SHLD2/FAM35A co‐operates with REV7 to coordinate DNA double‐strand break repair pathway choice

DNA double‐strand breaks (DSBs) can be repaired by two major pathways: non‐homologous end‐joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)‐based approach, we identify 11 high‐confidence REV7 interactors and elucidate the role of SHLD2 (previously annotated as FAM35A and RINN2) as an effector of REV7 in the NHEJ pathway. FAM35A depletion impairs NHEJ‐mediated DNA repair and compromises antibody diversification by class switch recombination (CSR) in B cells. FAM35A accumulates at DSBs in a 53BP1‐, RIF1‐, and REV7‐dependent manner and antagonizes HR by limiting DNA end resection. In fact, FAM35A is part of a larger complex composed of REV7 and SHLD1 (previously annotated as C20orf196 and RINN3), which promotes NHEJ and limits HR. Together, these results establish SHLD2 as a novel effector of REV7 in controlling the decision‐making process during DSB repair.     

ZMYM2 restricts 53BP1 at DNA double-strand breaks to favor BRCA1 loading and homologous recombination

An inability to repair DNA double-strand breaks (DSBs) threatens genome integrity and can contribute to human diseases, including cancer. Mammalian cells repair DSBs mainly through homologous recombination (HR) and nonhomologous end-joining (NHEJ). The choice between these pathways is regulated by the interplay between 53BP1 and BRCA1, whereby BRCA1 excludes 53BP1 to promote HR and 53BP1 limits BRCA1 to facilitate NHEJ. Here, we identify the zinc-finger proteins (ZnF), ZMYM2 and ZMYM3, as antagonizers of 53BP1 recruitment that facilitate HR protein recruitment and function at DNA breaks. Mechanistically, we show that ZMYM2 recruitment to DSBs and suppression of break-associated 53BP1 requires the SUMO E3 ligase PIAS4, as well as SUMO binding by ZMYM2. Cells deficient for ZMYM2/3 display genome instability, PARP inhibitor and ionizing radiation sensitivity and reduced HR repair. Importantly, depletion of 53BP1 in ZMYM2/3-deficient cells rescues BRCA1 recruitment to and HR repair of DSBs, suggesting that ZMYM2 and ZMYM3 primarily function to restrict 53BP1 engagement at breaks to favor BRCA1 loading that functions to channel breaks to HR repair. Identification of DNA repair functions for these poorly characterized ZnF proteins may shed light on their unknown contributions to human diseases, where they have been reported to be highly dysregulated, including in several cancers.     

Role for RIF1-interacting partner DDX1 in BLM recruitment to DNA double-strand breaks

Human Rap1-interacting factor 1 (RIF1) is an important player in the repair of DNA double strand breaks (DSBs). RIF1 acts downstream of 53BP1, with well-documented roles in class switch recombination in B-cells and inhibition of end resection initiation in BRCA1-defective cells. Here, we report that DEAD Box 1 (DDX1), a RNA helicase also implicated in DSB repair, interacts with RIF1, with co-localization of DDX1 and RIF1 observed throughout interphase. Recruitment of DDX1 to DSBs is dependent on RIF1, with RIF1 depletion abolishing DDX1-mediated facilitation of homologous recombination at DSBs. As previously demonstrated for RIF1, DDX1 is also required for chromatin loading of Bloom syndrome helicase (BLM) to ionizing radiation-induced DSBs, a RIF1-related activity that is independent of 53BP1. We show that DDX1 and RIF1 have different nucleic acid requirements for accumulation at DSBs, with RNA-DNA hybrids required for DDX1 accrual at DSBs, and single-strand RNA required for accumulation of RIF1 at these sites. Our data suggest both convergent and divergent roles for DDX1 and RIF1 in DSB repair, and may help explain why RIF1 depletion does not fully mimic 53BP1 ablation in the restoration of homologous recombination defects in BRCA1-deficient cells.     

REV7/MAD2L2: the multitasking maestro emerges as a barrier to recombination

REV7/MAD2L2 plays important roles in translesion DNA synthesis and mitotic control. Two new papers extend its gamut by revealing its unexpected participation in pathway choice during DNA double‐strand break repair. By inhibiting 5′ DNA end resection downstream of 53BP1 and RIF1, REV7/MAD2L2 promotes non‐homologous end joining at the expense of homologous recombination. Importantly, loss of REV7/MAD2L2 renders PARP inhibitors ineffective in BRCA1‐deficient tumours, suggesting another possible mechanism for the acquisition of resistance to this important new class of drug.     

Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining

DNA double strand breaks (DSBs) formed during S phase are preferentially repaired by homologous recombination (HR), whereas G₁ DSBs, such as those occurring during immunoglobulin class switch recombination (CSR), are repaired by non-homologous end joining (NHEJ). The DNA damage response proteins 53BP1 and BRCA1 regulate the balance between NHEJ and HR. 53BP1 promotes CSR in part by mediating synapsis of distal DNA ends, and in addition, inhibits 5’ end resection. BRCA1 antagonizes 53BP1 dependent DNA end-blocking activity during S phase, which would otherwise promote mutagenic NHEJ and genome instability. Recently, it was shown that supra-physiological levels of the E3 ubiquitin ligase RNF168 results in the hyper-accumulation of 53BP1/BRCA1 which accelerates DSB repair. Here, we ask whether increased expression of RNF168 or 53BP1 impacts physiological versus mutagenic NHEJ. We find that the anti-resection activities of 53BP1 are rate-limiting for mutagenic NHEJ but not for physiological CSR. As heterogeneity in the expression of RNF168 and 53BP1 is found in human tumors, our results suggest that deregulation of the RNF168/53BP1 pathway could alter the chemosensitivity of BRCA1 deficient tumors.     

RIF1 Is Essential for 53BP1-Dependent Nonhomologous End Joining and Suppression of DNA Double-Strand Break Resection

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Highlights? RIF1 is essential for 53BP1-dependent CSR and fusion of dysfunctional telomeres ? BRCA1 antagonizes RIF1 in S phase to prevent error-prone repair by toxic NHEJ ? N-terminal phospho-SQ/TQ domain of 53BP1 interacts with and recruits RIF1 to DSBs ? RIF1 and 53BP1 promote NHEJ in G1 by blocking 5′ end resection of DSBs     

The interplay between BRCA1 and 53BP1 influences death,aging, senescence and cancer

In proliferating cells DNA double strand breaks (DSBs) are a common occurrence during DNA replication. DSB repair using homologous recombination is essential for the error-free repair of such breaks and proliferating cells require some level of HR activity for their viability. The BRCA1 tumour suppressor has an important role in this process and is believed to channel the DSBs into the HR pathway. The related 53BP1 gene is known to positively regulate repair of DSBs outside of S phase, but via the NHEJ pathway. Two new studies suggest a new role for 53BP1 as an inhibitor of HR [1], [2]. These genetic studies establish that 53BP1, but not other components of the NHEJ machinery, can inhibit the early resection step of HR. In cells defective for BRCA1, which is required for efficient HR, the balance between promoting and inhibiting HR is thrown towards inhibition. Simultaneous loss of 53BP1 can rescue the HR defect of BRCA1-defective cells and restore cellular viability. Here, I provide an overview of these studies and discuss their implications for tumourigenesis.     

RIF1: A novel regulatory factor for DNA replication and DNA damage response signaling

DNA double strand breaks (DSBs) are highly toxic to the cells and accumulation of DSBs results in several detrimental effects in various cellular processes which can lead to neurological, immunological and developmental disorders. Failure of the repair of DSBs spurs mutagenesis and is a driver of tumorigenesis, thus underscoring the importance of the accurate repair of DSBs. Two major canonical DSB repair pathways are the non-homologous end joining (NHEJ) and homologous recombination (HR) pathways. 53BP1 and BRCA1 are the key mediator proteins which coordinate with other components of the DNA repair machinery in the NHEJ and HR pathways respectively, and their exclusive recruitment to DNA breaks/ends potentially decides the choice of repair by either NHEJ or HR. Recently, Rap1 interacting factor 1 has been identified as an important component of the DNA repair pathway which acts downstream of the ATM/53BP1 to inhibit the 5′–3′ end resection of broken DNA ends, in-turn facilitating NHEJ repair and inhibiting homology directed repair. Rif1 is conserved from yeast to humans but its function has evolved from telomere length regulation in yeast to the maintenance of genome integrity in mammalian cells. Recently its role in the maintenance of genomic integrity has been expanded to include the regulation of chromatin structure, replication timing and intra-S phase checkpoint. We present a summary of these important findings highlighting the various aspects of Rif1 functions and discuss the key implications for genomic integrity.     

SET8 methyltransferase activity during the DNA double-strand break response is required for recruitment of 53BP1

DNA double-strand breaks (DSBs) activate a signaling pathway known as the DNA damage response (DDR) which via protein–protein interactions and post-translational modifications recruit signaling proteins, such as 53BP1, to chromatin flanking the lesion. Depletion of the SET8 methyltransferase prevents accumulation of 53BP1 at DSBs; however, this phenotype has been attributed to the role of SET8 in generating H4K20 methylation across the genome, which is required for 53BP1 binding to chromatin, prior to DNA damage. Here, we report that SET8 acts directly at DSBs during the DNA damage response (DDR). SET8 accumulates at DSBs and is enzymatically active at DSBs. Depletion of SET8 just prior to the induction of DNA damage abrogates 53BP1’s accumulation at DSBs, suggesting that SET8 acts during DDR. SET8’s occupancy at DSBs is regulated by histone deacetylases (HDACs). Finally, SET8 is functionally required for efficient repair of DSBs specifically via the non-homologous end-joining pathway (NHEJ). Our findings reveal that SET8’s active role during DDR at DSBs is required for 53BP1’s accumulation.     

HP1 promotes tumor suppressor BRCA1 functions during the DNA damage response

The DNA damage response (DDR) involves both the control of DNA damage repair and signaling to cell cycle checkpoints. Therefore, unraveling the underlying mechanisms of the DDR is important for understanding tumor suppression and cellular resistance to clastogenic cancer therapeutics. Because the DDR is likely to be influenced by chromatin regulation at the sites of DNA damage, we investigated the role of heterochromatin protein 1 (HP1) during the DDR process. We monitored double-strand breaks (DSBs) using the γH2AX foci marker and found that depleting cells of HP1 caused genotoxic stress, a delay in the repair of DSBs and elevated levels of apoptosis after irradiation. Furthermore, we found that these defects in repair were associated with impaired BRCA1 function. Depleting HP1 reduced recruitment of BRCA1 to DSBs and caused defects in two BRCA1-mediated DDR events: (i) the homologous recombination repair pathway and (ii) the arrest of cell cycle at the G₂/M checkpoint. In contrast, depleting HP1 from cells did not affect the non-homologous end-joining (NHEJ) pathway: instead it elevated the recruitment of the 53BP1 NHEJ factor to DSBs. Notably, all three subtypes of HP1 seemed to be almost equally important for these DDR functions. We suggest that the dynamic interaction of HP1 with chromatin and other DDR factors could determine DNA repair choice and cell fate after DNA damage. We also suggest that compromising HP1 expression could promote tumorigenesis by impairing the function of the BRCA1 tumor suppressor.     

DNA repair pathway choice—a PTIP of the hat to 53BP1

In the June issue of Cell, Nussenzweig and colleagues identify PTIP/PAXIP as a 53BP1 effector protein in the regulatory network that controls DSB repair pathway choice.Cell (2013) 153 6, 1266–1280 doi: 10.1016/j.cell.2013.05.023DNA double-stranded breaks (DSBs) are highly cytotoxic lesions that can induce genome rearrangements if not accurately repaired. DSBs can be repaired either through homologous recombination (HR) or non-homologous end-joining (NHEJ). HR is the preferred repair pathway during the S and G2 cell cycle phases because a sister chromatid provides a perfect template for ‘error-free'' repair. During G1, when HR is suppressed to prevent recombination with homologues, repair is achieved primarily by NHEJ. Molecularly, DSB repair pathway choice is largely regulated at the level of 5′ to 3′ DNA end resection, that is, the formation of the 3′ end single-stranded DNA overhangs that are used to initiate HR. End resection inhibits NHEJ and promotes HR.In the June issue of Cell, Nussenzweig and colleagues identified the protein PTIP (also known as PAXIP) as a new component of the regulatory network that controls DSB repair pathway choice [1]. This work has important implications for our understanding of the mechanisms by which genomic integrity is underpinned, and is especially germane to those interested in the genesis of breast and ovarian cancer caused by a defective BRCA1 protein, which is crucial for DSB repair by HR.53BP1 (also known as TP53BP1) is a key determinant of DSB repair pathway choice [2]. In response to DSBs, 53BP1 binds to chromatin at damaged sites, where it promotes NHEJ by blocking end resection. 53BP1 has a crucial role during class switch recombination (CSR) in B cells and the fusion of dysfunctional telomeres. An even more striking phenotype was observed in mice in which loss of 53BP1 reversed most of the phenotypes associated with BRCA1 deficiency, including cell and embryonic lethality as well as tumorigenesis [2]. These findings suggest that 53BP1 and BRCA1 battle each other to influence DSB repair pathway choice.Molecularly, 53BP1 is responsible for the defective HR seen in BRCA1-deficient cells. Furthermore, in those cells, 53BP1 promotes the formation of characteristic radial chromosomes that are caused by toxic NHEJ events, presumably during S phase. Understanding exactly how 53BP1 carries out its many functions has been a major challenge to the field as 53BP1 does not harbour any enzymatic activity. However, it has been shown that 53BP1 must accumulate on chromatin to be functional. In addition, a mutant 53BP1 allele in which all 28 ataxia telangiectasia-mutated (ATM) phosphorylation sites were changed to alanine (53BP1^28A) failed to rescue 53BP1 deficiency, suggesting that 53BP1 acts through phosphorylation-dependent protein interactions to promote NHEJ [2].RIF1 was identified as the first effector of 53BP1 in DSB repair [3,4,5,6,7]. RIF1 accumulates at DSB sites by binding to phosphorylated 53BP1 but, intriguingly, the loss of RIF1 has a milder effect than the loss of 53BP1 with respect to the fusion of dysfunctional telomeres [3], and RIF1 deficiency does not fully restore HR in BRCA1-deficient cells [7]. As the 53BP1^28A mutant is nearly as defective as the complete loss of 53BP1 for these activities, these observations indicate that additional 53BP1 effector proteins contribute to some of the 53BP1 functions.Nussenzweig and colleagues provide compelling evidence that the BRCT domain-containing protein PTIP is the missing 53BP1 effector protein [1]. The authors identified a separation-of-function mutation in 53BP1 that disrupted the first eight amino-terminal ATM sites (53BP1^8A). The 53BP1^8A mutant behaved the same as the wild-type protein with respect to CSR—a physiological process dependent on NHEJ—but failed to promote genome instability (radial chromosome formation) in BRCA1-deficient cells after treatment with a PARP inhibitor. Since RIF1-deficient cells have impaired CSR and RIF1 can localize to break sites in cells expressing the 53BP1^8A mutant, this suggests that a protein other than RIF1 binds to the N-terminal region of 53BP1 to inhibit HR.The newly identified 53BP1 effector protein PTIP is a multifunctional DNA repair factor that interacts with phosphorylated Ser 25 of 53BP1 through its tandem BRCT domains [8]—a site that was mutated in the 53BP1^8A allele. PTIP is also part of the MLL3/MLL4 histone H3 Lys 4 methyltransferase complexes but this function seems to be unrelated to its role as a 53BP1 co-factor.Nussenzweig and co-workers found that PTIP-deficient cells are sensitive to ionizing radiation but tolerant of DNA damaging agents that are toxic to HR-deficient cells, which suggests a role for PTIP in NHEJ. In agreement with this, the fusion frequency of uncapped telomeres was reduced in PTIP-deficient cells. Interestingly, as in the case of the 53BP1^8A allele, PTIP-deficient B cells were proficient in switching their immunoglobulin locus, although this switching event is impaired in RIF1^−/− B cells. This suggests that PTIP might participate selectively in pathological NHEJ.Nussenzweig and colleagues next generated a conditional BRCA1^−/− PTIP^−/− mouse to investigate the contribution of PTIP to the genome instability of BRCA1-deficient B cells. Loss of PTIP restored normal growth kinetics and genome stability to BRCA1-deficient cells treated with a PARP inhibitor. In addition, RAD51 IR-induced focus formation was restored in BRCA1^−/− PTIP^−/− cells. As the primary defect of BRCA1-deficient cells with respect to HR seems to be at the level of resection, the accumulation of the single-stranded DNA-binding protein RPA into IR-induced foci was then analysed. The finding that PTIP-deficient cells have an increased number of RPA foci per cell supports a role for PTIP in blocking resection. Together, this suggests that PTIP opposes DNA end resection and mutagenic DSB repair in BRCA1-deficient cells.These results were surprising as they revealed that the 53BP1 activities relating to physiological NHEJ (during CSR) and mutagenic NHEJ (after PARP inhibition) can be separated, and that they are carried out by two distinct proteins that ‘read'' ATM-dependent 53BP1 phosphorylation. The relationship between 53BP1, RIF1 and PTIP is probably complex, as suggested by the possible competition between RIF1 and PTIP, and the observation that both proteins contribute in an additive manner to the fusion of dysfunctional telomeres, downstream from 53BP1.According to these findings, multiple phosphorylation events in 53BP1 seem to integrate ATM activity to control distinct aspects of DSB repair pathway choice (Fig 1). Establishing exactly how an increase of ATM activity at break sites is translated into the coordination of 53BP1 phosphorylation, with RIF1 and PTIP binding, will be an important milestone towards understanding 53BP1 function. Indeed, multi-site phosphorylation and its recognition by binding proteins can be used to develop switch-like responses that might be important for organizing the chromatin at DSB sites.Open in a separate windowFigure 153BP1 phospho-dependent interactions involved in DSB repair. PTIP and RIF1 interact with chromatin-bound and ATM-phosphorylated 53BP1 at DSB sites. PTIP binds directly to 53BP1 phosphorylated on Ser 14;25 (within the first eight Ser/Thr-Q sites). RIF1 binds to phosphorylated 53BP1 either directly or through an intermediate factor (X). The carboxy-terminal seven Ser/Thr-Q sites (9–15 Ser/Thr-Q sites) are involved in the interaction of RIF1–53BP1, although the amino-terminal eight Ser/Thr-Q sites might stabilize the binding. It is unknown whether PTIP and RIF1 can associate simultaneously with 53BP1 (left side of the figure), or if the binding is exclusive, due to either differential phosphorylation of the Ser/Thr-Q sites or steric hindrance (right side of the figure). 53BP1, PTIP and RIF1 block DNA end-resection and promote NHEJ repair. Although both PTIP and RIF1 contribute to dysfunctional telomere fusions, they also have distinct functions downstream from 53BP1. While RIF1 is essential for CSR and has a milder effect on toxic NHEJ events, PTIP is dispensable for CSR and has a more prominent role in toxic NHEJ events that lead to genome instability in BRCA1-deficient cells. ATM, ataxia telangiectasia-mutated; CSR, class switch recombination; DSB, double-stranded break; NHEJ, non-homologous end-joining.The identification of PTIP as a new 53BP1 effector also deepens the mystery of DSB repair pathway choice regulation by 53BP1. Future studies are needed to elucidate how 53BP1 and its effector proteins block resection. Are PTIP and RIF1 blocking specific nucleases? Do they act in a temporally distinct fashion or are they distributed in distinct subdomains of the chromatin flanking DSB sites? What is the function of PTIP in relation to the cell cycle? Testing whether RIF1 binds directly to 53BP1, and if so to which phosphorylated site, might answer some of the above questions. The identification of a RIF1 mutation that selectively disrupts 53BP1 binding would enable surgical manipulation of the 53BP1–RIF1–PTIP circuit at DSB sites.Another unresolved issue is whether 53BP1 acts solely by recruiting RIF1 and PTIP, or whether 53BP1 has a more active role in blocking resection. We have shown that 53BP1 localizes to the chromatin flanking the DSBs by binding to methylated and ubiquitinated nucleosomes, in a wheel clamp-like manner [9]. This suggests that 53BP1 might modify the nucleosomal array structure in a way that makes it refractory to the resection machinery. Recognizing how nucleosomes modified by 53BP1 cooperate with RIF1 and PTIP might provide clues to the role of these two proteins in end protection.It is important to note that in human cells, PTIP might not be recruited to DSB sites in a 53BP1- and ATM-dependent manner [8]. Furthermore, in the avian B-cell line DT40, PTIP promotes HR instead of inhibiting it [10]. It will be important to revisit these studies to tease out whether these differences are due to context-, experiment- or species-specific effects.The identification of PTIP as a candidate genetic modifier of BRCA1-deficient tumours is an important finding. As noted by the authors, disabling the PTIP–53BP1 interaction pharmacologically might selectively restore HR in BRCA1-deficient cells, which might be useful in certain contexts, for example as a chemopreventive strategy.     

Impaired TIP60-mediated H4K16 acetylation accounts for the aberrant chromatin accumulation of 53BP1 and RAP80 in Fanconi anemia pathway-deficient cells

To rescue collapsed replication forks cells utilize homologous recombination (HR)-mediated mechanisms to avoid the induction of gross chromosomal abnormalities that would be generated by non-homologous end joining (NHEJ). Using DNA interstrand crosslinks as a replication barrier, we investigated how the Fanconi anemia (FA) pathway promotes HR at stalled replication forks. FA pathway inactivation results in Fanconi anemia, which is associated with a predisposition to cancer. FANCD2 monoubiquitination and assembly in subnuclear foci appear to be involved in TIP60 relocalization to the chromatin to acetylates histone H4K16 and prevents the binding of 53BP1 to its docking site, H4K20Me2. Thus, FA pathway loss-of-function results in accumulation of 53BP1, RIF1 and RAP80 at damaged chromatin, which impair DNA resection at stalled replication fork-associated DNA breaks and impede HR. Consequently, DNA repair in FA cells proceeds through the NHEJ pathway, which is likely responsible for the accumulation of chromosome abnormalities. We demonstrate that the inhibition of NHEJ or deacetylase activity rescue HR in FA cells.     

Opposing roles for 53BP1 during homologous recombination

Although DNA non-homologous end-joining repairs most DNA double-strand breaks (DSBs) in G2 phase, late repairing DSBs undergo resection and repair by homologous recombination (HR). Based on parallels to the situation in G1 cells, previous work has suggested that DSBs that undergo repair by HR predominantly localize to regions of heterochromatin (HC). By using H3K9me3 and H4K20me3 to identify HC regions, we substantiate and extend previous evidence, suggesting that HC-DSBs undergo repair by HR. Next, we examine roles for 53BP1 and BRCA1 in this process. Previous studies have shown that 53BP1 is pro-non-homologous end-joining and anti-HR. Surprisingly, we demonstrate that in G2 phase, 53BP1 is required for HR at HC-DSBs with its role being to promote phosphorylated KAP-1 foci formation. BRCA1, in contrast, is dispensable for pKAP-1 foci formation but relieves the barrier caused by 53BP1. As 53BP1 is retained at irradiation-induced foci during HR, we propose that BRCA1 promotes displacement but retention of 53BP1 to allow resection and any necessary HC modifications to complete HR. In contrast to this role for 53BP1 in HR in G2 phase, we show that it is dispensable for HR in S phase, where HC regions are likely relaxed during replication.     

BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair

Brca1 is required for DNA repair by homologous recombination (HR) and normal embryonic development. Here we report that deletion of the DNA damage response factor 53BP1 overcomes embryonic lethality in Brca1-nullizygous mice and rescues HR deficiency, as measured by hypersensitivity to polyADP-ribose polymerase (PARP) inhibition. However, Brca1,53BP1 double-deficient cells are hypersensitive to DNA interstrand crosslinks (ICLs), indicating that BRCA1 has an additional role in DNA crosslink repair that is distinct from HR. Disruption of the nonhomologous end-joining (NHEJ) factor, Ku, promotes DNA repair in Brca1-deficient cells; however deletion of either Ku or 53BP1 exacerbates genomic instability in cells lacking FANCD2, a mediator of the Fanconi anemia pathway for ICL repair. BRCA1 therefore has two separate roles in ICL repair that can be modulated by manipulating NHEJ, whereas FANCD2 provides a key activity that cannot be bypassed by ablation of 53BP1 or Ku.     

MRE11-RAD50-NBS1 Complex Dictates DNA Repair Independent of H2AX

DNA double-strand breaks (DSBs) represent one of the most serious forms of DNA damage that can occur in the genome. Here, we show that the DSB-induced signaling cascade and homologous recombination (HR)-mediated DSB repair pathway can be genetically separated. We demonstrate that the MRE11-RAD50-NBS1 (MRN) complex acts to promote DNA end resection and the generation of single-stranded DNA, which is critically important for HR repair. These functions of the MRN complex can occur independently of the H2AX-mediated DNA damage signaling cascade, which promotes stable accumulation of other signaling and repair proteins such as 53BP1 and BRCA1 to sites of DNA damage. Nevertheless, mild defects in HR repair are observed in H2AX-deficient cells, suggesting that the H2AX-dependent DNA damage-signaling cascade assists DNA repair. We propose that the MRN complex is responsible for the initial recognition of DSBs and works together with both CtIP and the H2AX-dependent DNA damage-signaling cascade to facilitate repair by HR and regulate DNA damage checkpoints.     

A new pathway that regulates 53BP1 stability implicates cathepsin L and vitamin D in DNA repair

Genomic instability due to telomere dysfunction and defective repair of DNA double-strand breaks (DSBs) is an underlying cause of ageing-related diseases. 53BP1 is a key factor in DNA DSBs repair and its deficiency is associated with genomic instability and cancer progression. Here, we uncover a novel pathway regulating the stability of 53BP1. We demonstrate an unprecedented role for the cysteine protease Cathepsin L (CTSL) in the degradation of 53BP1. Overexpression of CTSL in wild-type fibroblasts leads to decreased 53BP1 protein levels and changes in its cellular distribution, resulting in defective repair of DNA DSBs. Importantly, we show that the defects in DNA repair associated with 53BP1 deficiency upon loss of A-type lamins are due to upregulation of CTSL. Furthermore, we demonstrate that treatment with vitamin D stabilizes 53BP1 and promotes DNA DSBs repair via inhibition of CTSL, providing an as yet unsuspected link between vitamin D action and DNA repair. Given that CTSL upregulation is a hallmark of cancer and progeria, regulation of this pathway could be of great therapeutic significance for these diseases.     

Ring Finger Nuclear Factor RNF168 Is Important for Defects in Homologous Recombination Caused by Loss of the Breast Cancer Susceptibility Factor BRCA1

The RING finger nuclear factor RNF168 is required for recruitment of several DNA damage response factors to double strand breaks (DSBs), including 53BP1 and BRCA1. Because 53BP1 and BRCA1 function antagonistically during the DSB repair pathway homologous recombination (HR), the influence of RNF168 on HR has been unclear. We report that RNF168 depletion causes an elevated frequency of two distinct HR pathways (homology-directed repair and single strand annealing), suppresses defects in HR caused by BRCA1 silencing, but does not suppress HR defects caused by disruption of CtIP, RAD50, BRCA2, or RAD51. Furthermore, RNF168-depleted cells can form ionizing radiation-induced foci of the recombinase RAD51 without forming BRCA1 ionizing radiation-induced foci, indicating that this loss of BRCA1 recruitment to DSBs does not reflect a loss of function during HR. Additionally, we find that RNF168 and 53BP1 have a similar influence on HR. We suggest that RNF168 is important for HR defects caused by BRCA1 loss.     

BRCA1-Ku80 Protein Interaction Enhances End-joining Fidelity of Chromosomal Double-strand Breaks in the G1 Phase of the Cell Cycle

Quality control of DNA double-strand break (DSB) repair is vital in preventing mutagenesis. Non-homologous end-joining (NHEJ), a repair process predominant in the G₁ phase of the cell cycle, rejoins DSBs either accurately or with errors, but the mechanisms controlling its fidelity are poorly understood. Here we show that BRCA1, a tumor suppressor, enhances the fidelity of NHEJ-mediated DSB repair and prevents mutagenic deletional end-joining through interaction with canonical NHEJ machinery during G₁. BRCA1 binds and stabilizes Ku80 at DSBs through its N-terminal region, promotes precise DSB rejoining, and increases cellular resistance to radiation-induced DNA damage in a G₁ phase-specific manner. These results suggest that BRCA1, as a central player in genome integrity maintenance, ensures high fidelity repair of DSBs by not only promoting homologous recombination repair in G₂/M phase but also facilitating fidelity of Ku80-dependent NHEJ repair, thus preventing deletional end-joining of chromosomal DSBs during G₁.     

Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1) Promotes Non-homologous End Joining and Inhibits Homologous Recombination Repair upon DNA Damage

Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) has been shown to be involved in gene silencing and DNA damage. However, the exact mechanisms of how SMCHD1 participates in DNA damage remains largely unknown. Here we present evidence that SMCHD1 recruitment to DNA damage foci is regulated by 53BP1. Knocking out SMCHD1 led to aberrant γH2AX foci accumulation and compromised cell survival upon DNA damage, demonstrating the critical role of SMCHD1 in DNA damage repair. Following DNA damage induction, SMCHD1 depletion resulted in reduced 53BP1 foci and increased BRCA1 foci, as well as less efficient non-homologous end joining (NHEJ) and elevated levels of homologous recombination (HR). Taken together, these results suggest an important function of SMCHD1 in promoting NHEJ and repressing HR repair in response to DNA damage.