Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics

Chromatin accessibility in the nucleus is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with lower mitochondrial DNA and duplicated sequences compared to ATACsee. Using NicE-viewSeq we interrogated cell cycle G1, S and G2M specific accessible chromatin in mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosome, chromatin accessibility remained subtly altered and generally preserved. Genome-wide alteration of accessibility for TSS and enhancer gradually decreased as the cell progressed from G1 to G2M, with distinctive differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylase promoted accessible chromatin of the gene body, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for MYC oncogene pathway correlated with gene down regulation. Surprisingly, repetitive RNA expression remained unaltered following histone acetylation mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics. HCT116, HeLa, HUT78 and HT1080 cell line were routinely grown in McCoy's and DMEM media with 10% fetal bovine serum respectively, media being replaced every 3 days. Cell cycle studies were performed in HCT116 and HeLa. Cells were sorted using FACS and also used nocodazole. HUT78 were treated with 1 micromolar of Romidepsin for 6 hours.