Regulation of Histone Ubiquitination in Response to DNA Double Strand Breaks

Abstract

Eukaryotic cells are constantly exposed to both endogenous and exogenous stressors that promote the induction of DNA damage. Of this damage, double strand breaks (DSBs) are the most lethal and must be efficiently repaired in order to maintain genomic integrity. Repair of DSBs occurs primarily through one of two major pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these pathways is in part regulated by histone post-translational modifications (PTMs) including ubiquitination. Ubiquitinated histones not only influence transcription and chromatin architecture at sites neighboring DSBs but serve as critical recruitment platforms for repair machinery as well. The reversal of these modifications by deubiquitinating enzymes (DUBs) is increasingly being recognized in a number of cellular processes including DSB repair. In this context, DUBs ensure proper levels of ubiquitin, regulate recruitment of downstream effectors, dictate repair pathway choice, and facilitate appropriate termination of the repair response. This review outlines the current understanding of histone ubiquitination in response to DSBs, followed by a comprehensive overview of the DUBs that catalyze the removal of these marks.

Keywords: DNA damage response; DSBs; DUBs; deubiquitinases; deubiquitinating enzymes; double strand break repair; histones; ubiquitination.

Figure 1

Mediators of ubiquitination and deubiquitination following a double strand break (DSB). (A) DSB induction, represented by a lightning bolt, leads to phosphorylation of H2AX (γH2AX) by ataxia-telangiectasia mutated (ATM) kinase. γH2AX recruits MDC1, which in turn recruits RNF8. RNF8-mediated ubiquitination of H1 or L3MBTL2 has been proposed to recruit RNF168. The concerted actions of RNF8 and RNF168 result in the mono (green), K63-linked (purple), and K27-linked (dark pink) ubiquitination of lysines 13 and 15 on H2A-type histones. H2AK13/15 ubiquitination acts as a recruitment platform for downstream mediators of the DSB response including the BRCA1-A complex and 53BP1, the latter dually recognizing ubiquitin and H4K20 methylation (light pink). Deubiquitinating enzyme (DUB) activity towards H2AK13/15 influences the recruitment of these factors and ultimately impacts the efficiency of DSB repair. (B) A PRC1 catalytic heterodimer, most notably RNF2 and BMI1, catalyzes H2AK119 monoubiquitination. This mark facilitates transcriptional silencing and its removal by various DUBs can influence gene expression at sites surrounding DSBs. (C) Ubiquitination at H2AK125/127/129 is catalyzed by BRCA1-BARD1 in response to DSBs. This mark is subsequently recognized by SMARCAD1, which facilitates the repositioning of 53BP1 to promote DNA end resection and thus homologous recombination (HR). USP48 is currently the only identified DUB with specificity towards this residue. USP48 activity is most robust in the presence of auxiliary ubiquitin either at K119 or the BRCA1 site. While monoubiquitination is depicted in this figure, polyubiquitin chains may be synthesized at the BRCA1 site as well. (D) Monoubiquitination at H2BK120 is deposited by RNF20-RNF40. The reversal of this mark by several DUBs has been reported and may influence the accessibility of chromatin for downstream DSB mediators. While ubiquitination of H3 and H4 occurs, future studies warrant the investigation of these marks and the DUBs that reverse them in the context of DSB repair. Figure created with BioRender.com.