin Fejes Toth, Timothy Bestor, Gregory J Hannon (2008 Oct 17)

A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice.

Molecular cell : 785-99 : DOI : 10.1016/j.molcel.2008.09.003 En savoir plus
Résumé

piRNAs and Piwi proteins have been implicated in transposon control and are linked to transposon methylation in mammals. Here we examined the construction of the piRNA system in the restricted developmental window in which methylation patterns are set during mammalian embryogenesis. We find robust expression of two Piwi family proteins, MIWI2 and MILI. Their associated piRNA profiles reveal differences from Drosophila wherein large piRNA clusters act as master regulators of silencing. Instead, in mammals, dispersed transposon copies initiate the pathway, producing primary piRNAs, which predominantly join MILI in the cytoplasm. MIWI2, whose nuclear localization and association with piRNAs depend upon MILI, is enriched for secondary piRNAs antisense to the elements that it controls. The Piwi pathway lies upstream of known mediators of DNA methylation, since piRNAs are still produced in dnmt3L mutants, which fail to methylate transposons. This implicates piRNAs as specificity determinants of DNA methylation in germ cells.

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Shantha K Mahadevaiah, Déborah Bourc'his, Dirk G de Rooij, Timothy H Bestor, James M A Turner, Paul S Burgoyne (2008 Jul 30)

Extensive meiotic asynapsis in mice antagonises meiotic silencing of unsynapsed chromatin and consequently disrupts meiotic sex chromosome inactivation.

The Journal of cell biology : 263-76 : DOI : 10.1083/jcb.200710195 En savoir plus
Résumé

Chromosome synapsis during zygotene is a prerequisite for the timely homologous recombinational repair of meiotic DNA double-strand breaks (DSBs). Unrepaired DSBs are thought to trigger apoptosis during midpachytene of male meiosis if synapsis fails. An early pachytene response to asynapsis is meiotic silencing of unsynapsed chromatin (MSUC), which, in normal males, silences the X and Y chromosomes (meiotic sex chromosome inactivation [MSCI]). In this study, we show that MSUC occurs in Spo11-null mouse spermatocytes with extensive asynapsis but lacking meiotic DSBs. In contrast, three mutants (Dnmt3l, Msh5, and Dmc1) with high levels of asynapsis and numerous persistent unrepaired DSBs have a severely impaired MSUC response. We suggest that MSUC-related proteins, including the MSUC initiator BRCA1, are sequestered at unrepaired DSBs. All four mutants fail to silence the X and Y chromosomes (MSCI failure), which is sufficient to explain the midpachytene apoptosis. Apoptosis does not occur in mice with a single additional asynapsed chromosome with unrepaired meiotic DSBs and no disturbance of MSCI.

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David Monk, Alexandre Wagschal, Philippe Arnaud, Pari-Sima Müller, Layla Parker-Katiraee, Déborah Bourc'his, Stephen W Scherer, Robert Feil, Philip Stanier, Gudrun E Moore (2008 May 16)

Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing.

Genome research : 1270-81 : DOI : 10.1101/gr.077115.108 En savoir plus
Résumé

Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is organized around a maternally methylated CpG island comprising the promoters of the adjacent PEG10 and SGCE imprinted genes. Examination of Dnmt3l(-/+) conceptuses shows that imprinted expression for all genes of the cluster depends upon the germline methylation at this putative « imprinting control region » (ICR). Similarly as for other ICRs, we find its DNA-methylated allele to be associated with trimethylation of lysine 9 on histone H3 (H3K9me3) and trimethylation of lysine 20 on histone H4 (H4K20me3), whereas the transcriptionally active paternal allele is enriched in H3K4me2 and H3K9 acetylation. Our study reveals a novel placenta-specific transcript, TFPI2, which is expressed from the maternal allele in both humans and mice. Deficiency for the histone methyltransferase EHMT2 (also known as G9A) or for the Polycomb group protein EED, involved in repressive H3K9me2 and H3K27me3 respectively, leads to biallelic expression of Tfpi2 in the extra-embryonic lineages, whereas the other genes in the cluster maintain correct imprinting. Apart from the putative ICR, however, no other promoter regions within the domain exhibited allele-specific repressive histone modifications. This unexpected general lack of repressive histone modifications suggests that this domain may utilize a different silencing mechanism as compared to other imprinted domains.

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