Chromatin remodeling by RSC involves ATP-dependent DNA translocation

Abstract

Chromatin-remodeling complexes couple ATP hydrolysis to alterations in histone-DNA interactions and nucleosome mobility, allowing transcription factors access to chromatin. Here, we use triple-helix strand-displacement assays, DNA length-dependent ATPase assays, and DNA-minicircle ATPase assays to establish that RSC, as well as its isolated ATPase subunit Sth1, are DNA translocases. RSC/Sth1 ATPase activity is stimulated by single-stranded DNA, suggesting that Sth1 tracks along one strand of the DNA duplex. Each RSC complex appears to contain a single molecule of Sth1, and isolated Sth1 is capable of nucleosome remodeling. We propose that the remodeling enzyme remains in a fixed position on the octamer and translocates a segment of DNA (with accompanying DNA twist), which breaks histone-DNA contacts and propagates as a wave of DNA around the octamer. The demonstration of DNA translocation presented here provides a mechanistic basis for this DNA wave. To test the relative contribution of twist to remodeling, we use nucleosomes containing nicks in precise locations to uncouple twist and translocation. Nucleosomes bearing nicks are remodeled less efficiently than intact nucleosomes. These results suggest that RSC and Sth1 are DNA translocases that use both DNA translocation and twist to remodel nucleosomes efficiently.