Genomic occupancy of the INO80 complex [ChIP-seq]

We mapped 4 subunits of the INO80 complex using ChIP-seq in HepG2 and Huh7 liver cancer cell lines. We found a subclass of sites occupied by the INO80 ATPase subunit, but not by any accessory subunits that we call 'Autonomous' INO80 sites. These sites are present in both HepG2 and Huh7 cells and are characterized by repressed chromatin. Relief of reprissive histone modifications thorugh EZH2 inhbiition led to the increase in H3K27ac at INO80 targets. Overall design: ChIP-seq was performed for INO80 subunits in two cell lines and H3K27ac was mapped in one cell line by ChIP-seq following inhibition of H3K27me3 activity using EPZ-6438. Each experiment was performed twice, and cells were processed for ChIP as previously described (Raab et al 2015), followed by high throughput sequencing. Please note that the YY1_HepG2 processed data was generated from the ENCODE Accession ENCFF000PSE and ENCFF000PSD with the same pipeline as all the other data (and thus, no GEO sample records were created, and the re-processed data files are included as Series supplementary files). The author's note: The experiments are quantitative ChIP-seq using drosophila chromatin (Active Motif #53083). We spike this chromatin into each IP, and then use the amount of drosophila chromatin in each sample for calculating the appropriate normalizations between samples. For each experiment there is a bam file corresponding to the sample aligned against hg19 (for the experiment we care about) and against dm3 (for normalizing between sample; GSM2564091-98)