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Review
. 2019 Dec 20;47(6):1881-1893.
doi: 10.1042/BST20190534.

Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response

Alexander J Garvin  1
Affiliations
Review

Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response

Alexander J Garvin. Biochem Soc Trans. .

Abstract

The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein-protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.

Keywords: DNA synthesis and repair; DUB; SENP; double strand break; sumoylation; ubiquitin.

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Conflict of interest statement

The Author declares that there are no competing interests associated with this manuscript.

Figures

Figure 1.
Figure 1.. NHEJ occurs at all stages of the cell cycle.
Ku70/80 heterodimers bind and stabilise the ends of the DSB. Other factors are also recruited by the Ku dimer. DNA end processing chemically modifies the bases to allow re-ligation. Ligase 4 (LIG4), XLF and other repair factors ligate the broken DNA ends. HR is restricted to S/G2, initial DNA 3′ end resection is initiated by the MRN complex and CtIP. Further resection promoted by the BRCA1–BARD1 heterodimer, EXO1 and DNA2 promote long range resection. The ssDNA generated by end resection is coated in the RPA heterotrimeric complex, which is then displaced by RAD51 nucleofilaments with the aid of the BRCA1–PALB2–BRCA2 complex. After RAD51 filament formation, homology search followed by invasion of the sister chromatid and synthesis of new DNA occurs. As the biology of these later processes in the context of Ub/Ubl modifications is poorly understood they are not illustrated here. As NHEJ can also occur in S/G2 pathway choice between HR and NHEJ occurs. The pro-NHEJ factor 53BP1 is recruited by K15 Ub modified H2A/H2AX while modification of K125/K127 or K129 by mono-Ub aids in nucleosome remodelling and displacement of 53BP1, this favours DNA end-resection and HR. Thus maintaining the balance of Ub signals dictates repair pathway choice.
Figure 2.
Figure 2.. The DNA bound Ku70/80 heterodimer is ubiquinated and SUMOylated by multiple E3 ligases.
Ultimately this signals for Ku70/80 dimer removal from chromatin by VCP/p97. MDC1 is constitutively protected from excessive SUMOylation through its interaction with SENP2. This interaction is disrupted by ATM signalling which allows the DSB located MDC1 to be hyperSUMOylated by PIAS4 which also localises to DSBs. The SUMOylated MDC1 is then recognised by the SUMO directed Ub ligase RNF4 which ubiquitinates MDC1 and promotes extraction from chromatin by VCP. The RNF4 step can be countered by ATXN3, slowing MDC1 turnover at DSBs. RNF8 is recruited by MDC1 where it forms K63-Ub linkages on H1.2. HUWE1 also contributes to the generation of Ub chains on H1.2. OTUB1 inhibits RNF8 activity by disrupting Ub recognition by the E2 UBE2N. Conversely, HERC2 stimulates RNF8–UBE2N activity in a SUMOylation dependent manner. HERC2 also interacts with two DUBs, USP16 and USP20 both of which are involves in DSB repair signalling. ATXN3 counters RNF8 auto-ubiquitination. RNF168 interacts with RNF8 generated H1.2K63-Ub and amplifies this Ub signal through recognition of its own Ub product — K15 mono-ubiquitinated H2A or H2AX. Two DUBs, (A20 and USP14) interfere with RNF168's initial recruitment to H1.2. Two more DUBs (USP7 and USP34) are needed to protect RNF168 from auto-degradation. The paralog RNF169 competes with RNF168 for H2A/H2AXK15-Ub binding. 53BP1 recognises the K15-Ub modified H2A or H2AX generated by RNF168. Additionally, 53BP1 is recruited by H4K20me2, a modification that is competitively bound by L3MBTL1. Ubiquitination and extraction from chromatin of L3MBTL1 is required for efficient 53BP1 spreading along chromatin. The turnover of L3MBTL1 is antagonised by OTUB2. Multiple DUBs regulate the spread of 53BP1 via regulating the amplitude of Ub/UbK63 at DSBs, some of these DUBs directly counter the H2A/H2AXK15-Ub modification while others may act on other uncharacterised K63-Ub modified proteins. RAP80 and the BRCA1-A complex are recruited to DSBs in a K63-Ub dependent fashion, although RAP80 also recognises SUMO modifications (most likely generated by RNF4), suggesting that the RAP80–BRCA1-A complex may recognise a different signal to 53BP1. BRCA1 recruitment into the BRCA1-A complex is thought to divert its activity from promoting DNA end-resection. At least two DUBs (USP26 and USP37) specifically counter the Ub signal that promotes RAP80–BRCA1 accrual. USP13 trims Ub from the RAP80 UIM domain to allow efficient Ub recognition. BRCA1–BARD1 also recruit to DSBs independently of K63-Ub signalling. Ubiquitination inhibits the BARD1- HP1γ interaction needed for efficient accumulation of BRCA1–BARD1 at DSBs. This disruptive ubiquitination event is countered by USP15. The ubiquitination and turnover of BRCA1 is countered by USP9X. BRCA1–BARD1 also generates mono-Ub on the far C terminus of H2A (K125, K127 or K129). This signal promotes DNA end-resection and aids in the displacement of 53BP1 from DSBs. USP48 restricts the spread of H2AK125/127/129-Ub preventing excessive DNA end-resection. The MRN complex and CtIP, both of which are essential for the early steps in DNA end-resection are ubiquitinated, USP4 antagonises these modifications. SUMOylation promotes degradation of the DNA exonuclease EXO1, to control DNA end-resection which is countered by SENP6. The loading of the RPA hetero-trimer onto single stranded DNA (generated through DNA end-resection) and its exchange with RAD51 are essential steps in HR. The RPA70 subunit is SUMOylated and degraded by RNF4, this is countered by SENP6. Loading of RAD51 onto ssDNA is promoted by BRCA2 in the BRCA1–PALB2–BRCA2 complex. This complex can only form due to the activity of USP11 which removes an inhibitory Ub modification that is disruptive to BRCA1–PALB2 interactions. USP11 levels are cell cycle regulated by KEAP1. USP1–UAF1 non-catalytically aids in the loading of RAD51, UCHL3 de-ubiquitinates RAD51 promoting its ability to load onto DNA, while USP21 protects the unstable BRCA2 protein from degradation.
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References

    1. Scully R., Panday A., Elango R. and Willis N.A. (2019) DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat. Rev. Mol. Cell Biol. 20, 698–714 10.1038/s41580-019-0152-0 - DOI - PMC - PubMed
    1. Uckelmann M. and Sixma T.K. (2017) Histone ubiquitination in the DNA damage response. DNA Repair 56, 92–101 10.1016/j.dnarep.2017.06.011 - DOI - PubMed
    1. Garvin A.J. and Morris J.R. (2017) SUMO, a small, but powerful, regulator of double-strand break repair. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160281 10.1098/rstb.2016.0281 - DOI - PMC - PubMed
    1. Brown J.S., Lukashchuk N., Sczaniecka-Clift M., Britton S., le Sage C., Calsou P. et al. (2015) Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep. 11, 704–714 10.1016/j.celrep.2015.03.058 - DOI - PMC - PubMed
    1. Nishi R. (2017) Balancing act: to be, or not to be ubiquitylated. Mutat. Res. 803, 43–50 10.1016/j.mrfmmm.2017.07.006 - DOI - PubMed