Book Description

The mechanism of ATP-dependent chromatin remodeling was explored using the Saccharomyces cerevisiae ISW2 complex, a member of the ISWI subfamily of chromatin remodeling factors. Site-specific DNA photoaffinity labeling and peptide mapping were utilized to study the specific interactions between ISW2 and nucleosomes. The subunits of ISW2 that contact particular sites on nucleosomal and extranucleosomal DNA were identified. In an extensive scan, three DNA regions on the end-positioned nucleosome were shown to be the major contact sites of ISW2. The extranucleosomal DNA region was bound by the largest subunit Itc1 and one of the small histone fold subunits (Dpb4). The region around the DNA entry/exit site or the edge of the nucleosome was contacted by both Itc1 and the catalytic subunit Isw2. The internal site 2 helical turns from the dyad axis of the nucleosome, which has been shown to be critical for chromatin remodeling, was associated with the two large subunits Itc1 and Isw2. The contacts of specific Isw2 domains were determined by peptide mapping of photoaffinity labeled Isw2. The SLIDE domain was found to interact with extranucleosomal DNA 20 bp from the entry/exit site and the novel HAND domain contacts the DNA just 10 bp inside the nucleosome. The helicase domain containing the ATP binding pocket is bound at the critical internal site two helical turns from the dyad. Determination of the spatial arrangement of ISW2 with nucleosomes illustrates, for the first time, the interaction of a chromatin remodeling factor with the nucleosome and key structural information for understanding how ISW2 repositions mononucleosomes and generates regularly spaced nucleosome arrays. The interaction of ISW2 with the nucleosome was found to be affected by the length of the extranucleosomal DNA with an optimal length of ~70 bp and by the histone H4 tail in parallel pathways to direct ISW2 to the critical internal site of the nucleosome. The domains of Ume6 that binds to ISW2 was determined and to be sufficient to recruit ISW2 under limiting conditions. Finally, studies on the histone fold dimer of ISW2 have suggested roles in facilitating ISW2 interacting with extranucleosomal DNA, as well as nucleosome mobilization.