Abstract
The budding yeast genome is globally accessible to DNA methyltransferases in living cells, unlike in isolated nuclei, where it is mostly inaccessible. Here, we assess the roles of the RSC, ISW1 and CHD1 ATP-dependent chromatin remodelers in generating nucleosome dynamics in vivo. We compare DNA methylation rates in wild type cells and chromatin remodeler mutants by normalizing nuclear methylation rates to the non-nucleosomal mitochondrial DNA methylation rate in each strain. Depletion of subunits of the RSC, ISW1 or CHD1 ATP-dependent chromatin remodelers has little effect on normalized methylation rate. A decaying sine wave model used to fit nucleosome phasing data shows that nucleosome dynamics decrease with distance from the promoter in an Isw1/Chd1-dependent manner. Depletion of both Isw1 and Chd1 increases the methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at tRNA genes. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo.