A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions

Abstract The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.

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Databases and Bioinformatics Tools for the Study of DNA Repair

Molecular Biology International ◽

10.4061/2011/475718 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Kaja Milanowska ◽

Kristian Rother ◽

Janusz M. Bujnicki

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Uv Light ◽

Dna Lesions ◽

Environmental Chemicals ◽

Nonhomologous End Joining ◽

End Joining ◽

Repair Mechanisms ◽

Base Excision

DNA is continuously exposed to many different damaging agents such as environmental chemicals, UV light, ionizing radiation, and reactive cellular metabolites. DNA lesions can result in different phenotypical consequences ranging from a number of diseases, including cancer, to cellular malfunction, cell death, or aging. To counteract the deleterious effects of DNA damage, cells have developed various repair systems, including biochemical pathways responsible for the removal of single-strand lesions such as base excision repair (BER) and nucleotide excision repair (NER) or specialized polymerases temporarily taking over lesion-arrested DNA polymerases during the S phase in translesion synthesis (TLS). There are also other mechanisms of DNA repair such as homologous recombination repair (HRR), nonhomologous end-joining repair (NHEJ), or DNA damage response system (DDR). This paper reviews bioinformatics resources specialized in disseminating information about DNA repair pathways, proteins involved in repair mechanisms, damaging agents, and DNA lesions.

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The ATPase Domain but Not the Acidic Region of Cockayne Syndrome Group B Gene Product Is Essential for DNA Repair

Molecular Biology of the Cell ◽

10.1091/mbc.10.11.3583 ◽

1999 ◽

Vol 10 (11) ◽

pp. 3583-3594 ◽

Cited By ~ 30

Author(s):

Robert M. Brosh ◽

Adayabalam S. Balajee ◽

Rebecca R. Selzer ◽

Morten Sunesen ◽

Luca Proietti De Santis ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Uv Light ◽

Genetic Disorder ◽

Cockayne Syndrome ◽

Premature Aging ◽

Atpase Domain ◽

Acidic Region

Cockayne syndrome (CS) is a human genetic disorder characterized by UV sensitivity, developmental abnormalities, and premature aging. Two of the genes involved, CSA andCSB, are required for transcription-coupled repair (TCR), a subpathway of nucleotide excision repair that removes certain lesions rapidly and efficiently from the transcribed strand of active genes. CS proteins have also been implicated in the recovery of transcription after certain types of DNA damage such as those lesions induced by UV light. In this study, site-directed mutations have been introduced to the human CSB gene to investigate the functional significance of the conserved ATPase domain and of a highly acidic region of the protein. The CSB mutant alleles were tested for genetic complementation of UV-sensitive phenotypes in the human CS-B homologue of hamster UV61. In addition, theCSB mutant alleles were tested for their ability to complement the sensitivity of UV61 cells to the carcinogen 4-nitroquinoline-1-oxide (4-NQO), which introduces bulky DNA adducts repaired by global genome repair. Point mutation of a highly conserved glutamic acid residue in ATPase motif II abolished the ability of CSB protein to complement the UV-sensitive phenotypes of survival, RNA synthesis recovery, and gene-specific repair. These data indicate that the integrity of the ATPase domain is critical for CSB function in vivo. Likewise, the CSB ATPase point mutant failed to confer cellular resistance to 4-NQO, suggesting that ATP hydrolysis is required for CSB function in a TCR-independent pathway. On the contrary, a large deletion of the acidic region of CSB protein did not impair the genetic function in the processing of either UV- or 4-NQO-induced DNA damage. Thus the acidic region of CSB is likely to be dispensable for DNA repair, whereas the ATPase domain is essential for CSB function in both TCR-dependent and -independent pathways.

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Interactome analysis and docking sites prediction of (AtCHR8, AtCUL4 and AtERCC1/UVR7) proteins in Arabidopsis Thaliana

Heritage and Sustainable Development, ISSN 2712-0554 ◽

10.37868/hsd.v2i1.32 ◽

2020 ◽

Vol 2 (1) ◽

pp. 52-68

Author(s):

Mohamed Ragab Abdel Gawwad ◽

Ali Taha Ozdemir

Keyword(s):

Dna Damage ◽

Arabidopsis Thaliana ◽

Protein Interactions ◽

Excision Repair ◽

Dna Lesions ◽

Damage Recognition ◽

Nucleotide Excision ◽

Nucleotide Excision Repair Pathway ◽

Docking Sites ◽

Dna Damage Recognition

The UV irradiation is a major DNA damaging factor in plants. Arabidopsis thaliana uses various repair pathways for these kinds of DNA lesions. One of them is the nucleotide excision repair pathway. The AtCUL4, ERCC1/UVR7 and CHR8 are vital proteins for nucleotide excision pathway and mutations in these proteins cause flaws in the repair mechanism. Two of these proteins play crucial role during DNA damage recognition and the other is involved in the excision of damaged bases. During NER processes, Arabidopsis uses different sets of proteins during the DNA damage recognition for transcriptionally active and genomic DNA. In order to get better insight into these proteins, we used bioinformatics tools to predict, analyze, and validate 3D structures of ERCC1/UVR7, AtCUL4 and CHR8. We also predicted the subcellular and sub-nuclear localization of proteins. Subsequently, we predicted the docking sites for each individual proteins and searched for interacting residues which mediate the protein-protein interactions.

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The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair

10.1101/643874 ◽

2019 ◽

Author(s):

JT Barnett ◽

J Kuper ◽

W Koelmel ◽

C Kisker ◽

NM Kad

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Dna Binding ◽

Nucleotide Excision Repair ◽

Single Molecule ◽

Excision Repair ◽

Uv Light ◽

Dna Lesions ◽

The Core ◽

Nucleotide Excision

AbstractNucleotide excision repair (NER) protects the genome following exposure to diverse types of DNA damage, including UV light and chemotherapeutics. Mutations in mammalian NER genes lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, and Cockayne syndrome. In eukaryotes, the major transcription factor TFIIH is the central hub of NER. The core components of TFIIH include the helicases XPB, XPD, and five ‘structural’ subunits. Two of these structural TFIIH proteins, p44 and p62 remain relatively unstudied; p44 is known to regulate the helicase activity of XPD during NER whereas p62’s role is thought to be structural. However, a recent cryo-EM structure shows that p44, p62, and XPD make extensive contacts within TFIIH, with part of p62 occupying XPD’s DNA binding site. This observation implies a more extensive role in DNA repair beyond the structural integrity of TFIIH. Here, we show that p44 stimulates XPD’s ATPase but upon encountering DNA damage, further stimulation is only observed when p62 is part of the ternary complex; suggesting a role for the p44/p62 heterodimer in TFIIH’s mechanism of damage detection. Using single molecule imaging, we demonstrate that p44/p62 independently interacts with DNA; it is seen to diffuse, however, in the presence of UV-induced DNA lesions the complex stalls. Combined with the analysis of a recent cryo-EM structure we suggest that p44/p62 acts as a novel DNA-binding entity within TFIIH that is capable of recognizing DNA damage. This revises our understanding of TFIIH and prompts more extensive investigation into the core subunits for an active role during both DNA repair and transcription.

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DICER- and MMSET-catalyzed H4K20me2 recruits the nucleotide excision repair factor XPA to DNA damage sites

The Journal of Cell Biology ◽

10.1083/jcb.201704028 ◽

2017 ◽

Vol 217 (2) ◽

pp. 527-540 ◽

Cited By ~ 11

Author(s):

Shalaka Chitale ◽

Holger Richly

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Uv Light ◽

Dna Lesions ◽

Histone H4 ◽

Damage Site ◽

Nucleotide Excision ◽

Lesion Recognition

Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is nucleotide excision repair (NER). We have previously demonstrated that the endoribonuclease DICER facilitates chromatin decondensation during lesion recognition in the global-genomic branch of NER. Here, we report that DICER mediates the recruitment of the methyltransferase MMSET to the DNA damage site. We show that MMSET is required for efficient NER and that it catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2). H4K20me2 at DNA damage sites facilitates the recruitment of the NER factor XPA. Our work thus provides evidence for an H4K20me2-dependent mechanism of XPA recruitment during lesion recognition in the global-genomic branch of NER.

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Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair

Nature Communications ◽

10.1038/s41467-020-18705-0 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Cristina Ribeiro-Silva ◽

Mariangela Sabatella ◽

Angela Helfricht ◽

Jurgen A. Marteijn ◽

Arjan F. Theil ◽

...

Keyword(s):

Dna Damage ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Repair Process ◽

Dna Lesions ◽

Damage Recognition ◽

Nucleotide Excision ◽

Repair Factor ◽

Dna Damage Recognition ◽

Spatiotemporal Control

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.

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XAB2 Dynamics during DNA Damage-Dependent Transcription Inhibition

10.1101/2021.12.23.473962 ◽

2021 ◽

Author(s):

Lise-Marie DONNIO ◽

Elena Cerutti ◽

Charlene Magnani ◽

Damien Neuillet ◽

Pierre-Olivier Mari ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Uv Light ◽

Critical Role ◽

Functional Protein ◽

Cellular Processes ◽

Damage Recognition ◽

Fast Change ◽

Group A

Xeroderma Pigmentosum group A (XPA)-binding protein 2 (XAB2) is a multi-functional protein that plays a critical role in distinct cellular processes including transcription, splicing, DNA repair and mRNA export. In this study, we detailed XAB2 involvement during Nucleotide Excision Repair (NER), a repair pathway that guarantees genome integrity against UV light-induced DNA damage and that specifically removes transcription-blocking damage in a dedicated process known as Transcription-Coupled repair (TC-NER). Here, we demonstrated that XAB2 is involved specifically and exclusively in TC-NER reaction and solely for RNA Polymerase 2 transcribed genes. Surprisingly, contrary to all the other NER proteins studied so far, XAB2 does not accumulate on the local UV-C damage but on the contrary is remobilized after damage induction. This fast change in mobility is restored when DNA repair reactions are completed. By scrutinizing from which cellular complex/partner/structure XAB2 is released, we have identified that XAB2 is detached after DNA damage induction from the DNA:RNA hybrids, commonly known as R-loops, and the CSA and XPG protein and this release is thought to contribute to the DNA damage recognition step during TC-NER. Importantly, we have disclosed a role for XAB2 in retaining RNAP2 on its substrate.

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Mutational signatures are jointly shaped by DNA damage and repair

10.1101/686295 ◽

2019 ◽

Cited By ~ 2

Author(s):

Nadezda V Volkova ◽

Bettina Meier ◽

Víctor González-Huici ◽

Simone Bertolini ◽

Santiago Gonzalez ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Dna Lesions ◽

Single Nucleotide Variants ◽

Mutational Signatures ◽

Experimental Conditions ◽

Repair Deficiency ◽

Dna Repair Deficiency ◽

Mutation Spectra

AbstractMutations arise when DNA lesions escape DNA repair. To delineate the contributions of DNA damage and DNA repair deficiency to mutagenesis we sequenced 2,717 genomes of wild-type and 53 DNA repair defective C. elegans strains propagated through several generations or exposed to 11 genotoxins at multiple doses. Combining genotoxin exposure and DNA repair deficiency alters mutation rates or leads to unexpected mutation spectra in nearly 40% of all experimental conditions involving 9/11 of genotoxins tested and 32/53 genotypes. For 8/11 genotoxins, signatures change in response to more than one DNA repair deficiency, indicating that multiple genes and pathways are involved in repairing DNA lesions induced by one genotoxin. For many genotoxins, the majority of observed single nucleotide variants results from error-prone translesion synthesis, rather than primary mutagenicity of altered nucleotides. Nucleotide excision repair mends the vast majority of genotoxic lesions, preventing up to 99% of mutations. Analogous mutagenic DNA damage-repair interactions can also be found in cancers, but, except for rare cases, effects are weak owing to the unknown histories of genotoxic exposures and DNA repair status. Overall, our data underscore that mutation spectra are joint products of DNA damage and DNA repair and imply that mutational signatures computationally derived from cancer genomes are more variable than currently anticipated.

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Immune checkpoint inhibitor sensitivity of DNA repair deficient tumors

Immunotherapy ◽

10.2217/imt-2021-0024 ◽

2021 ◽

Vol 13 (14) ◽

pp. 1205-1213

Author(s):

Pauline Rochefort ◽

Françoise Desseigne ◽

Valérie Bonadona ◽

Sophie Dussart ◽

Clélia Coutzac ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Immune Checkpoint ◽

Genome Stability ◽

Immune Checkpoint Inhibitor ◽

Checkpoint Inhibitor ◽

Excision Repair ◽

Checkpoint Inhibitors ◽

Repair Deficiency ◽

Dna Repair Deficiency

Faithful DNA replication is necessary to maintain genome stability and implicates a complex network with several pathways depending on DNA damage type: homologous repair, nonhomologous end joining, base excision repair, nucleotide excision repair and mismatch repair. Alteration in components of DNA repair machinery led to DNA damage accumulation and potentially carcinogenesis. Preclinical data suggest sensitivity to immune checkpoint inhibitors in tumors with DNA repair deficiency. Here, we review clinical studies that explored the use of immune checkpoint inhibitor in patient harboring tumor with DNA repair deficiency.

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