PKCδ regulates chromatin remodeling and DNA repair through SIRT6

Abstract

Protein kinase C delta (PKC{delta}) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKC{delta} is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKC{delta} activity provides radioprotection in vivo. How nuclear PKC{delta} regulates DNA-damage induced cell death is poorly understood. Here we show that PKC{delta} regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKC{delta} promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKC{delta} increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKC{delta} depletion is associated with more open chromatin, while overexpression of PKC{delta} reduces chromatin accessibility. Epiproteome analysis revealed that PKC{delta} depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKC{delta}. PKC{delta}-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKC{delta}-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKC{delta}-depleted cells. Our studies describe a novel pathway whereby PKC{delta} orchestrates SIRT6- dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKC{delta}. One Sentence SummaryProtein kinase C delta modifies chromatin structure via SIRT6 to regulate DNA repair.