Most models for SWI/SNF remodeling have been based on assays that measure either the accessibility of DNA to nucleases or the level of DNA supercoiling. The Illinois team, however, directly measured where specific sites on the histone octamer surface contact DNA before and after remodeling by attaching photoreactive groups to sites within the histone fold regions.
SWI/SNF displaced the histone octamers so that they were hanging on to only about 100 bp of DNA as compared to the normal 146 bp. “The fact that it can move an extra 50 bp beyond the end says that it is not just sliding by pushing the DNA into the nucleosome but it displaces large stretches of DNA off the surface,” says Bartholomew. The stable remodeled nucleosome also forms an unusual intranucleosomal loop in which the free DNA end is efficiently looped back onto the exposed surface of the octamer.
Using their direct readout, the team estimated that a remodeling event may require less than 1 s and the hydrolysis of fewer than 10 ATP molecules. This is a considerably lower energy estimate than those made by others, and provides further evidence that remodeling may involve a limited number of steps. ▪