A hexasome is the preferred substrate for the INO80 chromatin remodeling complex allowing versatility of function

The INO80 chromatin remodeling complex plays critical roles in transcription that are commonly attributed to INO80's nucleosome sliding activity. Here we find that removal of INO80 in yeast cells disrupts the positions of hexasome-sized particles within genes. We show that in vitro INO80 remodels hexasomes ~60-fold faster than nucleosomes. INO80's preference for hexasomes is highest when the linker lengths approach the ~18 bp linker lengths found in gene bodies. Our data further suggest that the module formed by the Arp5 and Ies6 subunits promotes nucleosome sliding by dislodging an H2A/H2B dimer, thereby making a nucleosome transiently resemble a hexasome. We propose a model in which the action of the Arp5/Ies6 module allows INO80 to act rapidly on both nucleosome substrates at promoters and hexasome substrates in gene bodies. Rapid repositioning of hexasomes that are generated in the wake of transcription may mitigate spurious transcription. More generally, such versatility could explain how INO80 regulates chromatin architecture during diverse processes ranging from transcription to DNA repair. Overall design: MNase mapping of subnucleosomal and nucleosomal fragments in S. cerevisiae WT and ?ino80 strains with replicates Please note that these libraries are non-traditional in the sense that the library prep is very different from standard Illumina protocols, and so the raw fastqs have been subjected to non-standard adaptor trimming + read filtration (in addition to read deduplication), generating BAM files as only processed data.