Nucleosome sliding by the Chd1 chromatin remodeler relies on theintegrity of the DNA duplex

Abstract

Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers are biased by DNA sequences, suggesting that they may be sensitive to properties of the DNA duplex. Here, we present a high-throughput method for determining nucleosome positioning in vitro using site-specific DNA cleavage coupled with next-generation sequencing. This method allowed us to systematically test how the introduction of poly(dA:dT) tracts and other perturbations affected the distribution of nucleosomes remodeled by the Chd1 remodeler. We found that Chd1 is sensitive to poly(dA:dT) tracts as short as 3 bp, and that its nucleosome sliding activity is severely perturbed by DNA mismatches and single-nucleotide insertions. These results suggest that remodelers rely on the integrity of duplex DNA for nucleosome sliding. We also discovered that DNA on the nucleosome can shift in the absence of a remodeler when multiple mismatches are placed at superhelix location 2 (SHL2). This DNA movement in response to a disruption of the double helix may explain why SHL2 is the preferred site of engagement by most chromatin remodelers.