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. Chez-les, L'unité de base de la chromatine est le nucléosome, composé d'ADN entouré de protéines nommées histones. Ces histones peuvent exister sous différentes formes, les variants d'histones, ou porter des modifications post-traductionnelles. Ainsi, le nucléosome est un module porteur d'informations dites épigénétiques, et la présence de variants d'histones ou de modifications particulières peut délimiter différentes zones fonctionnelles du génome et réguler son expression

, qui doit d'une part dupliquer son matériel génétique, mais également reconstituer son paysage épigénétique. La transmission fidèle des caractéristiques épigénétiques, comme les variants d'histones et leurs modifications, permet de dupliquer l'identité parentale et donc garantit le maintien de l'identité cellulaire. En revanche, la réplication offre aussi une opportunité pour changer le paysage épigénétique, apportant des modifications parfois planifiées -comme dans un contexte de différenciation -, parfois inattenduescomme dans le cas de certaines pathologies, La réplication de l'ADN représente un défi pour la cellule

, En parallèle de nouvelles histones sont déposées afin de maintenir la densité nucléosomale. Si les mécanismes qui permettent de déposer de nouvelles histones sont bien connus, il reste de nombreuses questions concernant le recyclage des histones parentales. Pourtant, le recyclage est essentiel pour garantir la transmission de l

, Leur expression connaît un pic en phase S, permettant de fournir un stock d'histones disponibles pour la réplication. Le variant d'histone H3.3, aussi appelé histone de remplacement, en revanche, est exprimé tout au long du cycle cellulaire et est déposé indépendamment de la synthèse d'ADN lors de situations qui nécessitent un apport en histones. Par exemple, H3.3 est enrichi aux gènes actifs, promoteurs et éléments de régulation -et est ainsi souvent associé à la transcriptionou encore aux télomères. Les histones sont déposées par des protéines appelées chaperons d'histones. Les chaperons peuvent être plus ou moins dédiés à des variants particuliers. Le chaperon d'histone Chromatin Assembly Factor 1 (CAF-1) est dédié au variant H3.1 et le dépose de manière couplée à la synthèse d'ADN, par exemple au cours de la réplication ou de la réparation de l'ADN. Le variant d'histone H3.3 est déposé de manière indépendante de la synthèse, Au sein du nucléosome se trouvent huit histones: deux copies de H2A, H2B, H3 et H4. Pour l'histone H3, une première catégorie de variants est constituée de H3.1 et H3.2, aussi nommés variants réplicatifs

, D'autres chaperons, en revanche, peuvent s'associer à plusieurs variants. C'est le cas du chaperon d'H3-H4 Anti-Silencing Function 1 (ASF1), qui s'associe à la fois à H3

, ASF1 a deux paralogues chez l'homme, ASF1a et ASF1b, impliqués dans de nombreuses voies de gestion des histones. En effet, ASF1a et ASF1b ont été impliqués dans le stockage des histones solubles, ou encore dans la déposition de novo des histones en partenariat avec CAF-1 et HIRA. ASF1

, semble avoir un rôle particulièrement important lors de la réplication, et notamment pour le recyclage des histones parentales. La déplétion d'ASF1 ralentit la progression de la phase S. Par ailleurs, ASF1 forme un complexe avec la sous-unité MCM2 de l'hélicase réplicative MCM via, pp.3-4

, En revanche, quand j'ai commencé ma thèse, un certain nombre de questions demeurait: (i) ce modèle est-il valable dans des cellules? (ii) comment sont recyclés les deux variants H3.1 et H3.3? (iii) quel est le rôle exact d'ASF1 dans le recyclage des variants? (iv) quel est l'impact de défauts de recyclage des variants pour l'épigénome? Question Au cours de ma thèse, j'ai donc tenté de répondre à la question: Comment les variants d'histone H3.1 et H3.3 parentaux sont-ils recyclés au cours de la réplication de l'ADN? Approche Pour répondre à cette question, et est donc idéalement situé pour transférer les histones parentales. Après traitement avec de l'hydroxyurée, qui empêche la synthèse d'ADN, des complexes ASF1 contenant des histones portant des modifications typiques d'histones parentales s'accumulent

, (ii) de pouvoir marquer spécifiquement les histones parentales, et (iii) d'avoir une résolution suffisante pour suivre avec précision les histones aux sites de réplication

J. , Le SNAP-tag peut réagir de manière covalente avec la benzylguanine, et donc notamment avec des dérivés où la benzylguanine est couplée à un fluorophore. Ainsi, en fusionnant une protéine d'intérêt avec le SNAP-tag, on peut en observer des sous-populations spécifiques: nouvelles ou parentales. Dans mon cas, j'ai utilisé des lignées cellulaires exprimant soit H3.1-SNAP, soit H3.3-SNAP, me permettant par ailleurs de distinguer les variants. Pour observer les histones parentales, j'ai effectué des expériences de pulse-chase: le pulse permet de marquer toutes les histones SNAP disponibles avec un fluorophore; ensuite, un chase de 48h permet la synthèse de nouvelles histones SNAP non marquées; à la fin de l'expérience, on observe par microscopie uniquement les histones marquées, c'est-à-dire les histones parentales, SNAP pour suivre les variants d'histones parentaux

, Le système SNAP permet donc de visualiser en microscopie les variants d'histone parentaux

, J'ai choisi d'utiliser une technique de super-résolution: le STORM (STochastic Optical Reconstruction Microscopy). Le STORM repose sur le fait que certains fluorophores, dans des conditions particulières, alternent entre un état excité et non excité et, ainsi, clignotent. Ce phénomène étant stochastique, les fluorophores de l'échantillon s'allument à des moments distincts; ainsi, en filmant l'échantillon, on peut localiser individuellement les molécules avec une grande précision. Deux fluorophore très proches, qu'on ne pourrait habituellement pas résoudre, s'allument alors à des moment différents, et peuvent donc être résolus. Cette technologie permet d'obtenir une résolution de l'ordre de 10-40 nm, au lieu de 250-300 nm avec une technique de microscopie classique, Cependant, pour étudier leur recyclage aux sites de réplication, j'avais besoin d'une résolution élevée pour observer avec précision, en deux couleurs, les histones et les sites de réplication

. Mon and . Storm, High resolution visualization of H3 variants during replication reveals their controlled recycling, Le résultats biologiques de cette étude sont résumés ci-dessous

, Résultats Afin d'étudier le recyclage des variants d'histone au cours de la réplication, j'ai procédé en deux temps: (i) j'ai tout d'abord étudié la distributions des variants d'histones globaux

, Nous avons pu observer que le variant d'histone H3.3 était enrichi dans les régions qui se répliquent en début de phase S (que nous appellerons par la suite "early" et qui, de manière générale, correspondent à l'euchromatine), alors que H3.1 était au contraire enrichi dans les régions qui se répliquent en fin de phase S (que nous appellerons par la suite "late" et qui, de manière générale, correspondent à l'hétérochromatine). Nous avons voulu déterminer si la transcription était seule responsable de l'association de H3.3 avec les régions early. Pour cela, nous avons utilisé des données d'activité transcriptionnelle (nascent RNA-seq). De manière intéressante, nous avons observé que, si H3.3 était en effet associé à la transcription, la corrélation entre H3.3 et le timing de réplication est vraie indépendamment de l'activité transcriptionnelle, Pour déterminer la distribution génomique de H3.1 et H3.3, j'ai collaboré avec des membres de mon équipe pour effectuer une expérience de ChIP-seq

, la distribution en 3D des variants. J'ai donc utilisé la technologie STORM pour observer H3.1 global et H3.3 global dans le noyau. J'ai observé que ces deux variants formaient des clusters, et j'ai décidé d'étudier le volume et la densité de ces clusters dans des cellules en début de phase S et des cellules en fin de phase S. J'ai constaté des comportements opposés pour H3.3 et H3.1. J'ai tout d'abord observé que les clusters H3.3 étaient plus denses dans les régions early du génome par rapport aux régions late

, Par ailleurs, le volume des clusters H3.3 est indépendant du cycle et notamment de la phase S. En revanche, la densité de ces clusters diminue au cours de la phase S. De manière opposée, le volume des clusters H3.1 dépend du cycle cellulaire, et plus particulièrement de la phase S, et leur densité augmente au cours de la phase S. Une interprétation possible de ces observations est liée au caractère réplicatif du variant H3.1, et non H3.3: H3.1 étant déposé pendant la réplication, Ce résultat est en accord avec les résultats de l'analyse génomique

J. , Je me suis d'abord placée dans un contexte censé, a priori, perturber leur recyclage pour déterminer si je pouvais détecter un défaut de recyclage avec mon système. Pour cela, j'ai traité les cellules avec de l'hydroxyurée pour infliger un stress réplicatif. Après ce traitement, j'ai mesuré moins d'histones parentales aux sites répliqués par rapport au contrôle, ce qui suggère un défaut de recyclage. J'ai ensuite voulu tester le rôle du chaperon d'histone ASF1 dans le recyclage de H3.3 et H3.1 en déplétant ASF1 par siRNA. En l'absence d'ASF1, j'ai mesuré une baisse du nombre d'histones parentales aux sites répliqués à la fois pour H3

, De manière intéressante, j'ai observé que la distribution spatiale de H3.1, mais pas H3.3, était perturbée en l'absence d'ASF1 dans les régions early

, Un défaut de recyclage des histones parentales déséquilibre le paysage des variants

, Mon travail permet ainsi de montrer l'importance du recyclage contrôlé des variants d'histone pour le maintien de l'épigénome, et ouvre la question de l'impact pour l'identité cellulaire