Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips

Chromatin-remodeling complexes alter chromatin structure to facilitate, or in some cases repress, gene expression. Recent studies have suggested two p otential pathways by which such regulation might occur. In the first, the r emodeling complex repositions nucleosomes along DNA to open or occlude regu latory sites. In the second, the remodeling complex creates an altered dime ric form of the nucleosome that has altered accessibility to transcription factors. The extent of translational repositioning, the structure of the re modeled dimer, and the presence of dimers on remodeled polynucleosomes have been difficult to gauge by biochemical assays. To address these questions, ultrahigh-resolution carbon nanotube tip atomic force microscopy was used to examine the products of remodeling reactions carried out by the human SW I/SNF (hSWI/SNF) complex. We found that mononucleosome remodeling by hSWI/S NF resulted in a dimer of mononucleosomes in which 60 bp of DNA is more wea kly bound than in control nucleosomes. Arrays of evenly spaced nucleosomes that were positioned by 5S rRNA gene sequences were disorganized by hSWI/SN F, and this resulted in long stretches of bare DNA, as well as clusters of nucleosomes. The formation of structurally altered nucleosomes on the array is suggested by a significant increase in the fraction of closely abutting nucleosome pairs and by a general destabilization of nucleosomes on the ar ray. These results suggest that both the repositioning and structural alter ation of nucleosomes are important aspects of hSWI/SNF action on polynucleo somes.