To understand the remodeler mechanism, we purify remodeler complexes and examine their action on purified nucleosomes in vitro. The primary remodeler that we study is called RSC (remodels the structure of chromatin), which consists of 15 proteins in one large complex. Our published work has shown that the remodeler "engine" is an ATPase subunit that functions as a DNA translocase. The remodeler binds the nucleosome in a fixed orientation and then uses DNA translocation to pump DNA waves around the surface of the nucleosome, resulting in the movement of the histone octamer relative to the DNA.
We have collaborated with Eva Nogales (HHMI, University of California, Berkeley) to determine the EM structure of the entire RSC complex, which revealed a large flexible protein machine that contains a large pocket of nucleosome dimensions. We have collaborated with Yongli Zhang (Albert Einstein) and Carlos Bustamante (HHMI, UC Berkeley) to determine the speed and force of DNA translocation on individual RSC-nucleosome complexes. To determine how the ATPase subunit is regulated, we are studying the actin-related proteins (ARPs) Arp7 and Arp9, as we have shown that these proteins bind directly to the ATPase subunit of the RSC remodeler. Recent published work from Heather Szerlong and Kaede Hinata show a role for ARPs in promoting the activity of the translocase. Cedric Clapier and Kaede Hinata are now focusing on the precise mechanism of translocation, and how actin-related proteins impact that mechanism.