Assays for chromatin remodeling during nucleotide excision repair in Saccharomyces cerevisiae

How DNA repair proteins interact with the dynamic structure of chromatin is an emerging question. Chromatin structure impedes the access of repair proteins to sites of DNA damage. Several recent studies have implicated chromatin remodeling complexes in DNA repair. In this report we summarize the methods we used to investigate chromatin remodeling during nucleotide excision repair (NER) in vivo. We describe a procedure to analyze UV-induced chromatin remodeling at the silent mating-type locus HML using isolated nuclei from UV-treated yeast cells. In addition, a method to capture transient protein–protein associations in chromatin is outlined. We have used the methods described here to demonstrate that the SWI/SNF chromatin remodeling complex is involved in chromatin rearrangement during NER.