Les différents rôles critiques de la méthylation de l’ADN dans le développement de la lignée germinale mâle

La méthylation de l'ADN, associée à la répression des gènes et des éléments transposables (ET), joue un rôle essentiel dans la spermatogenèse. Le méthylome des futurs gamètes est reprogrammé : les profils de méthylation somatiques sont effacés, des profils spécifiques des cellules germinales sont établis. Trois de novo ADN méthyltransférases (DNMT) sont essentielles à la méthylation de l'ADN des cellules germinales mâles chez la souris : les enzymes DNMT3C et DNMT3A et leur cofacteur DNMT3L. Il a été montré que DNMT3C est l'enzyme qui méthyle sélectivement les ET les plus jeunes évolutivement. Cependant, les cibles et la fonction de DNMT3A étaient encore inconnues. Je me suis donc intéressée aux rôles de DNMT3A et DNMT3C dans la régulation épigénétique de la spermatogénèse. J'ai démontré (projet 1) une division de travail remarquable : alors que DNMT3C empêche les ET d'interférer avec la méiose, DNMT3A méthyle largement le génome, à l'exception des ET dépendants de DNMT3C. J'ai découvert que les cellules souches spermatogoniales (CSS) mutantes pour Dnmt3A ont perdu leur potentiel de différentiation à cause de l’activation erronée d’enhancers qui imposent un programme génétique de cellules souches. Ce travail révèle une nouvelle fonction de la méthylation de l'ADN dans la fertilité mâle. En parallèle (projet 2), j’ai étudié la nature de la spécificité de reconnaissance des jeunes ET par DNMT3C. Ces séquences présentent une dynamique chromatinienne unique: d’abord un profil bivalent de type H3K4me3-H3K9me3 qui évolue vers un enrichissement H3K9me3 exclusif. Mon travail a ainsi fourni des éléments nouveaux pour comprendre le rôle de la méthylation de l’ADN en reproduction.DNA methylation, associated with gene or transposable element (TE) repression, plays a key role in spermatogenesis. During germ cell development, their methylome is reprogrammed: somatic patterns are erased and germ cell-specific patterns are established. Three de novo DNA methyltransferases (DNMTs) are essential for shaping male germ cell DNA methylation in mice: DNMT3C and DNMT3A enzymes and DNMT3L co-factor. DNMT3C was shown to selectively methylate young TEs. However, the targets and function of DNMT3A was still unknown. During my PhD, I investigated the interplay between DNMT3A and DNMT3C in the epigenetic regulation of spermatogenesis. First (project 1), I reported a striking division of labor: while DNMT3C prevents TEs from interfering with meiosis, DNMT3A broadly methylates the genome—except DNMT3C-dependent TEs—and controls spermatogonial stem cell (SSC) plasticity. By single-cell RNA-seq and chromatin states profiling, I found that Dnmt3A mutant SSCs cannot differentiate due to spurious enhancer activation that enforces a stem cell gene program. I thus demonstrated a novel function for DNA methylation for SSC differentiation and life-long spermatogenesis supply. Second (project 2), I investigated the chromatin determinants of DNMT3C specificity towards young TEs. I found that these sequences present unique dynamics: first a bivalent H3K4me3-H3K9me3 enrichment, followed by a switch to H3K9me3-only. H3K9me3-enrichment was also a hallmark of the sequences that gain DNA methylation upon ectopic DNMT3C expression in cultured embryonic stem cells. As a whole, my work provided novel insights into the complexity of DNA methylation-based control of reproduction

Les différents rôles critiques de la méthylation de l’ADN dans le développement de la lignée germinale mâle

DNA methylation, associated with gene or transposable element (TE) repression, plays a key role in spermatogenesis. During germ cell development, their methylome is reprogrammed: somatic patterns are erased and germ cell-specific patterns are established. Three de novo DNA methyltransferases (DNMTs) are essential for shaping male germ cell DNA methylation in mice: DNMT3C and DNMT3A enzymes and DNMT3L co-factor. DNMT3C was shown to selectively methylate young TEs. However, the targets and function of DNMT3A was still unknown. During my PhD, I investigated the interplay between DNMT3A and DNMT3C in the epigenetic regulation of spermatogenesis. First (project 1), I reported a striking division of labor: while DNMT3C prevents TEs from interfering with meiosis, DNMT3A broadly methylates the genome—except DNMT3C-dependent TEs—and controls spermatogonial stem cell (SSC) plasticity. By single-cell RNA-seq and chromatin states profiling, I found that Dnmt3A mutant SSCs cannot differentiate due to spurious enhancer activation that enforces a stem cell gene program. I thus demonstrated a novel function for DNA methylation for SSC differentiation and life-long spermatogenesis supply. Second (project 2), I investigated the chromatin determinants of DNMT3C specificity towards young TEs. I found that these sequences present unique dynamics: first a bivalent H3K4me3-H3K9me3 enrichment, followed by a switch to H3K9me3-only. H3K9me3-enrichment was also a hallmark of the sequences that gain DNA methylation upon ectopic DNMT3C expression in cultured embryonic stem cells. As a whole, my work provided novel insights into the complexity of DNA methylation-based control of reproduction.La méthylation de l'ADN, associée à la répression des gènes et des éléments transposables (ET), joue un rôle essentiel dans la spermatogenèse. Le méthylome des futurs gamètes est reprogrammé : les profils de méthylation somatiques sont effacés, des profils spécifiques des cellules germinales sont établis. Trois de novo ADN méthyltransférases (DNMT) sont essentielles à la méthylation de l'ADN des cellules germinales mâles chez la souris : les enzymes DNMT3C et DNMT3A et leur cofacteur DNMT3L. Il a été montré que DNMT3C est l'enzyme qui méthyle sélectivement les ET les plus jeunes évolutivement. Cependant, les cibles et la fonction de DNMT3A étaient encore inconnues. Je me suis donc intéressée aux rôles de DNMT3A et DNMT3C dans la régulation épigénétique de la spermatogénèse. J'ai démontré (projet 1) une division de travail remarquable : alors que DNMT3C empêche les ET d'interférer avec la méiose, DNMT3A méthyle largement le génome, à l'exception des ET dépendants de DNMT3C. J'ai découvert que les cellules souches spermatogoniales (CSS) mutantes pour Dnmt3A ont perdu leur potentiel de différentiation à cause de l’activation erronée d’enhancers qui imposent un programme génétique de cellules souches. Ce travail révèle une nouvelle fonction de la méthylation de l'ADN dans la fertilité mâle. En parallèle (projet 2), j’ai étudié la nature de la spécificité de reconnaissance des jeunes ET par DNMT3C. Ces séquences présentent une dynamique chromatinienne unique: d’abord un profil bivalent de type H3K4me3-H3K9me3 qui évolue vers un enrichissement H3K9me3 exclusif. Mon travail a ainsi fourni des éléments nouveaux pour comprendre le rôle de la méthylation de l’ADN en reproduction

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation.

Cis-regulation plays an essential role in the control of gene expression, and is particularly complex and poorly understood for developmental genes, which are subject to multiple levels of modulation. In this study, we performed a global analysis of the cis-acting elements involved in the control of the zebrafish developmental gene krox20. krox20 encodes a transcription factor required for hindbrain segmentation and patterning, a morphogenetic process highly conserved during vertebrate evolution. Chromatin accessibility analysis reveals a cis-regulatory landscape that includes 6 elements participating in the control of initiation and autoregulatory aspects of krox20 hindbrain expression. Combining transgenic reporter analyses and CRISPR/Cas9-mediated mutagenesis, we assign precise functions to each of these 6 elements and provide a comprehensive view of krox20 cis-regulation. Three important features emerged. First, cooperation between multiple cis-elements plays a major role in the regulation. Cooperation can surprisingly combine synergy and redundancy, and is not restricted to transcriptional enhancer activity (for example, 4 distinct elements cooperate through different modes to maintain autoregulation). Second, several elements are unexpectedly versatile, which allows them to be involved in different aspects of control of gene expression. Third, comparative analysis of the elements and their activities in several vertebrate species reveals that this versatility is underlain by major plasticity across evolution, despite the high conservation of the gene expression pattern. These characteristics are likely to be of broad significance for developmental genes

Schematic of the <i>cis</i>-regulation of <i>krox20</i> expression in r3 and r5, illustrating differences between zebrafish and mouse.

<p><i>Cis</i>-acting elements are indicated by light blue boxes along the locus, with their position with respect to the site of transcription initiation underneath. The different types of activities of the elements are represented by arrows originating from the element: enhancer activities involved in the initiation of <i>krox20</i> expression are indicated by green arrows pointing toward the promoter, enhancer activities corresponding to direct autoregulation are indicated by blue arrows pointing back to the element and the potentiator activity of element C is represented by red arrows pointing toward element A. Question marks indicate that the activity is suspected, but not confirmed.</p

Evolution of enhancer A activity in vertebrates.

<p>The orthologues of element A from 6 vertebrate species, zebrafish (zA), koi carp (kA), spotted gar (sA), <i>Xenopus laevis</i> (xA), chicken (cA) and mouse (mA) were transferred into a GFP reporter construct and the corresponding plasmids were used to generate zebrafish transgenic lines, as indicated. <i>GFP</i> expression was analysed by in situ hybridization at 8s in embryos from each line, either in wild type (WT) or <i>krox20</i> null (<i>krox20*</i>) backgrounds, the latter being obtained by injection of Cas9 protein together with guide RNAs targeting the coding sequence of Krox20’s zinc fingers. Positions of r3 and r5 are shown. A phylogenetic tree with the indication of the node time distances from the present in millions of years (MYA) is shown underneath.</p

DNA accessibility and candidate enhancer sequences within and around the zebrafish <i>krox20</i> locus.

<p>UCSC genome browser view of the <i>krox20</i> locus showing gene positions (purple), repetitive sequences (black) and the sequences selected for enhancer activity tests (light blue), including those that showed activity (named A to F). Below are ATAC-seq data from experiments performed at the indicated stages, either on whole embryos (95% epiboly) or dissected hindbrain or posterior regions of the embryos (5s and 15s), as shown on the schematics on the right side. The seven mostly significant peaks located in non-coding sequences are highlighted in yellow. Underneath is a Vista browser view of sequence conservation between zebrafish and mouse (black) over the region.</p

Collaboration in <i>cis</i> between elements A and C for the control of autoregulation.

<p>Embryos carrying combinations of homozygous deletions of elements A (∆A), C (C*), D (D*), E (E*) and of heterozygous deletions of elements A (∆A/+) or C (∆C/+) were analysed for <i>krox20</i> expression by in situ hybridization at the indicated stages. The genotype (∆A/+ +/∆C) corresponds to heterozygous deletions of A and C affecting different chromosomes. Somatic deletions are indicated by the * symbol and positions of r3 and r5 are shown. Neural crest cells migrating from r5/r6 are indicated by an arrowhead.</p

<i>krox20</i> expression and enhancer dynamics.

<p>(A) Analysis of <i>krox20</i> expression by in situ hybridization at the indicated somite stages (s) in wild type (<i>krox20</i>^<i>+/+</i>) or <i>krox20</i> null (<i>krox20</i>^{<i>fh227/fh227</i>}) backgrounds. (B) Analysis of <i>GFP</i> expression by in situ hybridization at the indicated stages in 6 transgenic lines carrying GFP reporter constructs in which the different putative <i>krox20</i> enhancers have been inserted. Positions of r3, r4 and r5 are shown. Neural crest cells migrating from r5/r6 are indicated by arrowheads.</p

Three enhancer elements cooperate for <i>krox20</i> positive autoregulation.

<p>(A) Analysis of the dependence on Krox20 of the enhancer elements affecting late <i>krox20</i> expression. Four transgenes consisting of GFP reporter constructs, in which the indicated <i>krox20</i> enhancers were inserted, were transferred into wild type (<i>krox20</i>^<i>+/+</i>) and <i>krox20</i> null (<i>krox20</i>^{<i>fh227/fh227</i>}) backgrounds and embryos were analysed for <i>GFP</i> expression by in situ hybridization in at the 12s stage. Positions of r3, r4 and r5 are shown. (B) Embryos carrying combinations of deletions affecting both alleles of elements A, D and/or E, as indicated, were analysed for <i>krox20</i> expression by in situ hybridization at the indicated stages. Somatic deletions are indicated by the * symbol and positions of r3 and r5 are shown. Neural crest cells migrating from r5/r6 are indicated by an arrowhead.</p

<i>krox20</i> r5 expression involves cooperation between three enhancer elements.

<p>Embryos carrying combinations of deletions affecting both alleles of elements B, A and/or C, as indicated, were analysed for <i>krox20</i> expression by in situ hybridization at the indicated stages. Somatic deletions are indicated by the * symbol and positions of r3 and r5 are shown.</p