The nucleoplasmin (NPM) family of acidic histone chaperones and the FK506-binding (FKBP) peptidyl proline isomerases are both linked to chromatin regulation. In vertebrates, NPM and FKBP domains are found on separate proteins. In fungi, NPM-like and FKBP domains are expressed as a single polypeptide in nucleoplasmin-like FKBP (NPL-FKBP) histone chaperones. Saccharomyces cerevisiae has two NPL-FKBPs: Fpr3 and Fpr4. These paralogs are 72% similar and are clearly derived from a common ancestral gene. This suggests that they may have redundant functions. Their retention over millions of years of evolution also implies that each must contribute non-redundantly to organism fitness. The redundant and separate biological functions of these chromatin regulators have not been studied. In this dissertation I take a systems biology approach to fill this knowledge gap. First, I refine the powerful synthetic genetic array (SGA) method of annotating gene-gene interactions, making it amenable for the analyses of paralogous genes. Using these ‘paralog-SGA’ screens I define distinct genetic interactions unique to either Fpr3 or Fpr4, shared genetic interactions common to both paralogs, and masked genetic interactions which are direct evidence for processes where these enzymes are functionally redundant. I provide transcriptomic evidence that Fpr3 and Fpr4 cooperate to regulate genes involved in polyphosphate metabolism and ribosome biogenesis. I identify an important role for Fpr4 at the 5’ ends of protein coding genes and the non-transcribed spacers of ribosomal DNA. Finally, I show that yeast lacking Fpr4 exhibit a genome instability phenotype at rDNA, implying that this histone chaperone regulates chromatin structure and DNA access at this locus. Collectively, these data demonstrate that Fpr3 and Fpr4 operate separately, cooperatively and redundantly to regulate a variety of chromatin environments. This work is the first comprehensive and comparative study of NPL-FKBP chaperones and as such represents a significant contribution to our understanding of their biological functions. / Graduate

Le rôle fonctionnel des transcrits de l’hétérochromatine péricentromérique reste à ce jour largement incompris chez les eucaryotes supérieurs. Néanmoins, il a été montré que ces transcrits sont soumis à un contrôle très précis, fonction du cycle cellulaire. La régulation de la transcription est fortement contrôlée par la structure de la chromatine qui peut être modifiée localement en changeant la composition biochimique du nucléosome, notamment par l’utilisation des variantes d’histones. L’objectif de ma thèse a été de mieux comprendre le rôle de la protéine chaperonne d’histone DAXX et de sa variante d’histone H3.3 dans la régulation de la transcription des séquences répétées péricentromériques. Par la méthode de purification TAP-TAG, les partenaires spécifiques de DAXX ont été identifiés à partir d’extraits solubles nucléaires de fibroblastes embryonnaires murins. Ces analyses ont mis en évidence que CAF-1, classiquement associé à H3.1, et les facteurs de remodelage de la chromatine ATRX et CHD4 interagissent spécifiquement avec DAXX. Le rôle de ces protéines dans le contrôle de la transcription de l’hétérochromatine péricentromérique a ensuite été mis en évidence par une approche combinant l’interférence ARN et la Q-PCR. Enfin, les résultats suggèrent fortement que ces mécanismes de régulation ont lieu au niveau des corps nucléaires PML. L’ensemble de ces données montre qu’il existe une régulation spatio-temporel très fine de la structure de la chromatine régulant la transcription de l’hétérochromatine péricentromérique. / The functional role of pericentromeric heterochromatin transcripts remains largely unknown in higher eukaryotes. Nevertheless, it has been shown that these transcripts are subject to very precise control, depending on the cell cycle. Regulation of transcription is tightly controlled by chromatin structure that can be modified locally by changing the biochemical composition of the nucleosome, including the use of histone variants. The aim of my thesis was to better understand the role of the histone chaperone protein DAXX and its histone variant H3.3 in the regulation of transcription of pericentromeric repeats. By the method of TAP-TAG purification, DAXX specific partners were identified from soluble nuclear extracts of murine embryonic fibroblasts. These analyzes revealed that CAF-1, classically associated with H3.1, and the chromatin remodeling factors, ATRX and CHD4, specifically interact with DAXX. The role of these proteins in the control of transcription of pericentromeric heterochromatin was then highlighted by an approach combining RNAi and Q-PCR. Finally, the results strongly suggest that these regulatory mechanisms take place at PML nuclear bodies. Taken together, these data show that there is a spatio-temporal regulation of the fine structure of chromatin regulates transcription of pericentromeric heterochromatin.