Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming [RNA-seq]

Class IIa histone deacetylases (HDACs) are a family of enzymes that despite their name, do not have any measurable histone deacetylase activity but they function as multi-protein interaction hubs due to the presence of a prolonged N-terminal domain. Here we show that HDAC7, a member of the Class IIa HDAC family, is a chaperone for Histone H3.3 and, interacts with H3.3 and HIRA on chromatin. Specific inhibition of HDAC7 expression with subtype specific siRNAs results in inhibition of the interaction of H3.3 with HIRA, while the association of H3.3 with DAXX and H3K9me3 is significantly increased, resulting in H3.3 being deposited on H3K9me3+/DAPI+ heterochromatin nuclear foci with observed changes in RNA expression. This drives substantial alteration of cancer cell gene expression as well as inhibition of the stemness phenotype for cancer cells. To understand the genome wide effect on expression, we perform RNA-seq following HDAC7 knockdown. Overall design: We performed differential gene expression analysis in 2 patients dervied GSCs samples following siRNA knockdown of HDAC7 We compared sicontrol versus siHDAC7 samples using two different patients.