Mechanisms of ATP-dependent Chromatin Remodeling Revealed by Single-molecule Manipulation Studies

Abstract

Genome-wide chromatin structures, such as nucleosome positioning and various histone modifications, have recently been mapped relative to the underlying DNA sequences, revealing an exquisite and dynamic organization of chromatin. The chromatin structures are established and remodeled mainly by a large family of highly conserved and specialized ATP-dependent chromatin remodeling complexes (remodelers) in cooperation with histone-modifying enzymes. The core of these remodelers is a DNA translocase, a molecular motor capable of actively moving along DNA. It remains unclear how the energy of ATP hydrolysis is converted to the mechanical work for DNA translocation and in turn to nucleosome remodeling by remodelers, and how the remodeling process is regulated by different protein subunits of remodelers, nucleosome substrates, and histone modifications. Using high-resolution optical tweezers, we studied the nucleosome remodeling process by SWI/SNF and RSC, two prototypes of remodelers containing 11 and 15 subunits, respectively. We found that both remodelers can translocate along DNA at rates of ∼13 bp/s and generate forces up to ∼12 pN, producing DNA loops of a broad range of sizes (5-1200 bp) in a nucleosome-dependent manner. Interestingly, when attached by a strong DNA binding domain and anchored to a bare DNA molecule, the isolated ATPase subunit of RSC alone can efficiently translocate along DNA to produce DNA loops in a nucleosome-independent manner. Surprisingly, the tethered translocase can now move against forces as high as 26 pN, making the remodeler translocase one of the strongest molecular motors. Our single-molecule experiments revealed a powerful and versatile DNA translocase engine for remodelers, which may be crucial for their role of disrupting DNA-histone interactions in a regulatory fashion.