The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler

In the cell, genomic DNA is tightly packaged into chromatin, the most basic unit of which is a histone core wrapped by ~147 bp of DNA called the nucleosome. A class of ATP-dependent enzymes called chromatin remodelers tightly regulates access to genomic DNA through repositioning, eviction, or exchange of the histone core from the DNA. The monomeric chromatin remodeler Chromodomain Helicase DNA binding protein 1 (Chd1) is the simplest of the class, only containing regulatory chromodomains, a DNA-binding domain (DBD), and a conserved ATPase motor. In this work I show how nucleosomal DNA sequence impacts remodeling activity of Chd1, and uncover a twist defect mechanism for remodeling. I found that Chd1 repositions nucleosomes in a sequence-dependent fashion. To test this, I incorporated a rigid poly(dA:dT) tract in the interior of the nucleosome, which reversed the direction of asymmetric repositioning by Chd1. This change in direction resulted from a slowed rate of repositioning by Chd1 towards the poly(dA:dT) tract, and did not depend on the DNA-binding domain. Further, I found that even relatively minor sequence changes affected both remodeling and nucleosome binding of Chd1. Some DNA sequence changes altered activity even when outside the remodeler binding site, demonstrating that Chd1 is sensitive to nucleosome stability and dynamics. Nucleosomes have been hypothesized to move DNA via a twist defect mechanism where local DNA under- and over-twisting allows single base-pairs to spontaneously propagate around the histone core. Previously, it was not known how remodelers might stimulate diffusion of these DNA twist defects. I found that Chd1 stabilizes different twist states of DNA in a nucleotide-dependent fashion that correlates with different conformations of the ATPase motor. Thus, by cycling through ATP hydrolysis and exchange, Chd1 ratchets nucleosomal DNA around the histone core. This idea is distinct from the previously proposed “inchworm” model, and instead suggests that remodelers shift DNA past the histone core by harnessing the inherent properties of the nucleosome