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Article: XPG: a multitasking genome caretaker

Muniesa-Vargas, Alba / Theil, Arjan F. / Ribeiro-Silva, Cristina / Vermeulen, Wim / Lans, Hannes

Cellular and molecular life sciences. 2022 Mar., v. 79, no. 3

2022

Abstract: The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic ... ...

Abstract	The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
Keywords	DNA damage ; DNA repair ; genes ; homologous recombination ; photosensitivity disorders
Language	English
Dates of publication	2022-03
Size	p. 166.
Publishing place	Springer International Publishing
Document type	Article
Note	Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-022-04194-5
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Article ; Online: XPG: a multitasking genome caretaker.

Muniesa-Vargas, Alba / Theil, Arjan F / Ribeiro-Silva, Cristina / Vermeulen, Wim / Lans, Hannes

Cellular and molecular life sciences : CMLS

2022 Volume 79, Issue 3, Page(s) 166

Abstract	The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1-XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
MeSH term(s)	Animals ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Binding Proteins/genetics ; Endonucleases/genetics ; Genome/genetics ; Humans ; Nuclear Proteins/genetics ; Transcription Factors/genetics ; Xeroderma Pigmentosum/genetics
Chemical Substances	DNA excision repair protein ERCC-5 ; DNA-Binding Proteins ; Nuclear Proteins ; Transcription Factors ; Endonucleases (EC 3.1.-)
Language	English
Publishing date	2022-03-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-022-04194-5
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Article ; Online: SWI/SNF: Complex complexes in genome stability and cancer.

Ribeiro-Silva, Cristina / Vermeulen, Wim / Lans, Hannes

DNA repair

2019 Volume 77, Page(s) 87–95

Abstract: SWI/SNF complexes are among the most studied ATP-dependent chromatin remodeling complexes, mostly due to their critical role in coordinating chromatin architecture and gene expression. Mutations in genes encoding SWI/SNF subunits are frequently observed ... ...

Abstract	SWI/SNF complexes are among the most studied ATP-dependent chromatin remodeling complexes, mostly due to their critical role in coordinating chromatin architecture and gene expression. Mutations in genes encoding SWI/SNF subunits are frequently observed in a large variety of human cancers, suggesting that one or more of the multiple SWI/SNF functions protect against tumorigenesis. Chromatin remodeling is an integral component of the DNA damage response (DDR), which safeguards against DNA damage-induced genome instability and tumorigenesis by removing DNA damage through interconnected DNA repair and signaling pathways. SWI/SNF has been implicated in facilitating repair of double-strand breaks, by non-homologous end-joining as well as homologous recombination, and repair of helix-distorting DNA damage by nucleotide excision repair. Here, we review current knowledge on SWI/SNF activity in the DDR and discuss the potential of exploiting DDR-related vulnerabilities due to SWI/SNF dysfunction for precision cancer therapy.
MeSH term(s)	Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/metabolism ; DNA Damage ; Genomic Instability ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism
Chemical Substances	Chromosomal Proteins, Non-Histone
Language	English
Publishing date	2019-03-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2019.03.007
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Article ; Online: Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure.

Muniesa-Vargas, Alba / Davó-Martínez, Carlota / Ribeiro-Silva, Cristina / van der Woude, Melanie / Thijssen, Karen L / Haspels, Ben / Häckes, David / Kaynak, Ülkem U / Kanaar, Roland / Marteijn, Jurgen A / Theil, Arjan F / Kuijten, Maayke M P / Vermeulen, Wim / Lans, Hannes

Nature communications

2024 Volume 15, Issue 1, Page(s) 3490

Abstract: Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the ... ...

Abstract	Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
MeSH term(s)	Caenorhabditis elegans/metabolism ; Caenorhabditis elegans/genetics ; DNA Damage ; Humans ; Animals ; DNA Repair ; Transcription Factor TFIIH/metabolism ; Transcription Factor TFIIH/genetics ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/genetics ; Endonucleases/metabolism ; Endonucleases/genetics ; Caenorhabditis elegans Proteins/metabolism ; Caenorhabditis elegans Proteins/genetics ; Xeroderma Pigmentosum Group A Protein/metabolism ; Xeroderma Pigmentosum Group A Protein/genetics ; Protein Binding ; Transcription Factors/metabolism ; Transcription Factors/genetics ; Mutation ; Nuclear Proteins/metabolism ; Nuclear Proteins/genetics
Chemical Substances	Transcription Factor TFIIH (148710-81-0) ; DNA-Binding Proteins ; Endonucleases (EC 3.1.-) ; xeroderma pigmentosum group F protein ; Caenorhabditis elegans Proteins ; Xeroderma Pigmentosum Group A Protein ; DNA excision repair protein ERCC-5 ; Transcription Factors ; ERCC1 protein, human (EC 3.1.-) ; XPA protein, human ; Nuclear Proteins
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47935-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination.

Davó-Martínez, Carlota / Helfricht, Angela / Ribeiro-Silva, Cristina / Raams, Anja / Tresini, Maria / Uruci, Sidrit / van Cappellen, Wiggert A / Taneja, Nitika / Demmers, Jeroen A A / Pines, Alex / Theil, Arjan F / Vermeulen, Wim / Lans, Hannes

Nucleic acids research

2023 Volume 51, Issue 17, Page(s) 9055–9074

Abstract: The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are ... ...

Abstract	The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are functionally distinguished by their exclusive subunits. Accumulating evidence suggests that double-strand breaks (DSBs) in transcriptionally active DNA are preferentially repaired by a dedicated homologous recombination pathway. We show that different BAF, PBAF and ncBAF subunits promote homologous recombination and are rapidly recruited to DSBs in a transcription-dependent manner. The PBAF and ncBAF complexes promote RNA polymerase II eviction near DNA damage to rapidly initiate transcriptional silencing, while the BAF complex helps to maintain this transcriptional silencing. Furthermore, ARID1A-containing BAF complexes promote RNaseH1 and RAD52 recruitment to facilitate R-loop resolution and DNA repair. Our results highlight how multiple SWI/SNF complexes perform different functions to enable DNA repair in the context of actively transcribed genes.
MeSH term(s)	Chromatin Assembly and Disassembly/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; DNA ; DNA Repair/genetics ; Homologous Recombination/genetics ; R-Loop Structures ; Humans
Chemical Substances	Chromosomal Proteins, Non-Histone ; DNA (9007-49-2) ; RAD52 protein, human ; SWI-SNF-B chromatin-remodeling complex
Language	English
Publishing date	2023-09-26
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/gkad609
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Article ; Online: Detection of oxaliplatin- and cisplatin-DNA lesions requires different global genome repair mechanisms that affect their clinical efficacy.

Slyskova, Jana / Muniesa-Vargas, Alba / da Silva, Israel Tojal / Drummond, Rodrigo / Park, Jiyeong / Häckes, David / Poetsch, Isabella / Ribeiro-Silva, Cristina / Moretton, Amandine / Heffeter, Petra / Schärer, Orlando D / Vermeulen, Wim / Lans, Hannes / Loizou, Joanna I

NAR cancer

2023 Volume 5, Issue 4, Page(s) zcad057

Abstract: The therapeutic efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the ... ...

Abstract	The therapeutic efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection. Using a combination of genetic, transcriptomics and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ISSN	2632-8674
ISSN (online)	2632-8674
DOI	10.1093/narcan/zcad057
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Article ; Online: Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair.

Ribeiro-Silva, Cristina / Sabatella, Mariangela / Helfricht, Angela / Marteijn, Jurgen A / Theil, Arjan F / Vermeulen, Wim / Lans, Hannes

Nature communications

2020 Volume 11, Issue 1, Page(s) 4868

Abstract: DNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds ... ...

Abstract	DNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds to UV-induced lesions directly and facilitates efficient recognition by XPC. We show that not only lesion-binding but also timely DDB2 dissociation is required for DNA damage handover to XPC and swift progression of the multistep repair reaction. DNA-binding-induced DDB2 ubiquitylation and ensuing degradation regulate its homeostasis to prevent excessive lesion (re)binding. Additionally, damage handover from DDB2 to XPC coincides with the arrival of the TFIIH complex, which further promotes DDB2 dissociation and formation of a stable XPC-TFIIH damage verification complex. Our results reveal a reciprocal coordination between DNA damage recognition and verification within NER and illustrate that timely repair factor dissociation is vital for correct spatiotemporal control of a multistep repair process.
MeSH term(s)	Cell Nucleus/genetics ; Cell Nucleus/metabolism ; DNA Damage ; DNA Repair ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Transcription Factor TFIIH/genetics ; Transcription Factor TFIIH/metabolism ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	DDB2 protein, human ; DNA-Binding Proteins ; Ubiquitin ; Transcription Factor TFIIH (148710-81-0)
Language	English
Publishing date	2020-09-28
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/s41467-020-18705-0
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Article ; Online: Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage.

Slyskova, Jana / Sabatella, Mariangela / Ribeiro-Silva, Cristina / Stok, Colin / Theil, Arjan F / Vermeulen, Wim / Lans, Hannes

Nucleic acids research

2018 Volume 46, Issue 18, Page(s) 9537–9549

Abstract: Sensitivity and resistance of cells to platinum drug chemotherapy are to a large extent determined by activity of the DNA damage response (DDR). Combining chemotherapy with inhibition of specific DDR pathways could therefore improve treatment efficacy. ... ...

Abstract	Sensitivity and resistance of cells to platinum drug chemotherapy are to a large extent determined by activity of the DNA damage response (DDR). Combining chemotherapy with inhibition of specific DDR pathways could therefore improve treatment efficacy. Multiple DDR pathways have been implicated in removal of platinum-DNA lesions, but it is unclear which exact pathways are most important to cellular platinum drug resistance. Here, we used CRISPR/Cas9 screening to identify DDR proteins that protect colorectal cancer cells against the clinically applied platinum drug oxaliplatin. We find that besides the expected homologous recombination, Fanconi anemia and translesion synthesis pathways, in particular also transcription-coupled nucleotide excision repair (TC-NER) and base excision repair (BER) protect against platinum-induced cytotoxicity. Both repair pathways are required to overcome oxaliplatin- and cisplatin-induced transcription arrest. In addition to the generation of DNA crosslinks, exposure to platinum drugs leads to reactive oxygen species production that induces oxidative DNA lesions, explaining the requirement for BER. Our findings highlight the importance of transcriptional integrity in cells exposed to platinum drugs and suggest that both TC-NER and BER should be considered as targets for novel combinatorial treatment strategies.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; Cisplatin/adverse effects ; Cisplatin/chemistry ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; DNA Damage/drug effects ; DNA Repair/drug effects ; DNA Repair/genetics ; DNA Replication/drug effects ; Humans ; Oxaliplatin/adverse effects ; Oxaliplatin/chemistry ; Platinum/adverse effects ; Platinum/chemistry ; Reactive Oxygen Species/chemistry ; Transcription, Genetic/drug effects
Chemical Substances	Reactive Oxygen Species ; Oxaliplatin (04ZR38536J) ; Platinum (49DFR088MY) ; Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2018-09-01
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/gky764
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Article ; Online: Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features.

Sabatella, Mariangela / Theil, Arjan F / Ribeiro-Silva, Cristina / Slyskova, Jana / Thijssen, Karen / Voskamp, Chantal / Lans, Hannes / Vermeulen, Wim

Nucleic acids research

2018 Volume 46, Issue 18, Page(s) 9563–9577

Abstract: The structure-specific ERCC1-XPF endonuclease plays a key role in DNA damage excision by nucleotide excision repair (NER) and interstrand crosslink repair. Mutations in this complex can either cause xeroderma pigmentosum (XP) or XP combined with Cockayne ...

Abstract	The structure-specific ERCC1-XPF endonuclease plays a key role in DNA damage excision by nucleotide excision repair (NER) and interstrand crosslink repair. Mutations in this complex can either cause xeroderma pigmentosum (XP) or XP combined with Cockayne syndrome (XPCS-complex) or Fanconi anemia. However, most patients carry compound heterozygous mutations, which confounds the dissection of the phenotypic consequences for each of the identified XPF alleles. Here, we analyzed the functional impact of individual pathogenic XPF alleles on NER. We show that XP-causing mutations diminish XPF recruitment to DNA damage and only mildly affect global genome NER. In contrast, an XPCS-complex-specific mutation causes persistent recruitment of XPF and the upstream core NER machinery to DNA damage and severely impairs both global genome and transcription-coupled NER. Remarkably, persistence of NER factors at DNA damage appears to be a common feature of XPCS-complex cells, suggesting that this could be a determining factor contributing to the development of additional developmental and/or neurodegenerative features in XP patients.
MeSH term(s)	Alleles ; Cell Line ; Cockayne Syndrome/genetics ; Cockayne Syndrome/pathology ; DNA Damage/genetics ; DNA Repair/genetics ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; Endonucleases/chemistry ; Endonucleases/genetics ; Fanconi Anemia/genetics ; Fanconi Anemia/pathology ; Genome, Human/genetics ; Humans ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/genetics ; Mutation/genetics ; Protein Multimerization/genetics ; Xeroderma Pigmentosum/genetics
Chemical Substances	DNA-Binding Proteins ; Multiprotein Complexes ; xeroderma pigmentosum group F protein ; ERCC1 protein, human (EC 3.1.-) ; Endonucleases (EC 3.1.-)
Language	English
Publishing date	2018-10-25
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/gky774
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Article: Hypoxia-driven selective degradation of cellular proteins in jumbo squids during diel migration to the oxygen minimum zones

Trübenbach, Katja / da Costa, Gonçalo / Ribeiro-Silva, Cristina / Ribeiro, Raquel Mesquita / Cordeiro, Carlos / Rosa, Rui

Marine biology. 2014 Mar., v. 161, no. 3

2014

Abstract: The jumbo squid, Dosidicus gigas, is an oceanic top predator in the eastern tropical Pacific that undergoes diel vertical migrations into mesopelagic oxygen minimum zones (OMZs). Besides glycogen breakdown, the pathways of the squid’s metabolic ( ... ...

Abstract	The jumbo squid, Dosidicus gigas, is an oceanic top predator in the eastern tropical Pacific that undergoes diel vertical migrations into mesopelagic oxygen minimum zones (OMZs). Besides glycogen breakdown, the pathways of the squid’s metabolic (suppression) strategy are poorly understood. Here, juvenile D. gigas were exposed to oxygen levels found in the OMZ off Gulf of California (1� % O₂, 1� kPa at 10� °C) with the aim to identify, via proteomic tools, eventual anaerobic protein degradation as potential energy source at such depths. Under hypoxia, total protein concentration decreased nonsignificantly from 79.2� ±� 12.4� mg� g⁻¹ wet mass to 74.7� ±� 11.7� mg� g⁻¹ wet mass (p� >� 0.05). Yet, there was a significant decrease in heat-shock protein (Hsp) 90 and α-actinin contents (p� <� 0.05). The lower α-actinin concentration at late hypoxia was probably related to decreased protection of the Hsp90 chaperon machinery resulting in increased ubiquitination (p� <� 0.05) and subsequent degradation. Thus, the present findings indicate that D. gigas might degrade, at least under progressing hypoxia, specific mantle proteins anaerobically to increase/maintain anaerobic ATP production and extend hypoxia exposure time. Moreover, the ubiquitin–proteasome system seems to play an important role in hypoxia tolerance, but further investigations are necessary to discover its full potential and pathways.
Keywords	Dosidicus gigas ; adenosine triphosphate ; exposure duration ; heat shock proteins ; hypoxia ; oxygen ; protein degradation ; squid ; ubiquitination ; Gulf of California
Language	English
Dates of publication	2014-03
Size	p. 575-584.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	1117-4
ISSN	1432-1793 ; 0025-3162
ISSN (online)	1432-1793
ISSN	0025-3162
DOI	10.1007/s00227-013-2360-z
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