The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells

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 adenosine 5'-triphosphate-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 nonnucleosomal mitochondrial DNA methylation rate in each strain. Depletion of both Isw1 and Chd1 increases the normalized methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Separate depletion of Isw1, Chd1, or Rsc8 has little effect. 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. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at transfer RNA genes in vivo. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo.