Accelerated Adaptation through Stimulated Copy Number Variation in Saccharomyces cerevisiae Ryan Matthew Hull Repetitive regions of the genome, such as the centromeres, telomeres and ribosomal DNA account for a large proportion of the genetic variation between individuals. Differences in the number of repeat sequences between individuals is termed copy number variation (CNV) and is rife across eukaryotic genomes. CNV is of clinical importance as it has been implicated in many human disorders, in particularly cancers where is has been associated with tumour growth and drug resistance. The copper-resistance gene CUP1 in Saccharomyces cerevisiae is one such CNV gene. CUP1 is transcribed from a copper inducible promoter and encodes a protein involved in copper detoxification. In this work I show that yeast can regulate their repeat levels of the CUP1 gene through a transcriptionally stimulated CNV mechanism, as a direct adaptation response to a hostile environment. I characterise the requirement of the epigenetic mark Histone H3 Lysine 56 acetylation (H3K56ac) for stimulated CNV and its limitation of only working at actively transcribed genes. Based upon my findings, I propose a model for how stimulated CNV is regulated in yeast and show how we can pharmacologically manipulate this mechanism using drugs, like nicotinamide and rapamycin, to stimulate and repress a cell's ability to adapt to its environment. I further show that the model is not limited to high-copy CUP1 repeat arrays, but is also applicable to low-copy systems. Finally, I show that the model extends to other genetic loci in response to different challenging environments, such as formaldehyde stimulation of the formaldehyde-resistance gene SFA1. To the best of our knowledge, this is the first example of any eukaryotic cell undergoing genome optimisation as a novel means to accelerate its adaptation in direct response to its environment. If conserved in higher eukaryotes, such a mechanism could have major implications in how we consider and treat disorders associated with changes in CNV.

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Chez la levure Saccharomyces cerevisiae, l’acétylation de l’histone H3 sur la Lysine 56 (H3K56ac) a lieu sur toutes les histones H3 nouvellement synthétisées qui sont déposées derrière les fourches de réplication. L’acétylation de H3K56 joue un rôle primordial dans l’assemblage de l’ADN lors la réplication et la réparation. L’acétylation de H3K56 joue également un rôle important dans la stabilité génomique et la stabilisation des fourches de réplication bloquée. En effet, les cellules dépourvues de H3K56ac sont sensibles au méthane sulfonate de méthyle (MMS) et à d’autres agents génotoxiques qui causent du stress réplicatif. Notre projet visait à investiguer les liens entre la protéine du réplisome Ctf4 et l’acétyltransférase d’histone Rtt109. Dans un premier lieu, la délétion de CTF4 a partiellement contré la sensibilité des cellules rtt109Δ au MMS. Notre analyse génétique a aussi montré que Ctf4, Rtt109, et le complexe Rtt101-Mms1-Mms22 agissent dans la même voie de réponse face à un stress réplicative. Nos résultats montrent que les cellules ctf4Δ et rtt109Δ présentent des foyers intenses du complexe de liaison à l'ADN simple-brin RPA en réponse au stress réplicatif, suggérant la formation excessive de régions d'ADN simple-brin aux fourches de réplication bloquées, ce qui conduit à une hyper activation des points de contrôle des dommages à l'ADN. Ces mutants présentent des ponts anaphase et des foyers persistants des protéines de recombinaison homologues Rad51 et Rad52 en réponse aux génotoxines, suggérant ainsi que la structure anormale des réplisomes bloqués peut compromettre leur récupération. Nos résultats indiquent également que la délétion des gènes de la RH (RAD51, RAD52, RAD54, RAD55 et MUS81) avec ctf4Δ et rtt109Δ respectivement, engendre une sensibilité synergique au MMS, suggérant que les cellules qui sont déficientes en H3K56 acétylation utilisent la RH pour réparer les dommages causés suite à un stress réplicatif. En conclusion, nos résultats suggèrent que les cellules déficientes en H3K56ac présentent des défauts de RH en réponse aux dommages à l’ADN induits par le MMS durant la phase S. / In Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56ac) occurs on all newly synthesized histones H3 that are deposited behind DNA replication forks. H3K56ac plays critical role in chromatin assembly during DNA replication and repair. H3K56ac is also required for genome stability and stabilization of stalled replication fork. Cells lacking H3K56ac are sensitive to methyl methane sulfonate and other drugs that cause replicative stress. In this thesis, we investigated the links between the replisome protein Ctf4 and the H3K56 acetyltransferase Rtt109. Deletion of CTF4 partially rescued the sensitivity of rtt109Δ cells to methyl methane sulfonate. Genetic analyses also showed that Ctf4, Rtt109, and the Rtt101-Mms1-Mms22 complex act in the same pathway to response to replicative stress. ctf4Δ and rtt109Δ cells displayed intense foci of the single-stranded DNA binding complex RPA during replicative stress, suggesting formation of excess single-stranded DNA regions at stalled replication forks, leading to hyper activation of DNA damage checkpoints. These mutants accumulated anaphase bridges and persistent foci of the homologous recombination proteins Rad51 and Rad52 in response to genotoxins, suggesting that abnormal DNA structure formed at stalled replisome may compromise their recovery. Deletion of HR genes (RAD51, RAD52, RAD54, RAD55 and MUS81) together with ctf4Δ and rtt109Δ presents synergistic sensitivity to MMS, suggesting that H3K56ac deficient cells use HR to repair the damages caused by replicative stress. Overall our results demonstrate that H3K56ac deficient cells cannot recover MMS- induced damages because HR is compromised in these mutants.