Chromatin remodeling by RSC involves ATP-dependent DNA translocation

Abstract

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.

Chromatin remodeling: insights and intrigue from single-molecule studies

“…At that location, the strained 11-bp DNA loop or wave then propagates around the nucleosome by onedimensional diffusion and resolves in the distal linker, as proposed previously 9,35,41 . This model yields about one negative turn for each 100 bp translocated.…”

“…These models were intuitive and provided important initial concepts. However, all remodeler ATPases are classified as members of the SF2 family of DEAD/H-box helicase/translocases, and a significant advance was the demonstration that remodelers are indeed ATP-dependent DNA translocases 4,5,[35][36][37][38] . This indicated a possible motor force for breaking histone-DNA contacts and moving DNA on the octamer surface.…”

Chromatin remodeling by ATP‐dependent molecular machines

“…(56,(64)(65)(66)(67)(68)(69)(70) These findings indicate that the SNF2-like ATPase polypeptides possess an intrinsic chromatin-remodeling function.…”

“…(35,60,91) (7) RSC complex, ISWI and Rad54 have been found to exhibit triplex DNA displacement activity and thus appear to translocate along the DNA. (65,92) [In the triplex DNA displacement assay, a short oligonucleotide that binds in the major groove of a pyrimidine-rich target sequence is displaced by motor proteins that translocate through the sequence.] Furthermore, the ACF complex exhibits template commitment during chromatin assembly, which suggests that it functions as a DNA-translocating enzyme.…”

“…8,15,20,31,35,65,68,77,78,82,83,85,[91][92][93][94]. Most of the proposed mechanisms involve the generation of a DNA loop or bulge (of variable size) that is propagated across the surface of the histone octamer.…”