Reversible Protein Phosphorylation Modulates Nucleotide Excision Repair of Damaged DNA by Human Cell Extracts

ABSTRACT The Saccharomyces cerevisiae transcription factor IIH (TFIIH) is essential both for transcription by RNA polymerase II (RNAP II) and for nucleotide excision repair (NER) of damaged DNA. We have established cell extracts which support RNAP II transcription from the yeast CYC1 promoter or NER of transcriptionally silent damaged DNA on independent plasmid templates and substrates. When plasmid templates and substrates for both processes are simultaneously incubated with these extracts, transcription is significantly inhibited. This inhibition is strictly dependent on active NER and can be complemented with purified holo-TFIIH. These results suggest that in the presence of active NER, TFIIH is preferentially mobilized from the basal transcription machinery for use in NER. Inhibition of transcription in the presence of active NER requires theRAD26 gene, the yeast homolog of the human Cockayne syndrome group B gene (CSB).

Download Full-text

Faculty Opinions recommendation of Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1082804.535725 ◽

2007 ◽

Author(s):

Alan Lehmann

Keyword(s):

Nucleotide Excision Repair ◽

Excision Repair ◽

Nucleotide Excision ◽

Damaged Dna

Download Full-text

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events

BMC Genomics ◽

10.1186/s12864-021-07898-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Umit Akkose ◽

Veysel Ogulcan Kaya ◽

Laura Lindsey-Boltz ◽

Zeynep Karagoz ◽

Adam D. Brown ◽

...

Keyword(s):

Nucleotide Excision Repair ◽

Cell Lines ◽

Human Cell ◽

Excision Repair ◽

Mouse Lemur ◽

Repair Mechanism ◽

Damage Repair ◽

Genome Wide ◽

Repair Efficiency ◽

Nucleotide Excision

Abstract Background Nucleotide excision repair is the primary DNA repair mechanism that removes bulky DNA adducts such as UV-induced pyrimidine dimers. Correspondingly, genome-wide mapping of nucleotide excision repair with eXcision Repair sequencing (XR-seq), provides comprehensive profiling of DNA damage repair. A number of XR-seq experiments at a variety of conditions for different damage types revealed heterogenous repair in the human genome. Although human repair profiles were extensively studied, how repair maps vary between primates is yet to be investigated. Here, we characterized the genome-wide UV-induced damage repair in gray mouse lemur, Microcebus murinus, in comparison to human. Results We derived fibroblast cell lines from mouse lemur, exposed them to UV irradiation, and analyzed the repair events genome-wide using the XR-seq protocol. Mouse lemur repair profiles were analyzed in comparison to the equivalent human fibroblast datasets. We found that overall UV sensitivity, repair efficiency, and transcription-coupled repair levels differ between the two primates. Despite this, comparative analysis of human and mouse lemur fibroblasts revealed that genome-wide repair profiles of the homologous regions are highly correlated, and this correlation is stronger for highly expressed genes. With the inclusion of an additional XR-seq sample derived from another human cell line in the analysis, we found that fibroblasts of the two primates repair UV-induced DNA lesions in a more similar pattern than two distinct human cell lines do. Conclusion Our results suggest that mouse lemurs and humans, and possibly primates in general, share a homologous repair mechanism as well as genomic variance distribution, albeit with their variable repair efficiency. This result also emphasizes the deep homologies of individual tissue types across the eukaryotic phylogeny.

Download Full-text

Recruitment of the Nucleotide Excision Repair Endonuclease XPG to Sites of UV-Induced DNA Damage Depends on Functional TFIIH

Molecular and Cellular Biology ◽

10.1128/mcb.00695-06 ◽

2006 ◽

Vol 26 (23) ◽

pp. 8868-8879 ◽

Cited By ~ 56

Author(s):

Angelika Zotter ◽

Martijn S. Luijsterburg ◽

Daniël O. Warmerdam ◽

Shehu Ibrahim ◽

Alex Nigg ◽

...

Keyword(s):

Dna Damage ◽

Nucleotide Excision Repair ◽

Fluorescent Protein ◽

Core Protein ◽

Excision Repair ◽

Mammalian Cell Lines ◽

Nucleotide Excision ◽

Green Fluorescent ◽

Damaged Dna

ABSTRACT The structure-specific endonuclease XPG is an indispensable core protein of the nucleotide excision repair (NER) machinery. XPG cleaves the DNA strand at the 3′ side of the DNA damage. XPG binding stabilizes the NER preincision complex and is essential for the 5′ incision by the ERCC1/XPF endonuclease. We have studied the dynamic role of XPG in its different cellular functions in living cells. We have created mammalian cell lines that lack functional endogenous XPG and stably express enhanced green fluorescent protein (eGFP)-tagged XPG. Life cell imaging shows that in undamaged cells XPG-eGFP is uniformly distributed throughout the cell nucleus, diffuses freely, and is not stably associated with other nuclear proteins. XPG is recruited to UV-damaged DNA with a half-life of 200 s and is bound for 4 min in NER complexes. Recruitment requires functional TFIIH, although some TFIIH mutants allow slow XPG recruitment. Remarkably, binding of XPG to damaged DNA does not require the DDB2 protein, which is thought to enhance damage recognition by NER factor XPC. Together, our data present a comprehensive view of the in vivo behavior of a protein that is involved in a complex chromatin-associated process.

Download Full-text

Erratum to ‘Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA’

Mutation Research/DNA Repair ◽

10.1016/s0921-8777(01)00075-1 ◽

2001 ◽

Vol 485 (3) ◽

pp. 267-268 ◽

Cited By ~ 1

Author(s):

Kosuke Morikawa ◽

Masahiro Shirakawa

Keyword(s):

Nucleotide Excision Repair ◽

Excision Repair ◽

Dna Recognition ◽

Three Dimensional ◽

E Coli ◽

Endonuclease V ◽

Nucleotide Excision ◽

Repair Factor ◽

Nucleotide Excision Repair Factor ◽

Damaged Dna

Download Full-text

Nucleotide excision repair–induced H2A ubiquitination is dependent on MDC1 and RNF8 and reveals a universal DNA damage response

The Journal of Cell Biology ◽

10.1083/jcb.200902150 ◽

2009 ◽

Vol 186 (6) ◽

pp. 835-847 ◽

Cited By ~ 125

Author(s):

Jurgen A. Marteijn ◽

Simon Bekker-Jensen ◽

Niels Mailand ◽

Hannes Lans ◽

Petra Schwertman ◽

...

Keyword(s):

Dna Damage ◽

Nucleotide Excision Repair ◽

Dna Damage Response ◽

Excision Repair ◽

Strand Break ◽

Epigenetic Mark ◽

Histone H2a ◽

Nucleotide Excision ◽

Damage Response ◽

Damaged Dna

Chromatin modifications are an important component of the of DNA damage response (DDR) network that safeguard genomic integrity. Recently, we demonstrated nucleotide excision repair (NER)–dependent histone H2A ubiquitination at sites of ultraviolet (UV)-induced DNA damage. In this study, we show a sustained H2A ubiquitination at damaged DNA, which requires dynamic ubiquitination by Ubc13 and RNF8. Depletion of these enzymes causes UV hypersensitivity without affecting NER, which is indicative of a function for Ubc13 and RNF8 in the downstream UV–DDR. RNF8 is targeted to damaged DNA through an interaction with the double-strand break (DSB)–DDR scaffold protein MDC1, establishing a novel function for MDC1. RNF8 is recruited to sites of UV damage in a cell cycle–independent fashion that requires NER-generated, single-stranded repair intermediates and ataxia telangiectasia–mutated and Rad3-related protein. Our results reveal a conserved pathway of DNA damage–induced H2A ubiquitination for both DSBs and UV lesions, including the recruitment of 53BP1 and Brca1. Although both lesions are processed by independent repair pathways and trigger signaling responses by distinct kinases, they eventually generate the same epigenetic mark, possibly functioning in DNA damage signal amplification.

Download Full-text