The Dpb4 subunit of ISW2 is anchored to extranucleosomal DNA

Histone fold proteins Dpb4 and Dls1 are components of the yeast ISW2 chromatin remodeling complex that resemble the smaller subunits of the CHRAC (Chromatin Accessibility Complex) complex found in Drosophila and humans. DNA photoaffinity labeling found that the Dpb4 subunit contacts extranucleosomal DNA 37-53 bp away from the entry/exit site of the nucleosome. Binding of Dpb4 to Isw2 and Itc2, the two largest subunits of ISW2, was found to require Dls1. Even after remodeling and nucleosome movement, Dpb4 tends to remain bound to its original binding site and likely serves as an anchor point for ISW2 on DNA. In vitro, only minor differences can be detected in the nucleosome binding and mobilization properties of ISW2 with or without Dpb4 and Dls1. Changes in the contacts of the largest subunit Itc1 with extranucleosomal DNA have, however, been found upon deletion of the Dpb4 and Dls1 dimer that may affect the nucleosome spacing properties of ISW2.