Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming

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. Inhibition of HDAC7 triggers a significant increase of heterochromatin marks H3K9me3 and H3K27me3, global heterochromatin spreading in cancer cells, and reprogramming of the H3.3 chromatin landscape. This drives substantial alteration of cancer cell gene expression as well as inhibition of the stemness phenotype for cancer cells. Our work demonstrates the involvement of HDAC7 in the euchromatic H3.3 chaperone network and shows that inhibiting HDAC7 induces H3.3 landscape reprogramming, heterochromatin spreading, and epigenetic restriction in cancer cells.