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

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

bioRxiv : the preprint server for biology

2023

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 ... ...

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.
Language	English
Publishing date	2023-09-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.05.556391
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Article ; Online: DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance.

Rother, Magdalena B / van Attikum, Haico

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2017 Volume 372, Issue 1731

Abstract: Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational ... ...

Abstract	Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
MeSH term(s)	Animals ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/metabolism ; DNA Breaks, Double-Stranded ; DNA Helicases/metabolism ; DNA Repair ; DNA-Binding Proteins/metabolism ; Humans ; Transcription Factors/metabolism
Chemical Substances	Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Transcription Factors ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2017-08-25
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2016.0285
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Article ; Online: Poly(ADP-ribosyl)ation temporally confines SUMO-dependent ataxin-3 recruitment to control DNA double-strand break repair.

Pfeiffer, Annika / Herzog, Laura K / Luijsterburg, Martijn S / Shah, Rashmi G / Rother, Magdalena B / Stoy, Henriette / Kühbacher, Ulrike / van Attikum, Haico / Shah, Girish M / Dantuma, Nico P

Journal of cell science

2021 Volume 134, Issue 3

Abstract: DNA damage-induced SUMOylation serves as a signal for two antagonizing proteins that both stimulate repair of DNA double-strand breaks (DSBs). Here, we demonstrate that the SUMO-dependent recruitment of the deubiquitylating enzyme ataxin-3 to DSBs, ... ...

Abstract	DNA damage-induced SUMOylation serves as a signal for two antagonizing proteins that both stimulate repair of DNA double-strand breaks (DSBs). Here, we demonstrate that the SUMO-dependent recruitment of the deubiquitylating enzyme ataxin-3 to DSBs, unlike recruitment of the ubiquitin ligase RNF4, additionally depends on poly [ADP-ribose] polymerase 1 (PARP1)-mediated poly(ADP-ribosyl)ation (PARylation). The co-dependence of ataxin-3 recruitment on PARylation and SUMOylation temporally confines ataxin-3 to DSBs immediately after occurrence of DNA damage. We propose that this mechanism ensures that ataxin-3 prevents the premature removal of DNA repair proteins only during the early phase of the DSB response and does not interfere with the subsequent timely displacement of DNA repair proteins by RNF4. Thus, our data show that PARylation differentially regulates SUMO-dependent recruitment of ataxin-3 and RNF4 to DSBs, explaining how both proteins can play a stimulatory role at DSBs despite their opposing activities.
MeSH term(s)	Ataxin-3/genetics ; Cell Line, Tumor ; DNA ; DNA Breaks, Double-Stranded ; DNA Damage ; DNA Repair/genetics ; Humans ; Poly (ADP-Ribose) Polymerase-1/genetics ; Poly ADP Ribosylation
Chemical Substances	DNA (9007-49-2) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; Ataxin-3 (EC 3.4.19.12)
Language	English
Publishing date	2021-02-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.247809
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Article ; Online: Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining.

Singh, Jenny Kaur / Smith, Rebecca / Rother, Magdalena B / de Groot, Anton J L / Wiegant, Wouter W / Vreeken, Kees / D'Augustin, Ostiane / Kim, Robbert Q / Qian, Haibin / Krawczyk, Przemek M / González-Prieto, Román / Vertegaal, Alfred C O / Lamers, Meindert / Huet, Sébastien / van Attikum, Haico

Nature communications

2021 Volume 12, Issue 1, Page(s) 6560

Abstract: DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for ... ...

Abstract	DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for DSB repair in human cells, involving the DNA-binding proteins XRCC6 (Ku70) and XRCC5 (Ku80). Other DNA-binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair, but their role in cNHEJ remained elusive. Here we show that ZNF384, a member of the C2H2 family of ZnF proteins, binds DNA ends in vitro and is recruited to DSBs in vivo. ZNF384 recruitment requires the poly(ADP-ribosyl) polymerase 1 (PARP1)-dependent expansion of damaged chromatin, followed by binding of its C2H2 motifs to the exposed DNA. Moreover, ZNF384 interacts with Ku70/Ku80 via its N-terminus, thereby promoting Ku70/Ku80 assembly and the accrual of downstream cNHEJ factors, including APLF and XRCC4/LIG4, for efficient repair at DSBs. Altogether, our data suggest that ZNF384 acts as a 'Ku-adaptor' that binds damaged DNA and Ku70/Ku80 to facilitate the build-up of a cNHEJ repairosome, highlighting a role for ZNF384 in DSB repair and genome maintenance.
MeSH term(s)	DNA/metabolism ; DNA Breaks, Double-Stranded ; Humans ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Trans-Activators ; Transcription Factors ; ZNF384 protein, human ; DNA (9007-49-2)
Language	English
Publishing date	2021-11-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-26691-0
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Article ; Online: CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks.

Rother, Magdalena B / Pellegrino, Stefania / Smith, Rebecca / Gatti, Marco / Meisenberg, Cornelia / Wiegant, Wouter W / Luijsterburg, Martijn S / Imhof, Ralph / Downs, Jessica A / Vertegaal, Alfred C O / Huet, Sébastien / Altmeyer, Matthias / van Attikum, Haico

Nature communications

2020 Volume 11, Issue 1, Page(s) 5775

Abstract: Chromatin structure is dynamically reorganized at multiple levels in response to DNA double-strand breaks (DSBs). Yet, how the different steps of chromatin reorganization are coordinated in space and time to differentially regulate DNA repair pathways is ...

Abstract	Chromatin structure is dynamically reorganized at multiple levels in response to DNA double-strand breaks (DSBs). Yet, how the different steps of chromatin reorganization are coordinated in space and time to differentially regulate DNA repair pathways is insufficiently understood. Here, we identify the Chromodomain Helicase DNA Binding Protein 7 (CHD7), which is frequently mutated in CHARGE syndrome, as an integral component of the non-homologous end-joining (NHEJ) DSB repair pathway. Upon recruitment via PARP1-triggered chromatin remodeling, CHD7 stimulates further chromatin relaxation around DNA break sites and brings in HDAC1/2 for localized chromatin de-acetylation. This counteracts the CHD7-induced chromatin expansion, thereby ensuring temporally and spatially controlled 'chromatin breathing' upon DNA damage, which we demonstrate fosters efficient and accurate DSB repair by controlling Ku and LIG4/XRCC4 activities. Loss of CHD7-HDAC1/2-dependent cNHEJ reinforces 53BP1 assembly at the damaged chromatin and shifts DSB repair to mutagenic NHEJ, revealing a backup function of 53BP1 when cNHEJ fails.
MeSH term(s)	Cell Line, Tumor ; Chromatin/metabolism ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; DNA Helicases/metabolism ; DNA Ligase ATP/metabolism ; DNA-Binding Proteins/metabolism ; Green Fluorescent Proteins/metabolism ; Histone Deacetylase 1/metabolism ; Humans ; Ku Autoantigen/metabolism ; Poly (ADP-Ribose) Polymerase-1 ; Tumor Suppressor p53-Binding Protein 1/metabolism ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Chromatin ; DNA-Binding Proteins ; LIG4 protein, human ; RNF8 protein, human ; TP53BP1 protein, human ; Tumor Suppressor p53-Binding Protein 1 ; Green Fluorescent Proteins (147336-22-9) ; RNF168 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; HDAC1 protein, human (EC 3.5.1.98) ; Histone Deacetylase 1 (EC 3.5.1.98) ; DNA Helicases (EC 3.6.4.-) ; CHD7 protein, human (EC 3.6.4.12) ; Ku Autoantigen (EC 4.2.99.-) ; DNA Ligase ATP (EC 6.5.1.1)
Language	English
Publishing date	2020-11-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-19502-5
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Article ; Online: PHF2 regulates homology-directed DNA repair by controlling the resection of DNA double strand breaks.

Alonso-de Vega, Ignacio / Paz-Cabrera, Maria Cristina / Rother, Magdalena B / Wiegant, Wouter W / Checa-Rodríguez, Cintia / Hernández-Fernaud, Juan Ramón / Huertas, Pablo / Freire, Raimundo / van Attikum, Haico / Smits, Veronique A J

Nucleic acids research

2020 Volume 48, Issue 9, Page(s) 4915–4927

Abstract: Post-translational histone modifications and chromatin remodelling play a critical role controlling the integrity of the genome. Here, we identify histone lysine demethylase PHF2 as a novel regulator of the DNA damage response by regulating DNA damage- ... ...

Abstract	Post-translational histone modifications and chromatin remodelling play a critical role controlling the integrity of the genome. Here, we identify histone lysine demethylase PHF2 as a novel regulator of the DNA damage response by regulating DNA damage-induced focus formation of 53BP1 and BRCA1, critical factors in the pathway choice for DNA double strand break repair. PHF2 knockdown leads to impaired BRCA1 focus formation and delays the resolution of 53BP1 foci. Moreover, irradiation-induced RPA phosphorylation and focus formation, as well as localization of CtIP, required for DNA end resection, to sites of DNA lesions are affected by depletion of PHF2. These results are indicative of a defective resection of double strand breaks and thereby an impaired homologous recombination upon PHF2 depletion. In accordance with these data, Rad51 focus formation and homology-directed double strand break repair is inhibited in cells depleted for PHF2. Importantly, we demonstrate that PHF2 knockdown decreases CtIP and BRCA1 protein and mRNA levels, an effect that is dependent on the demethylase activity of PHF2. Furthermore, PHF2-depleted cells display genome instability and are mildly sensitive to the inhibition of PARP. Together these results demonstrate that PHF2 promotes DNA repair by homologous recombination by controlling CtIP-dependent resection of double strand breaks.
MeSH term(s)	BRCA1 Protein/genetics ; BRCA1 Protein/metabolism ; Cell Line ; DNA Breaks, Double-Stranded ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Gene Expression Regulation ; Genomic Instability ; HeLa Cells ; Histone Demethylases/metabolism ; Histone Demethylases/physiology ; Homeodomain Proteins/metabolism ; Homeodomain Proteins/physiology ; Humans ; Recombinational DNA Repair
Chemical Substances	BRCA1 Protein ; Homeodomain Proteins ; PHF2 protein, human ; Histone Demethylases (EC 1.14.11.-) ; Endodeoxyribonucleases (EC 3.1.-) ; RBBP8 protein, human (EC 3.1.-)
Language	English
Publishing date	2020-03-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa196
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Article ; Online: CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks

Magdalena B. Rother / Stefania Pellegrino / Rebecca Smith / Marco Gatti / Cornelia Meisenberg / Wouter W. Wiegant / Martijn S. Luijsterburg / Ralph Imhof / Jessica A. Downs / Alfred C. O. Vertegaal / Sébastien Huet / Matthias Altmeyer / Haico van Attikum

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 19

Abstract: Chromatin is dynamically remodeled in response to DNA damage in favour of repair. Here the authors reveal how the chromatin remodeler CHD7 and chromatin binding protein 53BP1 regulate distinct DNA repair pathways. ...

Abstract	Chromatin is dynamically remodeled in response to DNA damage in favour of repair. Here the authors reveal how the chromatin remodeler CHD7 and chromatin binding protein 53BP1 regulate distinct DNA repair pathways.
Keywords	Science ; Q
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 19

Abstract	Chromatin is dynamically remodeled in response to DNA damage in favour of repair. Here the authors reveal how the chromatin remodeler CHD7 and chromatin binding protein 53BP1 regulate distinct DNA repair pathways.
Keywords	Science ; Q
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article ; Online: PHF6 promotes non-homologous end joining and G2 checkpoint recovery.

Warmerdam, Daniël O / Alonso-de Vega, Ignacio / Wiegant, Wouter W / van den Broek, Bram / Rother, Magdalena B / Wolthuis, Rob Mf / Freire, Raimundo / van Attikum, Haico / Medema, René H / Smits, Veronique Aj

EMBO reports

2019 Volume 21, Issue 1, Page(s) e48460

Abstract: The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DNA damage using an RNAi library of chromatin regulators. ...

Abstract	The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DNA damage using an RNAi library of chromatin regulators. We identified genes involved in chromatin remodeling, sister chromatid cohesion, and histone acetylation not previously associated with checkpoint recovery. Among these is the PHD finger protein 6 (PHF6), a gene mutated in Börjeson-Forssman-Lehmann syndrome and leukemic cancers. We find that loss of PHF6 dramatically compromises checkpoint recovery in G2 phase cells. Moreover, PHF6 is rapidly recruited to sites of DNA lesions in a PARP-dependent manner and required for efficient DNA repair through classical non-homologous end joining. These results indicate that PHF6 is a novel DNA damage response regulator that promotes end joining-mediated repair, thereby stimulating timely recovery from the G2 checkpoint.
MeSH term(s)	Cell Line, Tumor ; DNA End-Joining Repair ; G2 Phase Cell Cycle Checkpoints ; Growth Disorders ; Humans ; Hypogonadism ; Mental Retardation, X-Linked ; Repressor Proteins/genetics
Chemical Substances	PHF6 protein, human ; Repressor Proteins
Language	English
Publishing date	2019-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.201948460
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Article ; Online: Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining

Jenny Kaur Singh / Rebecca Smith / Magdalena B. Rother / Anton J. L. de Groot / Wouter W. Wiegant / Kees Vreeken / Ostiane D’Augustin / Robbert Q. Kim / Haibin Qian / Przemek M. Krawczyk / Román González-Prieto / Alfred C. O. Vertegaal / Meindert Lamers / Sébastien Huet / Haico van Attikum

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 21

Abstract: Classical non-homologous end-joining (cNHEJ) is the dominant pathway used by human cells to repair DNA double-strand breaks (DSBs) and maintain genome stability. Here the authors show that PARP1-driven chromatin expansion allows the recruitment of ZNF384, ...

Abstract	Classical non-homologous end-joining (cNHEJ) is the dominant pathway used by human cells to repair DNA double-strand breaks (DSBs) and maintain genome stability. Here the authors show that PARP1-driven chromatin expansion allows the recruitment of ZNF384, which in turn recruits Ku70/Ku80 to facilitate cNHEJ.
Keywords	Science ; Q
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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