The broad objective of the Smerdon Lab is to understand the molecular details of an important defense mechanism (DNA repair) against phenotypic changes in cells, and its modulation by different chromatin domains. Such changes are an important etiological factor in cell survival and cancer. DNA damage results from a wide variety of exogenous agents, such as ultraviolet (UV) radiation and chemical carcinogens, and endogenous agents, such as reactive oxygen species. Therefore, we use UV radiation and benzo[a]pyrene diol epoxide (BPDE) as prototype environmental agents for studies on nucleotide excision repair. In addition, formation of uracil or methylated bases is used to elicit base excision repair, which requires less processing at the chromatin level. We are examining the relationship between repair of these lesions and chromatin structure in yeast and mammalian cells.
Our studies employ novel analyses to follow repair at specific sites in different chromatin locations, including transcribed genes and replication origins. For example, we are currently examining DNA repair in positioned nucleosomes in cell-free extracts to answer well-defined questions about repair at the DNA-histone interface, and developing genome-wide methods to map the formation and repair of DNA damage in repair proficient and repair deficient human and yeast cells. Thus, we use a multifaceted approach, employing disciplines as distinct as yeast genetics and molecular biophysics, to examine the role of chromatin structure and transcription in DNA damage and its repair in eukaryotes.