Author ORCID Identifier

0000-0001-6203-5725

Date of Graduation

5-2017

Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Jessica Tyler

Committee Member

Bin Wang

Committee Member

Xiaobing Shi

Committee Member

Grzegorz Ira

Committee Member

Nayun Kim

Committee Member

Jessica Tyler

Abstract

Inaccurate repair of DNA double-strand breaks (DSBs) can lead to DNA mutation and chromosome rearrangements, causing human diseases such as cancer. Although we know the basic mechanisms of DSB repair, the added complexities in the chromatin context are unclear. This is partially due to the lack of unbiased systems for identifying proteins and post-translational modifications (PTMs) involved in DSB repair. In this work, we established a novel method, termed DSB-ChAP-MS (Double Strand Break-Chromatin Affinity Purification with Mass Spectrometry), for the affinity purification of a sequence-specific single copy endogenous chromosomal locus containing a DSB, followed by the proteomic identification of enriched proteins and histone PTMs. Providing validation of the DSB-ChAP-MS approach, we found many histone PTMs that had been previously implicated in the DNA damage response, as well as multiple new histone PTMs enriched on chromatin bearing a DSB from budding yeast. One of these, methylation of histone H3 on lysine 125, has not previously been reported. Among the novel proteins enriched at a DSB were the phosphatase Sit4, the RNA pol II degradation factor Def1, the mRNA export protein Yra1 and the HECT E3 ligase Tom1. Each of these proteins was required for resistance to radiomimetics. Yra1 and Def1 were required for DSB repair per se, while Sit4 was required for rapid inactivation of the DNA damage checkpoint after DSB repair. Thus, our unbiased proteomics approach has led to the unexpected discovery of novel roles for these and other proteins in the DNA damage response.

Keywords

DSB, PTM, Affinity Purification, Mass Spectrometry, Yeast, DNA repair, Checkpoint

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