Cockayne syndrome (CS) is a rare, segmental premature aging disorder in which the majority of cases are caused by mutations in the Cockayne syndrome group B protein (CSB). CSB is a multifunctional protein implicated in DNA repair, transcription and chromatin remodeling. The results presented here demonstrate that CSB plays an important role in telomere maintenance and DSB repair. We find that CS cells accumulate telomere doublets, have increased telomere-bound TRF1, decreased TERRA levels and a defect in telomerase-dependent telomere lengthening. These results imply that CS patients may be defective in telomere maintenance. We also uncover a novel and important role of CSB in DNA DSB repair. We show that CSB facilitates HR and supresses NHEJ during S and G2 phase. We find that CSB interacts with RIF1 and is recruited by RIF1 to DSBs in S phase. At DSBs, CSB remodels the chromatin extensively, which in turn limits RIF1 recruitment and promotes BRCA1 accumulation. The chromatin remodeling activity of CSB requires not only damage-induced phosphorylation on S10 by ATM but also cell cycle-dependent phosphorylation of S158 by cyclin A-CDK2. Both modifications are needed for the intramolecular interaction of CSB N-terminal domain with its ATPase domain. This intramolecular interaction has previously been reported to regulate the ATPase activity of CSB. Taken together, these results suggest that ATM and CDK2 control of CSB to promote chromatin remodeling, which in turn inhibits RIF1 in DNA DSB repair pathway choice. / Thesis / Doctor of Philosophy (PhD)

The Mre11/Rad50 complex has been implicated in the early steps of DNA double-strand break (DSB) repair through homologous recombination in several organisms. However, the enzymatic properties of this complex are incompatible with the generation of 3’ single-stranded DNA for recombinase loading and strand exchange. In thermophilic Archaea, the mre11 and rad50 genes cluster in an operon with genes encoding a bidirectional DNA helicase, HerA, and a 5’ to 3’ exonuclease, NurA, suggesting these four enzymes function in a common pathway. I show that purified Mre11 and Rad50 from Pyrococcus furiosus act cooperatively with HerA and NurA to resect the 5’ strand at a DNA end under physiological conditions in vitro where HerA and NurA alone do not show detectable activity. Furthermore, I demonstrate that HerA and NurA physically interact, and this interaction stimulates both helicase and nuclease activities. The products of HerA/NurA long-range resection are oligonucleotide products and HerA/NurA activity demonstrates both sequence specificity and a preference to cut at a specific distance from the DNA end. I demonstrate a novel activity of Mre11/Rad50 to make an endonucleolytic cut on the 5’ strand, which is consistent with a role for the Mre11 nuclease in the removal of 5’ protein conjugates. I also show that Mre11/Rad50 stimulates HerA/NurA-mediated resection through two different mechanisms. The first involves an initial Mre11 nucleolytic processing event of the DNA to generate a 3’ ssDNA overhang, which is then resected by HerA/NurA in the absence of Mre11/Rad50. The second mechanism likely involves local unwinding of the DNA end in a process dependent on Rad50 ATPase activity. I propose that this unwinding step facilitates binding of HerA/NurA to the DNA end and efficient resection of the break. Furthermore, the binding affinity of NurA for 3’ overhang and unwound DNA end substrates partially explains the efficiency of the two resection mechanisms. Lastly, 3’ single-stranded DNA generated by these enzymes can be used by the Archaeal RecA homolog RadA to catalyze strand exchange. This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in Archaea, and may serve as a model for DSB processing in eukaryotes. / text

Les cassures Double-brin de l'ADN (DSBs) sont une menace majeure pour la stabilité du génome. Afin de se protéger des effets délétères de ces dommages, les cellules activent une voie de réponse aux cassures double-brins (DDR) qui comprend des évènements qui conduisent à la reconnaissance et à la réparation de ces cassures ainsi qu'à un délai du cycle cellulaire. Cette DDR repose largement sur 2 membres de la famille des PI3K-like kinase, ataxia telangiectasia mutated (ATM) et DNA Protein Kinase (DNAPK) dont les fonctions respectives lors de la réparation restent controversées. Grâce à l'utilisation d'une lignée cellulaire contenant l'enzyme de restriction AsiSI combinée à de la cartographie par ChIP-chip, de l'analyse de la réparation de cassures séquence-spécifique ainsi qu'à de la microscopie haute résolution, j'ai pu, au cours de ma thèse mettre en évidence que aussi bien ATM que DNAPK sont recrutées sur une région confinée autour des DSBs. Cependant, une fois recrutées, elles présentent des fonctions non-redondantes que ce soit pour la ligation des cassures ou pour l'établissement des domaines yH2AX. Concernant la réparation, DNAPK est absolument requise pour la ligation des extrémités de la cassure alors que ATM est dispensable mais promeut la fidélité. En revanche, ATM est la principale kinase requise pour l'établissement des domaines yH2AX et ce quelque soit la cassure. J'ai aussi pu mettre en évidence le fait que plusieurs cassures induites par AsiSI sont capables de se regrouper au sein d'un "foyer de réparation" et ce de manière dépendante d'ATM et indépendante de DNAPK. Cette étude éclaircit les rôles respectifs des kinases ATM et DNAPK que ce soit pour la ligation des extrémités ou l'établissement des domaines yH2AX. Enfin elle a permis de mettre en évidence un nouveau rôle d'ATM dans l'organisation spatiale de la réparation et plus précisemment dans le regroupement de plusieurs DSBs au sein de "foyers de réparation" afin d'être réparées. / DNA Double Strand Breaks (DSBs) form a major threat to the genome stability. To circumvent the deleterious effects of DSBs, cells activate the DNA damage response (DDR), which comprises events that lead to detection and repair of these lesions, as well as a delay in cell cycle progression. This DDR largely rely on two members of the PI3K-like kinase family : ataxia telangiectasia mutated (ATM) and DNA Protein Kinase (DNAPK), whose respective functions during the DDR remains controversial. Using a cell line, expressing the AsiSI restriction enzyme, combined with high resolution ChIP-chip mapping, sequence-specific DSB repair kinetics analysis and advanced high resolution microscopy, we uncovered that both ATM and DNA-PK are recruited to a confined region surrounding DSBs. However, once present at the DSB site, they exhibit non-overlapping functions on end-joining and yH2AX domain establishment. At the repair level, DNAPK is absolutely required for end-joining while ATM is dispensable although promoting repair fidelity. By contrast, ATM is the main kinase required for the establishment of the histone mark yH2AX at all breaks. We also clearly demonstrated that multiple AsiSI-induced DSBs are able to associate within "repair foci", in a manner that strictly depends on ATM, but not DNAPK, activity. Our study shed light on the respective roles of ATM and DNAPK regarding end joining and yH2AX domain establishment. Lastly it allowed us to uncover a function of ATM in the spatial organisation of the repair, more precisely in the clustering of multiple breaks within "repair foci" in order to be repaired.

The amino acid proline is unique – within a polypeptide chain, proline adopts either a cis or trans peptide bond conformation while all other amino acids are sterically bound primarily in the trans configuration. In proteins, the isomeric state of a single proline can have dramatic consequences on structure and function. Consequently, cis-trans interconversion confers both barrier and opportunity – on one hand, isomerization is a rate limiting step in de novo protein folding and on the other can be utilized as a post-translational regulatory switch. Peptidyl-prolyl isomerases (PPIs) are a ubiquitous superfamily that catalyzes the interconversion between conformers. Although pervasive, the functions and substrates of most PPIs are unknown. The two largest subfamilies, FKBPs and cyclophilins, are the intracellular receptors of clinically relevant immunosuppressant drugs that also show promise in the treatment of neurodegenerative disorders and cancer. Therefore, narrowing the knowledge gap has significant potential to benefit human health. FKBP25 is a high-affinity binder of the PPI inhibitor rapamycin and is one of few nuclear-localized isomerases. While it has been shown to bind DNA and associate with chromatin, its function has remained largely uncharacterized. I hypothesized that FKBP25 targets prolines in nuclear proteins to regulate chromatin-templated processes. To explore this, I performed high-throughput transcriptomic and proteomic studies followed by detailed molecular characterizations of FKBP25’s function. Here, I discover that FKBP25 is a multifunctional protein required for the maintenance of genomic stability. In Chapter 2, I characterize the unique N-terminal Basic Tilted Helical Bundle (BTHB) domain of FKBP25 as a novel dsRNA binding module that recruits FKBP25’s prolyl isomerase activity to pre-ribosomal particles in the nucleolus. In Chapter 3, I show for the first time that FKBP25 associates with the mitotic spindle apparatus and acts to stabilize the microtubule cytoskeleton. In this chapter, I also present evidence that this function influences the stress response, cell cycle, and chromosomal stability. Additionally, I characterize the regulation of FKBP25’s localization and nucleic acid binding activity throughout the cell cycle. Finally, in Chapter 4, I uncover a role for FKBP25 in the repair of DNA double-stranded breaks. Importantly, this function requires FKBP25’s catalytic activity, identifying for the first time a functional requirement for cis-trans prolyl isomerization by FKBP25. Collectively, this work identifies FBKP25 as a multifunctional protein that is required for the maintenance of genomic stability. The knowledge gained contributes to the exploration of PPIs as important drug targets. / Graduate

Deinococcus radiodurans est une bactérie à gram-positive connue pour son extrême résistance à une grande variété d'agents endommageant l'ADN. Parmi ces derniers, les rayonnements ionisants et la dessiccation sont les plus nocifs pour la cellule, car ils introduisent des cassures dans le génome. Les cassures double brin (CDB) sont particulièrement dangereuses et doivent être réparées de façon très efficace, afin d'éviter l'apparition de mutations pouvant mener à la mort de la cellule ou de l'organisme. La recombinaison homologue (RH) est le mécanisme le plus efficace pour la réparation des CDBs. D. radiodurans est capable de restaurer entièrement son génome en à peine 3 heures, et elle accomplit la totalité du processus par la voie RecFOR. Afin d'être réparées, les CDBs doivent d'abord être reconnu. Cette étape importante, qui a lieu peu de temps après l'apparition du dommage dans la cellule, implique la protéine RecN. RecN est recrutée dès les premières étapes de la réparation de l'ADN et des études in vivo ont démontré qu'elle avait tendance à se localiser dans des foyers discrets. Des études in vitro suggèrent également que RecN favorise l'assemblage de fragments d'ADN, une fonction décrite précédemment pour les protéines SMC (telle que cohesin), qui sont structurellement similaires à RecN. De nombreuses études structurales ont été effectuées sur la protéine de type SMC, Rad50, alors qu'à présent aucune information structurale n'est disponible pour RecN. Le travail présenté ici a porté sur la caractérisation structurale de RecN et de ses domaines. Nous avons obtenu les structures cristallines de trois constructions (se chevauchant partiellement) de RecN et une étude de diffusions des rayons X aux petits angles a été effectuée sur les domaines séparés de RecN et sur la protéine entière. Les données obtenues en solution ont complété notre étude cristallographique et nous ont permis de construire un modèle atomique de la protéine entière. Des mutations ont été conçues et les protéines mutées ont été produites et utilisées pour la caractérisation de l'activité d'hydrolyse de l'ATP caractéristique de cette famille de protéines. Des études biochimiques approfondies ont été effectuées sur les différentes constructions et mutants de RecN afin de déterminer le rôle de chacun des ses domaines. Nos résultat nous ont permis de proposer un modèle qui explique comment RecN reconnaît les CDB, maintient les deux extrémités de l'ADN, et prépare l'ADN pour la réparation par les protéines RecFOR. / Deinococcus radiodurans is a Gram-positive bacterium known for its extreme resistance to a broad variety of DNA damaging agents. Among these, Ionizing Radiations and desiccation are the most harmful for the cell, since they introduce breaks in the genome. Double Strand Breaks (DSB) are particularly hazardous for the cell and they need to be repaired very efficiently, in order to avoid mutations leading to altered, if not lethal, phenotypes. Homologous Recombination (HR) is the most efficient mechanism by which DSBs are repaired. D. radiodurans is able to completely restore its genome in only 3 hours, and it accomplishes the entire process through the RecFOR pathway. In order to be repaired, DSBs first need to be recognized. The protein believed to be responsible for this important step that takes place soon after the damage occurs in the cell, is RecN. RecN is recruited at the early stages of DNA repair and in vivo studies have demonstrated its propensity to localize to discrete foci. In vitro studies also suggest that RecN possesses a DNA end-joining activity previously observed for SMC proteins (such as cohesin), which are structurally related to RecN. Several structural studies have been carried out on the SMC-like protein, Rad50, but so far no structural information is available for RecN. The work presented here focused on the structural characterization of RecN and its constitutive domains. We obtained crystal structures of three partially overlapping constructs of RecN and Small Angle X-ray Scattering was performed on the individual domains and the full-length protein. The study of RecN in solution complemented our crystallographic study and enabled us to build a reliable, atomic model of the full-length protein. Mutations were designed and the mutant RecN proteins were produced in order to characterize the ATP hydrolysis activity of RecN, which is a conserved feature of this family of proteins. Extensive biochemical studies were carried out on wild-type and mutants of both the full-length protein and the single domains, in order to determine the role and function of each of the domains. Our results led us to propose a model for how RecN might recognize DSBs, tether two broken DNA ends and prepare the DNA for subsequent repair by the RecFOR machinery.

京都大学 / 0048 / 新制・課程博士 / 博士(医科学) / 甲第22700号 / 医科博第115号 / 新制||医科||8(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 遊佐 宏介, 教授 近藤 玄, 教授 齊藤 博英 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19401号 / 医博第4052号 / 新制||医||1012(附属図書館) / 32426 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙田 穣, 教授 平岡 眞寛, 教授 松本 智裕 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム / 京都大学 / 新制・課程博士 / 博士(医学) / 甲第24520号 / 医博第4962号 / 新制||医||1065(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 生田 宏一, 教授 万代 昌紀, 教授 松田 文彦 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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