STUDY OF EXO1-DEPENDENT AND EXO1-INDEPENDENT MISMATCH REPAIR MECHANISMS IN HETEROCHROMATIN AND EUCHROMATIN

Author

Basanta Krishna Dahal, Southern Illinois University CarbondaleFollow

Date of Award

8-1-2019

Degree Name

Doctor of Philosophy

Department

Molecular Biology, Microbiology and Biochemistry

First Advisor

Kadyrov, Farid

Abstract

DNA mismatch repair (MMR) is an important intracellular mechanism that corrects DNA mismatches generated during DNA replication. If left uncorrected, DNA mismatches are fixed as mutations in the next round of DNA replication. Thus, MMR significantly reduces the level of spontaneous mutations in genome. MMR deficiency is associated with the initiation and development of Lynch syndrome and many sporadic cancers. Mutations that predispose human to such cancers are produced in the chromatin environment. So, understanding the relationship between MMR and chromatin environment is important. Involvement of MMR in the maintenance of genomic stability at euchromatin has been extensively studied. However, involvement of MMR at heterochromatin is not well understood although heterochromatin constitutes a significant portion of nuclear DNA. In this study, we utilized genetic approaches to show that MMR is involved in the maintenance of heterochromatic DNA stability. Our study in Saccharomyces cerevisiae demonstrates that the major MMR proteins MutSα, MutLα, MutSβ and Exo1 are involved in MMR at heterochromatin. Interestingly, the repair of base-base mismatches is less efficient at heterochromatin compared to euchromatin. Like MMR at euchromatin, MMR at heterochromatin cooperates with reversible H3K56 acetylation and replicative polymerases in protection of DNA replication fidelity. Additionally, Exo1-independent MMR at heterochromatin frequently leads to the formation of Pol ζ-dependent mutations, which indicates that Exo1-independent MMR at heterochromatin is an error-prone process. Further analysis of Exo1-independent MMR at euchromatin provides additional evidence that the Exo1-independent MMR is error-prone in the chromatin environment. We also investigated the impact of nucleosome assembly in the suppression of spontaneous mutagenesis to understand the importance of nucleosomal environment for the maintenance of genomic stability. Our results provide genetic evidence that histone chaperones CAF-1 and HIR dependent nucleosome assembly protects genome from the MMR-dependent degradation and spontaneous mutagenesis.