PhD.Thesis Dissertation:Sezgi Kaya

GENOME-WIDE UV-INDUCED DNA DAMAGE AND NUCLEOTIDE EXCISION REPAIR IN THE CONTEXT OF R-LOOPS

Sezgi Kaya
Molecular Biology, Genetics and Bioengineering, PhD Dissertation, 2023

Thesis Jury

Asst. Prof. Ogün Adebali (Thesis Advisor),

Prof. Levent Öztürk,

Asst. Prof. Onur Öztaş,

Prof. Canan Atılgan,

Asst. Prof. Emrah Nikerel

Date & Time: December 28th, 2023 –  3 PM

Place: FASS 1079

Keywords : R-loop, UV, NER, CPD, ssDNA, DNA:RNA hybrid

Abstract

R-loops are three-stranded nucleic acid structures formed frequently during transcription when nascent RNA anneals on its complementary DNA strand, leaving the other DNA strand single-stranded. R-loops are dynamic structures that are formed and resolved by a number of regulator proteins such as helicases and endonucleases. Under this tight regulation, they play roles in important cellular processes such as gene expression regulation, transcription termination, immunoglobulin class switch recombination, telomere maintenance. However, upon accumulation, R-loops lead to double-strand breaks (DSBs) and genome instability.

UV exposure leads to formation of bulky lesions on DNA by triggering a photochemical reaction that results in covalent bonds between adjacent pyrimidines. These bulky lesions are cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine pyrimidone photoproducts ((6-4)PP) which might turn into mutations if not repaired. Nucleotide excision repair (NER) is the main mechanism for the repair of UV-induced lesions.  To date, there is no clear evidence on how R-loops affect UV-induced damage formation and their repair by NER mechanism. Here, a comprehensive look at the relationship between R-loops and UV-induced damage formation and repair in human Arabidopsis genomes is presented. Firstly, the R-loop locations determined by different methods and databases were compared in terms of genomic distribution and chromatin features, and the most reliable set of R-loops were selected for further analysis. Secondly, the aspects of UV-induced damage formation on R-loop are examined and the differences in CPD damage accumulation patterns between R-loop strands and other genomic regions are addressed with molecular dynamics (MD) simulations. Then, the efficiency of UV-induced damage repair is assessed comparatively between R-loop strands and other genomics regions. Additionally, repair efficiency on R-loops is examined from another perspective, mutational burden. To do this, the distribution of mutations on the genomes of melanoma patients on R-loops and other genomic regions is presented in comparison to other cancer genomes. In the final part, Hidden Markov Models (HMMs) is used to classify human genome into states considering the differential occupancy of R-loop regulatory proteins, and these states are compared in terms of damage formation and repair efficiency. Findings of this study provide a broadened sight for R-loop - NER relationship.