GRB2 enforces homology-directed repair initiation by MRE11

Ye, Zu; Xu, Shengfeng; Shi, Yin; Bacolla, Albino; Syed, Aleem; Moiani, Davide; Tsai, Chi Lin; Shen, Qiang; Peng, Guang; Leonard, Paul G.; Jones, Darin E.; Wang, Bin; Tainer, John A.; Ahmed, Zamal

doi:10.1126/sciadv.abe9254

Cited by 27 publications

(12 citation statements)

References 55 publications

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“…Lesion scanning, repair licensing, and DNA incision steps are complex structural mechanisms required to control DDR for genome integrity, as observed for many nucleases (42,53,54) and for dsDNA break repair pathways (55)(56)(57). NER must similarly be strictly coordinated because of the toxicity and mutagenicity of its intermediates and the S4 and S5.…”

Section: Discussionmentioning

confidence: 99%

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Bralić

Tehseen

Sobhy

et al. 2022

Nucleic Acids Research

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Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5′-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5′-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

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Section: Discussionmentioning

confidence: 99%

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Bralić

Tehseen

Sobhy

et al. 2022

Nucleic Acids Research

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“…Indeed, structure-specific nucleases FEN1, XPG, and MRE11 have key structural, DNA sculpting, and catalytic roles that are controlled in different complexes ( Shibata et al, 2014 ; Tsutakawa et al, 2017 ; Tsutakawa et al, 2020a ). An example of the significance of pathway choice in biological outcome, XRCC1 links MRE11 and PolQ helicase to promote error-prone alternative end joining of DNA breaks ( Eckelmann et al, 2020 ), but MRE11 initiation of homology-directed repair (HDR) at breaks is promoted by GRB2 adaptor ( Ye et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication

Tsutakawa

Bacolla

Katsonis³

et al. 2021

Front. Mol. Biosci.

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All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.

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“…DYNLL1 is constitutively associated with 53BP1 and is recruited to DSBs within minutes of damage, and this is dependent on 53BP1 and no other known associated protein. MRE11 is one earliest factors recruited to DSBs with multiple proteins involved in this process 33, 39 . DYNLL1 directly binds MRE11 to remove it from DNA lesions.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs

Zhou

Swift

Syed

et al. 2023

Preprint

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Extent and efficacy of DNA end resection at DNA double strand break (DSB)s determines the choice of repair pathway. Here we describe how the 53BP1 associated protein DYNLL1 works in tandem with Shieldin and the CST complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1 where it limits end resection by binding and disrupting the MRE11 dimer. The Shieldin complex is recruited to a fraction of 53BP1-positive DSBs hours after DYNLL1 predominantly in the G1 cells. Shieldin localization to DSBs is dependent on MRE11 activity and is regulated by the interaction of DYNLL1 with MRE11. BRCA1-deficient cells rendered resistant to PARP inhibitors by the loss of Shieldin proteins can be re-sensitized by the constitutive association of DYNLL1 with MRE11. These results define the temporal and functional dynamics of the 53BP1-centric DNA end resection factors in cells.

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GRB2 enforces homology-directed repair initiation by MRE11

Cited by 27 publications

References 55 publications

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication

Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs

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