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Eukaryotic genomes are assembled into a complex of DNA and proteins known as chromatin. The packaging of DNA into chromatin is the foundational strategy that cells use to both compress genomic DNA into nuclei and regulate access to its contents. The basic repeating subunit of chromatin is the nucleosome, composed of an octamer of two copies of each of the core histone proteins H2A, H2B, H3, and H4 around which 146 bp of DNA are tightly wrapped. While the compaction of genomes into chromatin offers cells significant advantages, it also presents serious challenges to fundamental processes that maintain genome integrity, including DNA repair and replication. Nucleosomes must be disrupted to allow access to damaged DNA by repair factors. Additionally, the millions of nucleosomes that package genomic DNA are displaced during DNA replication. After their displacement, nucleosomes must be faithfully restored to preserve proper chromatin compaction and regulation of access to DNA that underlie transcriptional programs and cellular identity. Thus, the processes that maintain genome and epigenome stability are intricately linked. In the first aim of this dissertation, I examined the role of the conserved SWI/SNF ATP-dependent nucleosome remodeler in the repair of DNA double-strand breaks (DSBs) in yeast. I demonstrated that SWI/SNF facilitates the actions of the MRX complex at the DSB, including the eviction of KU, initiation of DNA end resection, recruitment of long-range resection factors, and activation of the DNA damage response. Furthermore, I showed that this activity of SWI/SNF is related to its role in the efficient eviction of nucleosomes near a DSB. This study contributes to an understanding of the roles of the clinically relevant SWI/SNF complex in mediating accurate repair of DSBs in the context of chromatin. In the second aim, I examined the role of DNA Ligase I (Lig1) in coordinating chromatin assembly and maturation on newly replicated DNA i

Eukaryotic genomes are assembled into a complex of DNA and proteins known as chromatin. The packaging of DNA into chromatin is the foundational strategy that cells use to both compress genomic DNA into nuclei and regulate access to its contents. The basic repeating subunit of chromatin is the nucleosome, composed of an octamer of two copies of each of the core histone proteins H2A, H2B, H3, and H4 around which 146 bp of DNA are tightly wrapped. While the compaction of genomes into chromatin offers cells significant advantages, it also presents serious challenges to fundamental processes that maintain genome integrity, including DNA repair and replication. Nucleosomes must be disrupted to allow access to damaged DNA by repair factors. Additionally, the millions of nucleosomes that package genomic DNA are displaced during DNA replication. After their displacement, nucleosomes must be faithfully restored to preserve proper chromatin compaction and regulation of access to DNA that underlie transcriptional programs and cellular identity. Thus, the processes that maintain genome and epigenome stability are intricately linked. In the first aim of this dissertation, I examined the role of the conserved SWI/SNF ATP-dependent nucleosome remodeler in the repair of DNA double-strand breaks (DSBs) in yeast. I demonstrated that SWI/SNF facilitates the actions of the MRX complex at the DSB, including the eviction of KU, initiation of DNA end resection, recruitment of long-range resection factors, and activation of the DNA damage response. Furthermore, I showed that this activity of SWI/SNF is related to its role in the efficient eviction of nucleosomes near a DSB. This study contributes to an understanding of the roles of the clinically relevant SWI/SNF complex in mediating accurate repair of DSBs in the context of chromatin. In the second aim, I examined the role of DNA Ligase I (Lig1) in coordinating chromatin assembly and maturation on newly replicated DNA i