Insights into promoter chromatin remodeling from the structure of ISW1a complex bound to the dinucleosome

Nucleosomes, the basic repeating units of chromatin, form evenly spaced arrays inside the cell. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression. Here we report the cryoEM structure of the chromatin remodeler ISW1a complex bound to the dinucleosome. Both subunits of the complex recognize one nucleosome. The motor subunit binds at the canonical position of the nucleosome, with two arginine anchors recognizing the acidic patch. The DNA-binding module interacts with the entry linker DNA at the nucleosome edge, consistent with the protein ruler model in nucleosome spacing. The Ioc3 subunit recognizes the disk face of the adjacent nucleosome, being important for the spacing activity in vitro, and for chromatin organization in vivo. Together, our findings illustrate a new mode of chromatin remodeling in the context of higher-order chromatin MNase-seq in Saccharomyces cerevisiae. Compare nucleosome shift between WT-mutant(dIoc3, dAP, dH4), with an addition pair of WT-WT control group. Two biological replicates were sampled for each group.