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3. EXO1 protects BRCA1-deficient cells against toxic DNA lesions

Author

van de Kooij, Bert, Schreuder, Anne, Pavani, Raphael, Garzero, Veronica, Uruci, Sidrit, Wendel, Tiemen J., van Hoeck, Arne, San Martin Alonso, Marta, Everts, Marieke, Koerse, Dana, Callen, Elsa, Boom, Jasper, Mei, Hailiang, Cuppen, Edwin, Luijsterburg, Martijn S., van Vugt, Marcel A.T.M., Nussenzweig, André, van Attikum, Haico, and Noordermeer, Sylvie M.

Published
2024
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4. An atlas of substrate specificities for the human serine/threonine kinome

Author

Johnson, Jared L., Yaron, Tomer M., Huntsman, Emily M., Kerelsky, Alexander, Song, Junho, Regev, Amit, Lin, Ting-Yu, Liberatore, Katarina, Cizin, Daniel M., Cohen, Benjamin M., Vasan, Neil, Ma, Yilun, Krismer, Konstantin, Robles, Jaylissa Torres, van de Kooij, Bert, van Vlimmeren, Anne E., Andrée-Busch, Nicole, Käufer, Norbert F., Dorovkov, Maxim V., Ryazanov, Alexey G., Takagi, Yuichiro, Kastenhuber, Edward R., Goncalves, Marcus D., Hopkins, Benjamin D., Elemento, Olivier, Taatjes, Dylan J., Maucuer, Alexandre, Yamashita, Akio, Degterev, Alexei, Uduman, Mohamed, Lu, Jingyi, Landry, Sean D., Zhang, Bin, Cossentino, Ian, Linding, Rune, Blenis, John, Hornbeck, Peter V., Turk, Benjamin E., Yaffe, Michael B., and Cantley, Lewis C.

Published
2023
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5. FIRRM/C1orf112 is synthetic lethal with PICH and mediates RAD51 dynamics

Author

Stok, Colin, Tsaridou, Stavroula, van den Tempel, Nathalie, Everts, Marieke, Wierenga, Elles, Bakker, Femke J., Kok, Yannick, Alves, Inês Teles, Jae, Lucas T., Raas, Maximilian W.D., Huis in 't Veld, Pim J., de Boer, H. Rudolf, Bhattacharya, Arkajyoti, Karanika, Eleftheria, Warner, Harry, Chen, Mengting, van de Kooij, Bert, Dessapt, Julien, ter Morsche, Lars, Perepelkina, Polina, Fradet-Turcotte, Amelie, Guryev, Victor, Tromer, Eelco C., Chan, Kok-Lung, Fehrmann, Rudolf S.N., and van Vugt, Marcel A.T.M.

Published
2023
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8. The Fanconi anemia core complex promotes CtIP-dependent end resection to drive homologous recombination at DNA double-strand breaks

Author

van de Kooij, Bert; https://orcid.org/0000-0003-1042-8409, van der Wal, Fenna J, Rother, Magdalena B, Wiegant, Wouter W, Creixell, Pau, Stout, Merula; https://orcid.org/0000-0001-6643-7860, Joughin, Brian A; https://orcid.org/0000-0003-1022-9450, Vornberger, Julia, Altmeyer, Matthias; https://orcid.org/0000-0003-3780-1170, van Vugt, Marcel A T M; https://orcid.org/0000-0002-3202-4678, Yaffe, Michael B; https://orcid.org/0000-0002-9547-3251, van Attikum, Haico; https://orcid.org/0000-0001-8590-0240, van de Kooij, Bert; https://orcid.org/0000-0003-1042-8409, van der Wal, Fenna J, Rother, Magdalena B, Wiegant, Wouter W, Creixell, Pau, Stout, Merula; https://orcid.org/0000-0001-6643-7860, Joughin, Brian A; https://orcid.org/0000-0003-1022-9450, Vornberger, Julia, Altmeyer, Matthias; https://orcid.org/0000-0003-3780-1170, van Vugt, Marcel A T M; https://orcid.org/0000-0002-3202-4678, Yaffe, Michael B; https://orcid.org/0000-0002-9547-3251, and van Attikum, Haico; https://orcid.org/0000-0001-8590-0240

Abstract

During the repair of interstrand crosslinks (ICLs) a DNA double-strand break (DSB) is generated. The Fanconi anemia (FA) core complex, which is recruited to ICLs, promotes high-fidelity repair of this DSB by homologous recombination (HR). However, whether the FA core complex also promotes HR at ICL-independent DSBs, for example induced by ionizing irradiation or nucleases, remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen. Using isogenic cell line models, we further demonstrated an HR-promoting function of FANCL and Ube2T, and of their ubiquitination substrate FANCD2. We show that FANCL and Ube2T localize at DSBs in a FANCM-dependent manner, and are required for the DSB accumulation of FANCD2. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of CtIP at DSBs, thereby promoting end resection and Rad51 loading. Together, these data demonstrate a dual genome maintenance function of the FA core complex and FANCD2 in promoting repair of both ICLs and DSBs.

Published
2024

9. EXO1 protects BRCA1-deficient cells against toxic DNA lesions

Author

CMM Groep Snippert, CMM Groep Van Mil, van de Kooij, Bert, Schreuder, Anne, Pavani, Raphael, Garzero, Veronica, Uruci, Sidrit, Wendel, Tiemen J., van Hoeck, Arne, San Martin Alonso, Marta, Everts, Marieke, Koerse, Dana, Callen, Elsa, Boom, Jasper, Mei, Hailiang, Cuppen, Edwin, Luijsterburg, Martijn S., van Vugt, Marcel A.T.M., Nussenzweig, André, van Attikum, Haico, Noordermeer, Sylvie M., CMM Groep Snippert, CMM Groep Van Mil, van de Kooij, Bert, Schreuder, Anne, Pavani, Raphael, Garzero, Veronica, Uruci, Sidrit, Wendel, Tiemen J., van Hoeck, Arne, San Martin Alonso, Marta, Everts, Marieke, Koerse, Dana, Callen, Elsa, Boom, Jasper, Mei, Hailiang, Cuppen, Edwin, Luijsterburg, Martijn S., van Vugt, Marcel A.T.M., Nussenzweig, André, van Attikum, Haico, and Noordermeer, Sylvie M.

Published
2024

11. The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks

Author

van de Kooij, Bert, primary, van der Wal, Fenna J., additional, Rother, Magdalena B., additional, Creixell, Pau, additional, Stout, Merula, additional, Wiegant, Wouter, additional, Joughin, Brian A., additional, Vornberger, Julia, additional, van Vugt, Marcel A.T.M., additional, Altmeyer, Matthias, additional, Yaffe, Michael B., additional, and van Attikum, Haico, additional

Published
2023
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12. FIRRM/C1orf112 is synthetic lethal with PICH and mediates RAD51 dynamics

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Stok, Colin, Tsaridou, Stavroula, van den Tempel, Nathalie, Everts, Marieke, Wierenga, Elles, Bakker, Femke J, Kok, Yannick, Alves, Inês Teles, Jae, Lucas T, Raas, Maximilian W D, Huis In 't Veld, Pim J, de Boer, H Rudolf, Bhattacharya, Arkajyoti, Karanika, Eleftheria, Warner, Harry, Chen, Mengting, van de Kooij, Bert, Dessapt, Julien, Ter Morsche, Lars, Perepelkina, Polina, Fradet-Turcotte, Amelie, Guryev, Victor, Tromer, Eelco C, Chan, Kok-Lung, Fehrmann, Rudolf S N, van Vugt, Marcel A T M, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Stok, Colin, Tsaridou, Stavroula, van den Tempel, Nathalie, Everts, Marieke, Wierenga, Elles, Bakker, Femke J, Kok, Yannick, Alves, Inês Teles, Jae, Lucas T, Raas, Maximilian W D, Huis In 't Veld, Pim J, de Boer, H Rudolf, Bhattacharya, Arkajyoti, Karanika, Eleftheria, Warner, Harry, Chen, Mengting, van de Kooij, Bert, Dessapt, Julien, Ter Morsche, Lars, Perepelkina, Polina, Fradet-Turcotte, Amelie, Guryev, Victor, Tromer, Eelco C, Chan, Kok-Lung, Fehrmann, Rudolf S N, and van Vugt, Marcel A T M

Published
2023

13. Multi-pathway DNA-repair reporters reveal competition between end-joining, single-strand annealing and homologous recombination at Cas9-induced DNA double-strand breaks

Author

Massachusetts Institute of Technology. Department of Biology, van de Kooij, Bert, Kruswick, Alex, van Attikum, Haico, Yaffe, Michael B, Massachusetts Institute of Technology. Department of Biology, van de Kooij, Bert, Kruswick, Alex, van Attikum, Haico, and Yaffe, Michael B

Abstract

AbstractDNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to mutagenesis and genomic loss. DSB-repair pathway cross-talk and compensation is incompletely understood, despite its importance for genomic stability, oncogenesis, and genome editing using CRISPR/Cas9. To address this, we constructed and validated three fluorescent Cas9-based reporters, named DSB-Spectrum, that simultaneously quantify the contribution of multiple DNA repair pathways at a DSB. DSB-Spectrum reporters distinguish between DSB-repair by error-free canonical non-homologous end-joining (c-NHEJ) versus homologous recombination (HR; reporter 1), mutagenic repair versus HR (reporter 2), and mutagenic end-joining versus single strand annealing (SSA) versus HR (reporter 3). Using these reporters, we show that inhibiting the c-NHEJ factor DNA-PKcs increases repair by HR, but also substantially increases mutagenic SSA. Our data indicate that SSA-mediated DSB-repair also occurs at endogenous genomic loci, driven by Alu elements or homologous gene regions. Finally, we demonstrate that long-range end-resection factors DNA2 and Exo1 promote SSA and reduce HR, when both pathways compete for the same substrate. These new Cas9-based DSB-Spectrum reporters facilitate the comprehensive analysis of repair pathway crosstalk and DSB-repair outcome.

Published
2023

14. Limited Mitochondrial Permeabilization Causes DNA Damage and Genomic Instability in the Absence of Cell Death

Author

Ichim, Gabriel, Lopez, Jonathan, Ahmed, Shafiq U., Muthalagu, Nathiya, Giampazolias, Evangelos, Delgado, M. Eugenia, Haller, Martina, Riley, Joel S., Mason, Susan M., Athineos, Dimitris, Parsons, Melissa J., van de Kooij, Bert, Bouchier-Hayes, Lisa, Chalmers, Anthony J., Rooswinkel, Rogier W., Oberst, Andrew, Blyth, Karen, Rehm, Markus, Murphy, Daniel J., and Tait, Stephen W.G.

Published
2015
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17. A global atlas of substrate specificities for the human serine/threonine kinome

Author

Johnson, Jared L., primary, Yaron, Tomer M., additional, Huntsman, Emily M., additional, Kerelsky, Alexander, additional, Song, Junho, additional, Regev, Amit, additional, Lin, Ting-Yu, additional, Liberatore, Katarina, additional, Cizin, Daniel M., additional, Cohen, Benjamin M., additional, Vasan, Neil, additional, Ma, Yilun, additional, Krismer, Konstantin, additional, Robles, Jaylissa Torres, additional, van de Kooij, Bert, additional, van Vlimmeren, Anne E., additional, Andrée-Busch, Nicole, additional, Käufer, Norbert, additional, Dorovkov, Maxim V., additional, Ryazanov, Alexey G., additional, Takagi, Yuichiro, additional, Kastenhuber, Edward R., additional, Goncalves, Marcus D., additional, Elemento, Olivier, additional, Taatjes, Dylan J., additional, Maucuer, Alexandre, additional, Yamashita, Akio, additional, Degterev, Alexei, additional, Linding, Rune, additional, Blenis, John, additional, Hornbeck, Peter V., additional, Turk, Benjamin E., additional, Yaffe, Michael B., additional, and Cantley, Lewis C., additional

Published
2022
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21. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs

Author

Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Van de Kooij, Bert, Creixell Morera, Pau, Van Vlimmeren, Anne Elise, Joughin, Brian Alan, Yaffe, Michael B, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Van de Kooij, Bert, Creixell Morera, Pau, Van Vlimmeren, Anne Elise, Joughin, Brian Alan, and Yaffe, Michael B

Abstract

© van de Kooij et al. Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the -3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE- 4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phosphomotif amplifiers of Plk1 signaling., Dutch Cancer Society (Grant BUIT 2015-7546), National Cancer Institute (U.S.) (Grant K99CA226396), National Institutes of Health (U.S.) (Grant 01-GM104047), National Institutes of Health (U.S.) (Grant 01-ES015339), National Institutes of Health (U.S.) (Grant R35-ES028374), National Cancer Institute (U.S.) (Grant P30-CA14051), National Institute of Environmental Health Sciences (Grant P30-ES002109)

Published
2020

23. Author response: Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs

Author

van de Kooij, Bert, primary, Creixell, Pau, additional, van Vlimmeren, Anne, additional, Joughin, Brian A, additional, Miller, Chad J, additional, Haider, Nasir, additional, Simpson, Craig D, additional, Linding, Rune, additional, Stambolic, Vuk, additional, Turk, Benjamin E, additional, and Yaffe, Michael B, additional

Published
2019
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24. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output

Author

Miller, Chad J., primary, Lou, Hua Jane, additional, Simpson, Craig, additional, van de Kooij, Bert, additional, Ha, Byung Hak, additional, Fisher, Oriana S., additional, Pirman, Natasha L., additional, Boggon, Titus J., additional, Rinehart, Jesse, additional, Yaffe, Michael B., additional, Linding, Rune, additional, and Turk, Benjamin E., additional

Published
2019
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26. Proteasome Activation by Small Molecules

Author

Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, Ovaa, Huib, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Functional Genomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
0301 basic medicine, Proteasome Endopeptidase Complex, p38 mitogen-activated protein kinases, Proteolysis, Clinical Biochemistry, Biology, Biochemistry, p38 Mitogen-Activated Protein Kinases, Cell Line, 03 medical and health sciences, Enzyme activator, SDG 3 - Good Health and Well-being, Cell Line, Tumor, Drug Discovery, medicine, Journal Article, Humans, ASK1, Molecular Biology, Pharmacology, Tumor, medicine.diagnostic_test, Activity-based proteomics, Protein turnover, Imidazoles, Cell biology, Enzyme Activation, 030104 developmental biology, Proteasome, Molecular Medicine, Chemical genetics, Proteasome Inhibitors
Abstract

Drugs that increase 26S proteasome activity have potential therapeutic applications in the treatment of neurodegenerative diseases. A chemical genetics screen of over 2,750 compounds using a proteasome activity probe as a readout in a high-throughput live-cell fluorescence-activated cell sorting-based assay revealed more than ten compounds that increase proteasome activity, with the p38 MAPK inhibitor PD169316 being one of the most potent ones. Genetic and chemical inhibition of either p38 MAPK, its upstream regulators, ASK1 and MKK6, and downstream target, MK2, enhance proteasome activity. Chemical activation of the 26S proteasome increases PROTAC-mediated and ubiquitin-dependent protein degradation and decreases the levels of both overexpressed and endogenous α-synuclein, without affecting the overall protein turnover. In addition, survival of cells overexpressing toxic α-synuclein assemblies is increased in the presence of p38 MAPK inhibitors. These findings highlight the potential of activation of 26S proteasome activity and that this can be achieved through multiple mechanisms by distinct molecules.

Published
2016
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27. Proteasome Activation by Small Molecules

Author

Leestemaker, Yves, primary, de Jong, Annemieke, additional, Witting, Katharina F., additional, Penning, Renske, additional, Schuurman, Karianne, additional, Rodenko, Boris, additional, Zaal, Esther A., additional, van de Kooij, Bert, additional, Laufer, Stefan, additional, Heck, Albert J.R., additional, Borst, Jannie, additional, Scheper, Wiep, additional, Berkers, Celia R., additional, and Ovaa, Huib, additional

Published
2017
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28. NEK10tyrosine phosphorylates p53 and controls its transcriptional activity

Author

Haider, Nasir, Dutt, Previn, van de Kooij, Bert, Ho, Jason, Palomero, Luis, Pujana, Miquel Angel, Yaffe, Michael, and Stambolic, Vuk

Abstract

In response to genotoxic stress, multiple kinase signaling cascades are activated, many of them directed towards the tumor suppressor p53, which coordinates the DNA damage response (DDR). Defects in DDR pathways lead to an accumulation of mutations that can promote tumorigenesis. Emerging evidence implicates multiple members of the NimA-related kinase (NEK) family (NEK1, NEK10, and NEK11) in the DDR. Here, we describe a function for NEK10in the regulation of p53 transcriptional activity through tyrosine phosphorylation. NEK10loss increases cellular proliferation by modulating the p53-dependent transcriptional output. NEK10directly phosphorylates p53 on Y327, revealing NEK10’sunexpected substrate specificity. A p53 mutant at this site (Y327F) acts as a hypomorph, causing an attenuated p53-mediated transcriptional response. Consistently, NEK10-deficient cells display heightened sensitivity to DNA-damaging agents. Further, a combinatorial score of NEK10and TP53-target gene expression is an independent predictor of a favorable outcome in breast cancers.

Published
2020
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29. Proteasome Activation by Small Molecules

Author

Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, Ovaa, Huib, Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, and Ovaa, Huib

Published
2017

30. Proteasome Activation by Small Molecules

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, Ovaa, Huib, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, and Ovaa, Huib

Published
2017

31. Proteasome Activation by Small Molecules

Author

Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, Ovaa, Huib, Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Leestemaker, Yves, de Jong, Annemieke, Witting, Katharina F, Penning, Renske, Schuurman, Karianne, Rodenko, Boris, Zaal, Esther A, van de Kooij, Bert, Laufer, Stefan, Heck, Albert J R, Borst, Jannie, Scheper, Wiep, Berkers, Celia R, and Ovaa, Huib

Published
2017

32. The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks.

Author

van de Kooij B, van der Wal FJ, Rother MB, Creixell P, Stout M, Wiegant W, Joughin BA, Vornberger J, van Vugt MATM, Altmeyer M, Yaffe MB, and van Attikum H

Abstract

Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological DNA damaging processes. DSBs are also generated as intermediates during the repair of interstrand crosslinks (ICLs). In this context, the Fanconi anemia (FA) core complex, which is effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether the FA core complex also promotes HR at ICL-independent DSBs remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen with cells carrying the DSB-repair reporter DSB-Spectrum. Using isogenic cell-line models, we validated the HR-function of FANCL and Ube2T, and demonstrated a similar function for their ubiquitination-substrate FANCD2. We further show that FANCL and Ube2T are directly recruited to DSBs and are required for the accumulation of FANCD2 at these break sites. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of the nuclease CtIP at DSBs, and consequently for optimal end-resection and Rad51 loading. CtIP overexpression rescues HR in FANCL-deficient cells, validating that FANCL primarily regulates HR by promoting CtIP recruitment. Together, these data demonstrate that the FA core complex and FANCD2 have a dual genome maintenance function by promoting repair of DSBs as well as the repair of ICLs.

Published
2023
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