scholarly journals RNA Polymerase II Transcription Suppresses Nucleosomal Modulation of UV-Induced (6-4) Photoproduct and Cyclobutane Pyrimidine Dimer Repair in Yeast

1999 ◽  
Vol 19 (1) ◽  
pp. 934-940 ◽  
Author(s):  
Marcel Tijsterman ◽  
Remko de Pril ◽  
Judith G. Tasseron-de Jong ◽  
Jaap Brouwer
Keyword(s):  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Uv Light ◽  
Single Gene ◽  
Pyrimidine Dimer ◽  
Cyclobutane Pyrimidine Dimer ◽  
Mutagenic Potential ◽  
Dna Strand ◽  
Nucleotide Resolution ◽  
Transcription Coupled Repair

ABSTRACT The nucleotide excision repair (NER) pathway is able to remove a wide variety of structurally unrelated lesions from DNA. NER operates throughout the genome, but the efficiencies of lesion removal are not the same for different genomic regions. Even within a single gene or DNA strand repair rates vary, and this intragenic heterogeneity is of considerable interest with respect to the mutagenic potential of carcinogens. In this study, we have analyzed the removal of the two major types of genotoxic DNA adducts induced by UV light, i.e., the pyrimidine (6-4)-pyrimidone photoproduct (6-4PP) and the cyclobutane pyrimidine dimer (CPD), from the Saccharomyces cerevisiae URA3 gene at nucleotide resolution. In contrast to the fast and uniform removal of CPDs from the transcribed strand, removal of lesions from the nontranscribed strand is generally less efficient and is modulated by the chromatin environment of the damage. Removal of 6-4PPs from nontranscribed sequences is also profoundly influenced by positioned nucleosomes, but this type of lesion is repaired at a much higher rate. Still, the transcribed strand is repaired preferentially, indicating that, as in the removal of CPDs, transcription-coupled repair predominates in the removal of 6-4PPs from transcribed DNA. The hypothesis that transcription machinery operates as the rate-determining damage recognition entity in transcription-coupled repair is supported by the observation that this pathway removes both types of UV photoproducts at equal rates without being profoundly influenced by the sequence or chromatin context.

Blockage of RNA polymerase II at a cyclobutane pyrimidine dimer and 6–4 photoproduct

2004 ◽  
Vol 320 (4) ◽  
pp. 1133-1138 ◽  
Author(s):  
Joan Seah Mei Kwei ◽  
Isao Kuraoka ◽  
Katsuyoshi Horibata ◽  
Manabu Ubukata ◽  
Eiry Kobatake ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Pyrimidine Dimer ◽  
Cyclobutane Pyrimidine Dimer

scholarly journals Requirement of ELC1 for RNA Polymerase II Polyubiquitylation and Degradation in Response to DNA Damage in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (11) ◽  
pp. 3999-4005 ◽  
Author(s):  
Balazs Ribar ◽  
Louise Prakash ◽  
Satya Prakash
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Ubiquitin Ligase ◽  
Excision Repair ◽  
Uv Light ◽  
Yeast Cells ◽  
Pol Ii ◽  
Dna Damaging Agents ◽  
Nucleotide Excision

ABSTRACT Treatment of Saccharomyces cerevisiae and human cells with DNA-damaging agents such as UV light or 4-nitroquinoline-1-oxide induces polyubiquitylation of the largest RNA polymerase II (Pol II) subunit, Rpb1, which results in rapid Pol II degradation by the proteasome. Here we identify a novel role for the yeast Elc1 protein in mediating Pol II polyubiquitylation and degradation in DNA-damaged yeast cells and propose the involvement of a ubiquitin ligase, of which Elc1 is a component, in this process. In addition, we present genetic evidence for a possible involvement of Elc1 in Rad7-Rad16-dependent nucleotide excision repair (NER) of lesions from the nontranscribed regions of the genome and suggest a role for Elc1 in increasing the proficiency of repair of nontranscribed DNA, where as a component of the Rad7-Rad16-Elc1 ubiquitin ligase, it would promote the efficient turnover of the NER ensemble from the lesion site in a Rad23-19S proteasomal complex-dependent reaction.

scholarly journals Structural basis of the XPB helicase–Bax1 nuclease complex interacting with the repair bubble DNA

2020 ◽  
Vol 48 (20) ◽  
pp. 11695-11705
Author(s):  
Feng He ◽  
Kevin DuPrez ◽  
Eduardo Hilario ◽  
Zhenhang Chen ◽  
Li Fan
Keyword(s):  
Excision Repair ◽  
Uv Light ◽  
Dna Helicase ◽  
Dna Lesions ◽  
Structural Basis ◽  
Base Pairs ◽  
Dna Strands ◽  
Underlying Mechanisms ◽  
Dna Strand ◽  
Atp Binding And Hydrolysis

Abstract Nucleotide excision repair (NER) removes various DNA lesions caused by UV light and chemical carcinogens. The DNA helicase XPB plays a key role in DNA opening and coordinating damage incision by nucleases during NER, but the underlying mechanisms remain unclear. Here, we report crystal structures of XPB from Sulfurisphaera tokodaii (St) bound to the nuclease Bax1 and their complex with a bubble DNA having one arm unwound in the crystal. StXPB and Bax1 together spirally encircle 10 base pairs of duplex DNA at the double-/single-stranded (ds–ss) junction. Furthermore, StXPB has its ThM motif intruding between the two DNA strands and gripping the 3′-overhang while Bax1 interacts with the 5′-overhang. This ternary complex likely reflects the state of repair bubble extension by the XPB and nuclease machine. ATP binding and hydrolysis by StXPB could lead to a spiral translocation along dsDNA and DNA strand separation by the ThM motif, revealing an unconventional DNA unwinding mechanism. Interestingly, the DNA is kept away from the nuclease domain of Bax1, potentially preventing DNA incision by Bax1 during repair bubble extension.

Comparison of the Global Genomic and Transcription-Coupled Repair Rates of Different Lesions in Human Cells

2004 ◽  
Vol 59 (5-6) ◽  
pp. 445-453 ◽  
Author(s):  
Boyko Atanassov ◽  
Aneliya Velkova ◽  
Emil Mladenov ◽  
Boyka Anachkova ◽  
George Russev
Keyword(s):  
Dna Sequences ◽  
Chemical Nature ◽  
Excision Repair ◽  
Uv Light ◽  
Double Helix ◽  
Human Cells ◽  
The Other ◽  
Specific Sequence ◽  
Dna Double Helix ◽  
Transcription Coupled Repair

There are two subclasses of nucleotide excision repair (NER). One is the global genomic repair (GGR) which removes lesions throughout the genome regardless of whether any specific sequence is transcribed or not. The other is the transcription-coupled repair (TCR), which removes lesions only from the transcribed DNA sequences. There are data that GGR rates depend on the chemical nature of the lesions in a manner that the lesions inflicting larger distortion on the DNA double helix are repaired at higher rate. It is not known whether the TCR repair rates depend on the type of lesions and in what way. To address this question human cells were transfected with pEGFP and pEYFP plasmids treated with UV light, cis-diamminedichloroplatinum(II) (cisplatin) and angelicin and 24 h later the restored fluorescence was measured and used to calculate the respective NER rates. In a parallel series of experiments the same plasmids were incubated in repair-competent protein extracts to determine GGR rates in the absence of transcription. From the two sets of data, the TCR rates were calculated. We found out that cisplatin, UV light and angelicin lesions were repaired by GGR with different efficiency, which corresponded to the degree of DNA helix distortion induced by these agents. On the other hand the three lesions were repaired by TCR at very similar rates which showed that TCR efficiency was not directly connected with the chemical nature of the lesions.

scholarly journals The Drosophila melanogaster Homologue of the Xeroderma Pigmentosum D Gene Product Is Located in Euchromatic Regions and Has a Dynamic Response to UV Light-induced Lesions in Polytene Chromosomes

1999 ◽  
Vol 10 (4) ◽  
pp. 1191-1203 ◽  
Author(s):  
Enrique Reynaud ◽  
Hilda Lomelı́ ◽  
Martha Vázquez ◽  
Mario Zurita
Keyword(s):  
Dna Damage ◽  
Drosophila Melanogaster ◽  
Rna Polymerase Ii ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Uv Light ◽  
Polytene Chromosomes ◽  
Light Irradiation ◽  
Distribution Analysis ◽  
Uv Light Irradiation

The XPD/ERCC2/Rad3 gene is required for excision repair of UV-damaged DNA and is an important component of nucleotide excision repair. Mutations in the XPD gene generate the cancer-prone syndrome, xeroderma pigmentosum, Cockayne’s syndrome, and trichothiodystrophy. XPD has a 5′- to 3′-helicase activity and is a component of the TFIIH transcription factor, which is essential for RNA polymerase II elongation. We present here the characterization of the Drosophila melanogaster XPD gene (DmXPD). DmXPD encodes a product that is highly related to its human homologue. The DmXPD protein is ubiquitous during development. In embryos at the syncytial blastoderm stage, DmXPD is cytoplasmic. At the onset of transcription in somatic cells and during gastrulation in germ cells, DmXPD moves to the nuclei. Distribution analysis in polytene chromosomes shows that DmXPD is highly concentrated in the interbands, especially in the highly transcribed regions known as puffs. UV-light irradiation of third-instar larvae induces an increase in the signal intensity and in the number of sites where the DmXPD protein is located in polytene chromosomes, indicating that the DmXPD protein is recruited intensively in the chromosomes as a response to DNA damage. This is the first time that the response to DNA damage by UV-light irradiation can be visualized directly on the chromosomes using one of the TFIIH components.

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