Genome-wide chromatin interaction profiling with Hi-C following VPA treatment in HEK293 cells

Valproic acid (VPA), a histone deacetylase (HDAC) inhibitor induces epigenetic changes through histone hyperacetylation which lead to chromatin remodeling, including the alteration of compartments, TAD boundaries and chromatin loops. To determine the effects of VPA on 3D chromatin organization, we performed Hi-C sequencing on untreated and VPA-treated HEK293T cells. VPA treatment results in increased A compartments which represents regions associated with active transcription, with more switching from B-to-A compartments. In VPA-treated HEK293T cells, reduced TAD boundaries and increased chromatin loops were also observed, which supports the evidence of active transcription triggered upon histone hyperacetylation induced by VPA. Overall design: We performed Hi-C on untreated and VPA-treated HEK293T cells. Differential analysis was performed to elucidate the genomic changes triggered by VPA.