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Dissecting functions for the histone acetyltransferase Esa1 through suppression analysis


Posttranslational histone modifications contribute to chromatin-dependent processes such as transcriptional regulation and repair of DNA damage. Catalysis of these modifications is carried out by complexes that function in both targeting activities to specific genes and in regulating genome-wide levels of modifications. One form of histone modification is dynamic and reversible acetylation and deacetylation of lysines. In Saccharomyces cerevisiae, Esa1 is an essential histone acetyltransferase that belongs to the conserved MYST family. Esa1 is the catalytic subunit of two chromatin modifying complexes with key roles in transcriptional regulation and DNA repair. In this thesis, three different genetic suppressors of esa1 were identified and characterized, connecting the diverse nuclear functions of Esa1 with multiple cellular processes. NAB3 encodes an RNA binding protein that processes 3'-ends of non-polyadenylated transcripts. Overexpression of NAB3 suppressed the temperature-sensitivity of an esa1 mutant and its defects in rDNA and telomeric silencing. Nab3 was discovered to function in transcriptional silencing at the rDNA locus, cell cycle progression, and DNA damage repair. These are all processes in which Esa1 participates, providing evidence that RNA processing by Nab3 is functionally linked to acetylation by Esa1. Other genetic studies identified two closely-related histone deacetylases, Rpd3 and Hos2, that coordinate with Esa1 in its different functions. The first of these two studies demonstrates that Esa1 and Rpd3 coordinate acetylation of H4 lysine 12 (H4K12) to promote cell viability. RPD3, when deleted, suppressed mutant phenotypes of esa1 including temperature -sensitivity and silencing defects. In particular, growth rescue of esa1 by rpd3 depended specifically on H4K12 acetylation, defining a crucial yet previously unsuspected role for this residue. Notably, of the two biochemically defined Rpd3 complexes, it was Rpd3L that mediated suppression, providing a new distinction from the smaller Rpd3S complex. In contrast to RPD3, deletion of HOS2 suppressed esa1's sensitivity to DNA damaging agents. Initial characterization thus indicates that Esa1 partners with Hos2, and not Rpd3, in response to DNA damage. The work presented in this thesis applies the powerful tool of genetic suppression to important questions about biological roles for chromatin modifying enzymes

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