17 research outputs found
Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues.
BACKGROUND: Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from gametes. Imprinting is pervasive in murine extra-embryonic lineages, and uniquely, the imprinting of several genes has been found to be conferred non-canonically through maternally inherited repressive histone modification H3K27me3. However, the underlying regulatory mechanisms of non-canonical imprinting in post-implantation development remain unexplored. RESULTS: We identify imprinted regions in post-implantation epiblast and extra-embryonic ectoderm (ExE) by assaying allelic histone modifications (H3K4me3, H3K36me3, H3K27me3), gene expression, and DNA methylation in reciprocal C57BL/6 and CAST hybrid embryos. We distinguish loci with DNA methylation-dependent (canonical) and independent (non-canonical) imprinting by assaying hybrid embryos with ablated maternally inherited DNA methylation. We find that non-canonical imprints are localized to endogenous retrovirus-K (ERVK) long terminal repeats (LTRs), which act as imprinted promoters specifically in extra-embryonic lineages. Transcribed ERVK LTRs are CpG-rich and located in close proximity to gene promoters, and imprinting status is determined by their epigenetic patterning in the oocyte. Finally, we show that oocyte-derived H3K27me3 associated with non-canonical imprints is not maintained beyond pre-implantation development at these elements and is replaced by secondary imprinted DNA methylation on the maternal allele in post-implantation ExE, while being completely silenced by bi-allelic DNA methylation in the epiblast. CONCLUSIONS: This study reveals distinct epigenetic mechanisms regulating non-canonical imprinted gene expression between embryonic and extra-embryonic development and identifies an integral role for ERVK LTR repetitive elements
Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes
International audienceTranscriptional silencing of retrotransposons via DNA methylation is paramount for mammalian fertility and reproductive fitness. During germ cell development, most mammalian species utilize the de novo DNA methyltransferases DNMT3A and DNMT3B to establish DNA methylation patterns. However, many rodent species deploy a third enzyme, DNMT3C, to selectively methylate the promoters of young retrotransposon insertions in their germline. The evolutionary forces that shaped DNMT3C's unique function are unknown. Using a phylogenomic approach, we confirm here that Dnmt3C arose through a single duplication of Dnmt3B that occurred 60 Ma in the last common ancestor of muroid rodents. Importantly, we reveal that DNMT3C is composed of two independently evolving segments: the latter two-thirds have undergone recurrent gene conversion with Dnmt3B, whereas the N-terminus has instead evolved under strong diversifying selection. We hypothesize that positive selection of Dnmt3C is the result of an ongoing evolutionary arms race with young retrotransposon lineages in muroid genomes. Interestingly, although primates lack DNMT3C, we find that the N-terminus of DNMT3A has also evolved under diversifying selection. Thus, the N-termini of two independent de novo methylation enzymes have evolved under diversifying selection in rodents and primates. We hypothesize that repression of young retrotransposons might be driving the recurrent innovation of a functional domain in the N-termini on germline DNMT3s in mammals
Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naĂŻve pluripotency
International audienceDuring 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 naĂŻve 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 an 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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Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues.
BACKGROUND: Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from gametes. Imprinting is pervasive in murine extra-embryonic lineages, and uniquely, the imprinting of several genes has been found to be conferred non-canonically through maternally inherited repressive histone modification H3K27me3. However, the underlying regulatory mechanisms of non-canonical imprinting in post-implantation development remain unexplored. RESULTS: We identify imprinted regions in post-implantation epiblast and extra-embryonic ectoderm (ExE) by assaying allelic histone modifications (H3K4me3, H3K36me3, H3K27me3), gene expression, and DNA methylation in reciprocal C57BL/6 and CAST hybrid embryos. We distinguish loci with DNA methylation-dependent (canonical) and independent (non-canonical) imprinting by assaying hybrid embryos with ablated maternally inherited DNA methylation. We find that non-canonical imprints are localized to endogenous retrovirus-K (ERVK) long terminal repeats (LTRs), which act as imprinted promoters specifically in extra-embryonic lineages. Transcribed ERVK LTRs are CpG-rich and located in close proximity to gene promoters, and imprinting status is determined by their epigenetic patterning in the oocyte. Finally, we show that oocyte-derived H3K27me3 associated with non-canonical imprints is not maintained beyond pre-implantation development at these elements and is replaced by secondary imprinted DNA methylation on the maternal allele in post-implantation ExE, while being completely silenced by bi-allelic DNA methylation in the epiblast. CONCLUSIONS: This study reveals distinct epigenetic mechanisms regulating non-canonical imprinted gene expression between embryonic and extra-embryonic development and identifies an integral role for ERVK LTR repetitive elements
Identification d'une nouvelle ADN méthyltransférase « DNMT3C » qui protÚge les cellules germinales mùles de l'activité des transposons
Les transposons portent des gĂšnes codant pour des enzymes qui leur permettent de se multiplier, se dĂ©placer de façon alĂ©atoire dans le gĂ©nome, pouvant ainsi causer des mutations dĂ©lĂ©tĂšres. Il est donc particuliĂšrement important de neutraliser lâactivitĂ© des transposons dans le gĂ©nome, en particulier lors de certaines phases critiques de dĂ©veloppement de lâorganisme, par exemple la formation des cellules reproductrices (spermatozoĂŻdes et ovules). La mĂ©thylation de lâADN est un des principaux systĂšmes utilisĂ©s pour neutraliser lâactivitĂ© des transposons. La mĂ©thylation de leurs sĂ©quences promotrices inhibent lâexpression des gĂšnes des transposons empĂȘchant ainsi leurs multiplications et dĂ©placements. Cette mĂ©thylation est effectuĂ©e par des enzymes particuliĂšres, appelĂ©es DNA mĂ©thyl transfĂ©rases. On pensait quâelles Ă©taient au nombre de quatre dans les gĂ©nomes. Or, nous en avons dĂ©couvert une cinquiĂšme (appelĂ©e DMMT3C) dans le gĂ©nome de la souris. Elle prĂ©sente des propriĂ©tĂ©s singuliĂšres: Elle est spĂ©cifique des rongeurs, prĂ©sente uniquement dans les cellules germinales male, et cible spĂ©cifiquement des transposons les plus rĂ©cents et les plus actifs. Le niveau de spĂ©cialisation de cette DNA mĂ©thyl transfĂ©rase est trĂšs surprenant par rapport aux autres enzymes de ce type connues jusquâĂ prĂ©sent. Elle ne sâexprime que dans les cellules germinales pendant la vie fĆtale et protĂšge le gĂ©nome des futurs spermatozoĂŻdes contre lâeffet dĂ©lĂ©tĂšre des transposons. Elle mĂ©thyle uniquement la rĂ©gion promotrice de certains transposons les rendant inactifs. Chez la souris mutante qui nâexprime pas cette enzyme, les transposons sont massivement rĂ©activĂ©s au cours de la spermatogĂ©nĂšse, ce qui conduit Ă un arrĂȘt de la formation des spermatozoĂŻdes et Ă la stĂ©rilitĂ©. Enfin, cette enzyme est une innovation des rongeurs, elle serait apparue il y a quelques 46 millions dâannĂ©es par duplication du gĂšne dâune autre mĂ©thyl transfĂ©rase. Ainsi, la protection du gĂ©nome contre les transposons serait une force motrice dans lâĂ©volution de la mĂ©thylation de lâADN chez les mammifĂšres. Cette enzyme pose de nouvelles questions : quels sont les mĂ©canismes de cette spĂ©cificitĂ© ? Existe-t-il lâĂ©quivalent de cette enzyme chez les autres mammifĂšres pour protĂ©ger leur fertilitĂ©
The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates
International audienceGenomic 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
Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene
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DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation.
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
Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin
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.This work was supported by Ayuda Merck Serono- FundaciĂłn Salud 2000 de InvestigaciĂłn en EndocrinologĂa 2009 (to DM and IIP); Spanish Ministerio de EducaciĂłn y Ciencia (grant number SAF2008-1578 to DM); Centre National de la Recherche Scientifique ââProjects for International Scientific Cooperationââ 34622 (to PA and DM); Agence National de la Recherche (to RF); âLigue Contre le Cancerâ (to RF); Ligue contre le Cancer comitĂ© HĂ©rault and Association pour la
Recherche sur la cancer- ARC nu 4980- (for PA). DM is a Ramon y Cajal research fellow and AGA is funded by a FPU studentship. Research in the Neonatal Unit in Hospital Sant Joan de Déu is partially funded by an unrestricted grant from BebéDue Spai
MOESM2 of Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues
Additional file 2. Supplementary Tables S1-S6