Ultraviolet Damage and Nucleosome Folding of the 5S Ribosomal RNA Gene

Liu, Xiaoqi; Mann, David B.; Suquet, Christine; Springer, David L.; Smerdon, Michael J.

doi:10.1021/bi991771m

Cited by 24 publications

(37 citation statements)

References 37 publications

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“…This study used the 5S rDNA nucleosome positioning sequence with uracil residues at sites more than two or five helical turns away from the dyad center. As observed by these authors (54), a feature of 5S rDNA nucleosomes, demonstrated previously by others (55)(56)(57)(58)(59), is the presence of multiple translational settings of the DNA on the histone octamer surface. Thus, the transient exposure of uracil by variability in translational setting of the 5S rDNA, as well as increased ''breathing'' of DNA away from the dyad center of nucleosomes (8,52), makes the results of Nilsen et al (54) more difficult to interpret.…”

Section: Discussionsupporting

confidence: 63%

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

Beard

Wilson

Smerdon

2003

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

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141

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The majority of DNA in eukaryotic cells exists in the highly condensed structural hierarchy of chromatin, which presents a challenge to DNA repair enzymes in that recognition, incision, and restoration of the original sequence at most sites must take place within these structural constraints. To test base excision repair (BER) activities on chromatin substrates, an in vitro system was developed that uses human uracil DNA glycosylase (UDG), apyrimidinic͞apurinic endonuclease (APE), and DNA polymerase ␤ (pol ␤) on homogeneously damaged, rotationally positioned DNA in nucleosomes. We find that UDG and APE carry out their combined catalytic activities with reduced efficiency on nucleosome substrates (Ϸ10% of that on naked DNA). Furthermore, these enzymes distinguish between two different rotational settings of the lesion on the histone surface, showing a 2-to 3-fold difference in activity between uracil facing ''toward'' and ''away from'' the histones. However, UDG and APE will digest such substrates to completion in a concentration-dependent manner. Conversely, the synthesis activity of pol ␤ is inhibited completely by nucleosome substrates and is independent of enzyme concentration. These results suggest that the first two steps of BER, UDG and APE, may occur ''unassisted'' in chromatin, whereas downstream factors in this pathway (i.e., pol ␤) may require nucleosome remodeling for efficient DNA BER in at least some regions of chromatin in eukaryotic cells.chromatin ͉ glycosylase ͉ DNA polymerase ␤ ͉ apyrmidinic͞apurinic endonuclease

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Section: Discussionsupporting

confidence: 63%

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

Beard

Wilson

Smerdon

2003

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

Self Cite

141

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“…44). On the other hand, irradiation was shown to destabilize nucleosomes reconstituted on 5 S rDNA (45) and plasmids (46), whereas nucleosomes reconstituted on HISAT DNA and 5 S rDNA were not similarly affected (20,38,39). In the examples shown in this study, UV lesions were not sufficient to disrupt the nucleosomes.…”

Section: Resultsmentioning

confidence: 56%

“…CPD formation depends on the structure of DNA and can be altered by folding of DNA in nucleosomes (37)(38)(39). ATDED-long nucleosomes were analyzed by UV photo-footprinting during remodeling (Fig.…”

Section: Resultsmentioning

confidence: 99%

Chromatin Remodeling Activities Act on UV-damaged Nucleosomes and Modulate DNA Damage Accessibility to Photolyase

Gaillard

Fitzgerald

Smith

et al. 2003

Journal of Biological Chemistry

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Nucleosomes inhibit DNA repair in vitro, suggesting that chromatin remodeling activities might be required for efficient repair in vivo. To investigate how structural and dynamic properties of nucleosomes affect damage recognition and processing, we investigated repair of UV lesions by photolyase on a nucleosome positioned at one end of a 226-bp-long DNA fragment. Repair was slow in the nucleosome but efficient outside. No disruption or movement of the nucleosome was observed after UV irradiation and during repair. However, incubation with the nucleosome remodeling complex SWI/SNF and ATP altered the conformation of nucleosomal DNA as judged by UV photo-footprinting and promoted more homogeneous repair. Incubation with yISW2 and ATP moved the nucleosome to a more central position, thereby altering the repair pattern. This is the first demonstration that two different chromatin remodeling complexes can act on UV-damaged nucleosomes and modulate repair. Similar activities might relieve the inhibitory effect of nucleosomes on DNA repair processes in living cells.

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“…8); however, past biochemical and cellular studies have suggested that nucleosomes and DNA-binding proteins may significantly alter the formation of UV damage (11)(12)(13)(14). Previous attempts to measure initial CPD levels using microarray-based methods (15)(16)(17) suggested that UV damage formation is primarily influenced by the DNA sequence.…”

mentioning

confidence: 99%

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.

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133

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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Ultraviolet Damage and Nucleosome Folding of the 5S Ribosomal RNA Gene

Cited by 24 publications

References 37 publications

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

Chromatin Remodeling Activities Act on UV-damaged Nucleosomes and Modulate DNA Damage Accessibility to Photolyase

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

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