Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Hu, Jinchuan; Adar, Sheera; Selby, Christopher P.; Lieb, Jason D.; Sancar, Aziz

doi:10.1101/gad.261271.115

Cited by 231 publications

(421 citation statements)

References 66 publications

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“…Previous genomic studies have suggested that NER activity is affected by chromatin state and inhibited by transcription factor binding (7)(8)(9)(10). However, it is not known how these and other features of the chromosomal landscape affect initial UV damage formation.…”

Section: Discussionmentioning

confidence: 95%

“…In these studies, a high-throughput sequencing method, known as excision repair-sequencing (XR-seq), was used to analyze oligonucleotide fragments excised during NER of CPDs or 6-4PPs. These studies found increased repair activity associated with TC-NER of the TS of actively expressed genes and noncoding transcripts (7,8). There was also more rapid repair in active chromatin domains (i.e., enhancers and promoters) and DNase I hypersensitivity regions, and slower repair associated with repressed and heterochromatin regions (8).…”

mentioning

confidence: 99%

“…Differences in repair rates between transcribed and nontranscribed DNA, and between accessible and inaccessible chromatin domains, have been invoked to explain the mutational heterogeneity in many cancer genomes (4-6). To gain new insight into the mutational processes that lead to human cancer, however, a more detailed understanding is needed of the complex interplay of UV damage formation and repair across the genome.Our understanding of how NER operates in different sequence and chromatin contexts has been aided by two recent genome-wide surveys of NER activity in UV-irradiated human fibroblasts (7,8). In these studies, a high-throughput sequencing method, known as excision repair-sequencing (XR-seq), was used to analyze oligonucleotide fragments excised during NER of CPDs or 6-4PPs.…”

mentioning

confidence: 99%

“…Our understanding of how NER operates in different sequence and chromatin contexts has been aided by two recent genome-wide surveys of NER activity in UV-irradiated human fibroblasts (7,8). In these studies, a high-throughput sequencing method, known as excision repair-sequencing (XR-seq), was used to analyze oligonucleotide fragments excised during NER of CPDs or 6-4PPs.…”

mentioning

confidence: 99%

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Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Mao

Smerdon

Roberts

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

134

236

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UV-induced DNA lesions are important contributors to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. Genome-wide profiling of repair activity in UV irradiated cells has revealed significant variations in repair kinetics across the genome, not only among large chromatin domains, but also at individual transcription factor binding sites. Here we report that there is also a striking but predictable variation in initial UV damage levels across a eukaryotic genome. We used a new high-throughput sequencing method, known as CPD-seq, to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution throughout the yeast genome. This analysis revealed that individual nucleosomes significantly alter CPD formation, protecting nucleosomal DNA with an inward rotational setting, even though such DNA is, on average, more intrinsically prone to form CPD lesions. CPD formation is also inhibited by DNAbound transcription factors, in effect shielding important DNA elements from UV damage. Analysis of CPD repair revealed that initial differences in CPD damage formation often persist, even at later repair time points. Furthermore, our high-resolution data demonstrate, to our knowledge for the first time, that CPD repair is significantly less efficient at translational positions near the dyad of strongly positioned nucleosomes in the yeast genome. These findings define the global roles of nucleosomes and transcription factors in both UV damage formation and repair, and have important implications for our understanding of UV-induced mutagenesis in human cancers.DNA repair | DNA damage | nucleosome | chromatin | transcription factor U ltraviolet (UV) light causes extensive damage to DNA by inducing the formation of cyclobutane pyrimidine dimers (CPDs) and, to a lesser extent, 6-4 pyrimidine-pyrimidone photoproducts (6-4PPs). If unrepaired, these DNA lesions block normal DNA replication and are major contributors to mutagenesis in skin cancers (1). CPDs and 6-4PPs are primarily repaired in cells by the nucleotide excision repair (NER) pathway (1). CPD lesions in actively transcribed strands (TS) of DNA are repaired rapidly by the transcription coupled-NER (TC-NER) branch of this repair pathway, which is triggered by RNA polymerase II stalling at UV damage (2, 3). In contrast, CPD lesions in the remainder of the genome are repaired by the global genome NER (GG-NER) subpathway. Differences in repair rates between transcribed and nontranscribed DNA, and between accessible and inaccessible chromatin domains, have been invoked to explain the mutational heterogeneity in many cancer genomes (4-6). To gain new insight into the mutational processes that lead to human cancer, however, a more detailed understanding is needed of the complex interplay of UV damage formation and repair across the genome.Our understanding of how NER operates in different sequence and chromatin contexts has been aided by two recent genome-wide surveys of NER ac...

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Section: Discussionmentioning

confidence: 95%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Mao

Smerdon

Roberts

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

134

236

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“…A genome-wide comparison of open chromatin status, histone modifications, RNA expression, and DNA damage and repair would allow inference of how these processes are coordinated. We recently developed an assay for mapping DNA excision repair at nucleotide resolution across the human genome called eXcision Repair sequencing (XR-seq) (11). In XR-seq, the excised oligonucleotides, released during repair in vivo, are isolated and sequenced, resulting in a stranded, single-nucleotide resolution map of repair (Fig.…”

mentioning

confidence: 99%

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis

Adar

Lieb

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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We recently developed a high-resolution genome-wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) and have now used XR-seq to determine which regions of the genome are subject to repair very soon after UV exposure and which regions are repaired later. Over a time course, we measured repair of the UV-induced damage of cyclobutane pyrimidine dimers (CPDs) (at 1, 4, 8, 16, 24, and 48 h) and (6-4)pyrimidinepyrimidone photoproducts [(6-4)PPs] (at 5 and 20 min and 1, 2, and 4 h) in normal human skin fibroblasts. Each type of damage has distinct repair kinetics. The (6-4)PPs are detected as early as 5 min after UV treatment, with the bulk of repair completed by 4 h. Repair of CPDs, which we previously showed is intimately coupled to transcription, is slower and in certain regions persists even 2 d after UV irradiation. We compared our results to the Encyclopedia of DNA Elements data regarding histone modifications, chromatin state, and transcription. For both damage types, and for both transcription-coupled and general excision repair, the earliest repair occurred preferentially in active and open chromatin states. Conversely, repair in regions classified as "heterochromatic" and "repressed" was relatively low at early time points, with repair persisting into the late time points. Damage that remains during DNA replication increases the risk for mutagenesis. Indeed, laterepaired regions are associated with a higher level of cancer-linked mutations. In summary, we show that XR-seq is a powerful approach for studying relationships among chromatin state, DNA repair, genome stability, mutagenesis, and carcinogenesis.DNA repair | DNA damage | chromatin | transcription | mutation D NA damage blocks transcription and replication and compromises the integrity of the genome. Bulky adducts in DNA, the focus of this work, are caused by a variety of genotoxic agents including UV radiation in sunlight. In human cells, this damage is removed exclusively by the nucleotide excision repair mechanism (1-3). In nucleotide excision repair, a single-stranded oligomer that contains the bulky adduct is excised by dual incisions bracketing the lesion. The resulting gap is filled in by DNA polymerases, and the newly synthesized repair patch is then sealed by DNA ligase. In general excision repair, damage recognition is achieved by the repair factors xeroderma pigmentosum (XP) complementation group C (XPC) together with replication protein A (RPA) and XPA (4-6). In DNA that is being actively transcribed, damage recognition can also be achieved by a stalled RNA polymerase II, which, with the aid of the Cockayne Syndrome B (CSB) protein, accelerates the recruitment of the excision repair factors. This recognition process leads to transcription-coupled repair (7,8). The subsequent dual-incision reaction is carried out by the core excision repair factors RPA, XPA, transcription factor II H (TFIIH), XPG, and XPF-ERCC1, releasing an excised oligomer that is 24-32 nucleotides (nt) in length (6, 9).The mechanism of DNA...

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cis ‐Regulatory Driver Mutations in Cancer Genomes

Poulos

Wong

2017

Encyclopedia of Life Sciences

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The increasing availability of large‐scale whole cancer genome sequencing data sets has enabled research efforts to focus on cancer driver mutations within the noncoding genome. cis ‐Regulatory elements are sites responsible for the control of gene expression. Mutations at such loci may modify transcription factor binding sites, disrupt enhancer–promoter interactions or affect epigenetic marks. cis ‐Regulatory driver mutations have been found in some cancer types to‐date, with initial discoveries of point mutations in the TERT promoter, small insertions creating an enhancer regulating TAL1 and genomic rearrangements leading to simultaneous enhancer dysregulation of EVI1 and GATA2 . However, recent discoveries have also revealed mechanisms responsible for the accumulation of recurrent, and even functional, somatic single‐nucleotide mutations in regulatory regions, wholly apart from selective pressure. Close scrutiny of candidate cis ‐regulatory mutations is necessary in order to effectively identify mutations that have undergone positive selection and to accurately distinguish driver from passenger mutations. Key Concepts Improvements in DNA sequencing technology, and the commencement of large‐scale cancer genome sequencing projects, have made discoveries in the noncoding genome possible. cis ‐Regulatory elements, such as promoters and enhancers, are responsible for the control of gene expression. Transcription factors bind to cis ‐regulatory elements, influencing the rate of transcription of DNA to mRNA. Mutations in cis ‐regulatory elements can drive cancer development by altering transcription factor binding sites, enhancer–promoter interactions or the epigenetic landscape of the cell. Alterations to cis ‐regulatory elements can lead to gene dysregulation, potentially impacting the expression of oncogenes or tumour suppressor genes. Recurrent somatic driver mutations affecting cis ‐regulatory elements have already been identified in cancer genomes, including point mutations, insertions and deletions (indels) and structural rearrangements. cis ‐Regulatory elements may appear recurrently mutated in cancer due to selective pressures or due to other mechanisms driving the formation of mutation hot spots. Transcription factor binding can inhibit access to nucleotide excision repair (NER) enzymes, leading to increased mutation rates at transcription factor binding sites in some cancers. DNA modifications and nucleotide composition can both influence the propensity for certain sites to become mutated. Close scrutiny of candidate cis ‐regulatory mutations is necessary in order to effectively identify sites under selective pressure and to accurately distinguish driver from passenger mutations.

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Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Cited by 231 publications

References 66 publications

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis

cis ‐Regulatory Driver Mutations in Cancer Genomes

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