Histone H1, or linker histone, are unique histones that bind to the nucleosome to facilitate higher order chromatin structure. The linker histones, when compared to the core histones that make up the nucleosome, are poorly understood especially in plants. Linker histones are vital for plant development as well as for cell cycle regulation, sharing many qualities with animal linker histones. In this report, the first two parts introduce the current literature of H1, including result from non-plant systems, and the third section is a research proposal describing a research project to elucidate the roles of linker histones on the regulation of FLOWERING LOCUS C (FLC) in Arabidopsis thaliana. / text

Comprendre la structure et l’organisation de la chromatine est une question fondamentale dans le domaine de la régulation de l’expression des gènes. La cristallographie par rayons-X et d’autres techniques biophysiques on permit de comprendre la structure du nucléosome avec une précision quasi atomique. Malgré de nombreuses études, les données structurelles au delà de la particule de cœur nucléosomale (NCP) demeurent imprécises. Au cours des dernières décennies plusieurs tentatives ont été faites pour montrer comment l’histone de liaison H1 interagit avec les particules nucléosomales pour les condenser en fibre de chromatine. Ces études ont mené à différents modèle décrivant la position de l’histone de liaison H1 sur la chromatine. De récentes avancées sur l’histone de liaison H1 suggèrent que le domaine globulaire de H1 (GH1) et la partie C-terminale interagit avec la dyade du nucléosome et les 2 bouts d’ADN de liaison (modèle à 3 contacts) qui sont contraintes de former une structure en tige. Cependant, la conformation et la position précise de l’histone de liaison H1 reste inconnues et la controverse à ce sujet persiste.Dans cette étude, nous avons déterminé la structure tridimensionnelle de nucléosomes contenant H1 par des techniques de cryo-microscopie électronique (cryo-EM) et de diffraction aux rayons-X dans des cristaux. Nous avons utilisé le chaperons d’histone, NAP1, pour déposer l’histone de liaison H1 sur les nucléosomes reconstitué à partir des histones de cœur recombinant et la séquence d’ADN positionnante 601 de 197 paires de bases (dite de Widom). Nos résultats de cryo-EM montrent que l’association de H1 compacte le nucléosome en réduisant la mobilité des ADNs et stabilisant ainsi les contacts entre les nucléotides précédant la sortie NCP et l’octamer d’histones. Nos résultats par diffusion de rayon-x dans des cristaux à une résolution de 7Ä montrent que la partie globulaire de H1 (GH1) est située sur la dyade et interagie simultanément avec les petits sillons de l’ADN à la dyade et les ADN de liaison à l’entrée et à la sortie du nucléosome. Les parties N- et C-terminales de H1 sont orientées vers l’extérieur du cœur du nucléosome à travers les différents ADN de liaison. Nous avons validé l’orientation de GH1 par des expériences de pontages ADN-proteine, après substitutions de cystéine par mutagénèse dirigée, empreinte par radicaux hydroxyles et « amarrage moléculaire ». Nos résultats révèlent l’effet de H1 sur la dynamique du nucléosome et apporte une vision détaillé de la conformation du « stem du nucléosome » lors de l’incorporation de H1.Nous avons également étudié l’association spécifique du facteur de transcription Sox6 à ces de reconnaissance consensus présent à l’intérieur du nucléosome, associé ou non avec l’histone de liaison H1 par une empreinte biphotonique avec laser UV. Nos résultats montrent que le domaine HMG de Sox6 se fixe spécifiquement sur son motif consensus situé profondément à l’intérieur du nucléosome à l’exception sur la dyade. Cette association n’est pas influencée par la « fermeture » des ADN de liaison avec l’histone H1 démontrant l’existence d’un autre façon de reconnaissance que le modèle de Widom basés sur fluctuations thermodynamiques des ADN de liaison. Le résultat que Sox6 est capable de surmonter la barrière nucléosomale (avec ou sans H1) suggère fortement que les facteurs de transcription de la famille Sox, de domaine de liaison de type HMG, jouent le rôle de facteurs « pionnier » dans la régulation de la transcription et en particulier dans l’initiation de la différentiation. / Understanding the structural organization of chromatin is a fundamental issue in the field of gene regulation. X-ray crystallography and other biophysical techniques have enabled understanding of the nucleosome structure nearly at atomic precision. Despite numerous studies, the structural information beyond the nucleosome core particle (NCP) remains elusive. Over the last few decades several attempts have been made to reveal how the linker histone H1 interacts with the nucleosome particles and condenses them into a chromatin fiber. These studies have led to different models describing the position of linker histone H1 on chromatin. Recent advancements in linker histone H1 studies suggest that globular domain of histone H1 (GH1) interacts with the nucleosomal dyad and its C-terminal domain interacts with the linker DNA forming a stem like structure. However, the precise conformation of linker histone H1 and position of other domains still remains unknown.In this study, we resolved the three-dimensional structure of H1-containing nucleosomes by using cryo-electron microscopy (cryo-EM) and X-ray crystallography. We have used the chaperone NAP-1 to deposit linker histone H1 onto nucleosomes reconstituted from recombinant core histones and 197 base-pair of 601 strong nucleosome positioning DNA sequence. Our cryo-EM results showed that association of H1 gives a more compact appearance of the nucleosome as it restricts the mobility of the two linker DNAs keeping them in close proximity and thereby stabilizing contacts between the histone core and nucleotides preceding NCP exit. Our X-ray crystallography results at 7 Ä resolution reveal that the globular domain of histone H1 (GH1) is positioned onto the nucleosome pseudodyad and recognizes the nucleosome core and both linker arms by contacting the DNA backbone in the minor groove. The N- and C-terminal domains of H1 are oriented away from the nucleosome core towards different DNA linkers. We further validated the orientation of GH1 by cross-linking experiments followed after cysteine substitutions mutagenesis, hydroxyl radical footprinting and by molecular docking. Our results reveal the effect of H1 on nucleosome dynamics and also provide a detailed view of the nucleosome stem conformation upon H1 incorporation.We also studyed the nucleosome accessibility of transcription factor Sox6 and the impact of linker histone H1 incorporation to Sox6 binding on nucleosome by using UV laser biphotonic footprinting. Our results reveal that Sox6 HMG domain binds specifically to its consensus binding located deep inside of the nucleosomal DNA, but not at the nucleosomal dyad. Our in vitro footprinting results reveal that the “locking” of DNA linkers by incorporation of histone H1 on nucleosome does not show any impact on Sox6 HMG domain binding, evidencing an alternative to the Widom model based on thermal fluctuation “opening” of the nucleosome at the linkers.. The finding that Sox6 is able to overcome nucleosome (chromatosome) barrier in presence or absence of H1, strongly suggest that the HMG domain - based Sox family proteins it can act as a pioneer factor in transcription regulation, in particular in initiation of cell differentiation.

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Methyl-CpG binding protein 2 (MeCP2) and histone H1 are important chromatin associated proteins. Both exhibit their own extent of complexity as MeCP2 is an intrinsically disordered protein (IDP) that interacts with many different partners involved in several cellular processes and histone H1 consists of 11 different subtypes each of them associated with different posttranslational modifications (PTMs). An interesting avenue for the study of these proteins is in neurons where MeCP2 is very abundant and histone H1 level is half that observed in other somatic tissues. Several reports in the past have proposed that this lower level of histone H1 is due to the abundance of MeCP2 which displaces histone H1. However, this hypothesis has been debated and there is no clear consensus. In an attempt to study this controversy, a cell model system ReNCell WT and MeCP2-KO was used that can be induced to differentiate into neurons. The protein levels, transcript levels and localization of histone H1 subtypes in these cells were analyzed using HPLC, RT-qPCR and immunofluorescence, respectively. The results show that ReNCell WT and MeCP2-KO do not exhibit significant differences in their relative amount of histone H1 protein and transcript level neither at the proliferative nor at the later differentiated stages. However, HPLC analyses show that the histone H1 subtypes of these two cell types exhibit significant elution differences probably resulting from differences in their PTM content. Immunofluorescence analyses show that WT ReNCell differentiation as determined by extension of dendritic or axonic processes can be seen to occur over the course of one week and there is a significant difference in the nuclear area of these two cells at 8 DIV. This study provides important preliminary data for future research in MeCP2 and histone H1 using this cell model system and show that MeCP2 may have a bearing on histone H1 PTMs. / Graduate

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Linker histone H1 plays a key role in facilitating folding of higher order chromatin structure. Previous studies have shown that deletion of three somatic H1 subtypes together leads to embryonic lethality and that H1c/H1d/H1e triple knockout (TKO) embryonic stem cells (ESCs) display bulk chromatin decompaction. Following this initial work, we investigated the role of H1 and chromatin compaction in stem cell pluripotency and differentiation, as well as the regulation of Hox genes expression. We find that H1 TKO ESCs are more resistant to spontaneous differentiation, impaired in embryoid body differentiation, and largely blocked in neural differentiation. We present evidence that H1 contributes to efficient repression of the expression of pluripotency factors, Oct4 and Nanog, and participates in establishment and maintenance of DNA methylation and histone modification necessary for silencing pluripotency genes during stem cell differentiation and embryogenesis. In addition, we find reduced expression of a distinct set of Hox genes in embryos and ESCs, respectively. Furthermore, by characterizing H1c−/−; H1d−/−; and H1e−/− single-H1 null ESCs established in this study, we showed that individual H1 subtypes regulated specific Hox genes in ESCs. Finally, we demonstrate that the levels of H3K4me3 were significantly diminished at the affected Hox genes in H1 TKO- and single-H1 KO- ESCs, whereas H3K27me3 occupancy is modestly increased at specific Hox genes. Our results suggest that marked reduction of H1 levels and decondensation of bulk chromatin affect the expression of pluripotency genes and Hox genes in embryos and ESCs, which may be in part mediated through establishment and maintenance of epigenetic marks.

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Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.