The Chd1 Chromatin Remodeler can Sense a Protein Bound at the Edge of the Nucleosome and is Sensitive to DNA Unwrapping

Abstract

Chromatin remodelers are essential for establishing and maintaining the placement of nucleosomes along genomic DNA. However, how remodelers respond to transcription factors and other bound factors that might influence chromatin organization is poorly understood. Here we use the Lac repressor to investigate how the Chd1 remodeler responds to a protein bound to the edge of a nucleosome. We found that Lac repressor effectively provided a barrier for nucleosome sliding by Chd1. This barrier did not require an absolute block in sliding, but instead was achieved through the bidirectional movement of nucleosomes, with a higher preference for sliding nucleosomes away from occupied Lac repressor sites. The presence of Lac repressor did not markedly diminish the affinity of Chd1 for nucleosomes, suggesting that Lac repressor is sensed after nucleosome sliding has been initiated. Nucleosome sliding rates were also reduced by DNA unwrapping, suggesting a mechanism by which Chd1 may indirectly sense factors bound at the edge of the nucleosome.