Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase III-transcribed genes in Saccharomyces cerevisiae

Aboussekhra, Abdelilah; Thoma, Fritz

doi:10.1101/gad.12.3.411

Cited by 28 publications

(23 citation statements)

References 48 publications

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“…In human fibroblasts, CPDs present in tRNA genes were repaired by NER but TCR was not observed (50). Different results were found in yeast, where the NTS was actually repaired faster than the TS of the SNR6 gene (51). In yeast, the pol III-transcribed 5S rRNA gene is located between rDNA transcription units (Fig.…”

Section: Discussionmentioning

confidence: 77%

Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

Conconi

Bespalov

Smerdon

2002

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

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Nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers (CPDs) was measured in the individual strands of transcriptionally active and inactive ribosomal genes of yeast. Ribosomal genes (rDNA) are present in multiple copies, but only a fraction of them is actively transcribed. Restriction enzyme digestion was used to specifically release the transcriptionally active fraction from yeast nuclei, and selective psoralen crosslinking was used to distinguish between active and inactive rDNA chromatin. Removal of CPDs was followed in both rDNA populations, and the data clearly show that strand-specific repair occurs in transcriptionally active rDNA while being absent in the inactive rDNA fraction. Thus, transcription-coupled repair occurs in RNA polymerase I-transcribed genes in yeast. Moreover, the nontranscribed strand of active rDNA is repaired faster than either strand of inactive rDNA, implying that NER has preferred access to the active, non-nucleosomal rDNA chromatin. Finally, restriction enzyme accessibility to active rDNA varies during NER, suggesting that there is a change in ribosomal gene chromatin structure during or soon after CPD removal. N ucleotide excision repair (NER) removes different types of lesions from DNA, including bulky adducts caused by chemicals, interstrand or intrastrand crosslinks, and the UV photoproducts cis-syn cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone (1). If DNA lesions are not removed, mutations can occur after translesion replication (2). It is now well established that many transcriptionally active genes are repaired faster than inactive DNA (3, 4). Furthermore, preferential removal of CPDs from active genes is caused mainly by an increased rate of repair of the transcribed strand (TS). This transcription-coupled repair (TCR) was first discovered in mammalian cells (5), then in Escherichia coli (6) and yeast (7). Elongation by RNA polymerase II (pol II) is required for TCR (8, 9), and it is thought that only pol II-transcribed genes are subject to TCR (10).RNA polymerase I (pol I) transcribes ribosomal genes (rDNA) at a very high rate. The rDNA is localized in the nucleolus, which is a dense chromatin region composed of rDNA, pol I, rRNA, assembling ribosomes, and proteins involved in cell-cycle regulation (11,12). It is known that mammalian cells repair rDNA damaged by UV radiation (13) and chemicals (14-16). However, in rodent and human cells, CPDs are less efficiently repaired in rDNA than in either total genomic DNA or pol II-transcribed genes (16)(17)(18)(19)(20). Moreover, DNA repair does not exhibit strand bias in the rDNA of these cells (17,19). To the contrary, CPDs are rapidly removed from both strands of total rDNA in yeast (21,22). In addition, a strand bias during repair of total rDNA was observed in rad7 and rad16 mutants, even though strand-specific repair was not observed in total rDNA of wild-type cells (21).Ribosomal genes are present in multiple copies organized in long tandem repeats (11), and in most cells only a f...

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Section: Discussionmentioning

confidence: 77%

Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

Conconi

Bespalov

Smerdon

2002

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

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“…RNAP-II stalled at a DNA lesion may serve as a damage recognition enzyme and promote NER (1,16). Transcriptioncoupled repair was found in genes transcribed by RNAP-II, while genes transcribed by RNAP-III lack transcription-coupled repair in mammalian cells (24) and show a slight inhibition of NER on the transcribed strand in yeast (12).…”

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confidence: 99%

“…Photolyase is fast in nucleosome-free regions and slow in nucleosomes and therefore is an ideal molecular tool to investigate DNA accessibility in chromatin of living cells (9 -11). There is preferential repair of the nontranscribed strands in genes transcribed by RNAP-II and RNAP-III, whereas photoreactivation of the transcribed strands is partially inhibited by RNAP-II and RNAP-III blocked at CPDs (9,12,13). In contrast to photolyase, NER is a multistep mechanism that removes a large range of DNA lesions including CPDs and 6-4PPs (5).…”

mentioning

confidence: 99%

“…NER is divided in two subpathways, global genome repair and transcription-coupled repair (1, 14 -16). Global genome repair refers to repair in nontranscribed parts of the genome and is modulated by nucleosomes (17,18) and other protein/DNA interactions (11,12,19,20). Transcription-coupled repair refers to preferential repair of the transcribed strand, an observation that was originally made in mammalian and hamster cells (21) and later in many more organisms including yeast (22,23).…”

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confidence: 99%

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Repair of Active and Silenced rDNA in Yeast

Meier¹,

Livingstone‐Zatchej²,

Thoma³

2002

Journal of Biological Chemistry

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DNA repair by photolyase (photoreactivation) and nucleotide excision repair (NER) are the major pathways to remove UV-induced cyclobutane-pyrimidine dimers (CPDs). The nucleolus is a nuclear subcompartment containing the ribosomal RNA genes (rDNA) of which a fraction is transcribed by RNA polymerase I (RNAP-I), and the rest is silenced. Here yeast was used to investigate how photoreactivation and NER contribute to repair of active and inactive rDNA. Cells were irradiated with UV light and exposed to different repair conditions. Nuclei were isolated, and the active genes were separated from the inactive genes by restriction endonuclease digestion. CPDs were measured in total rDNA, in both fractions, and in the GAL10 gene. Repair in rDNA was as efficient as in GAL10 indicating that both pathways have unrestricted access to the nucleolus. Photoreactivation was much faster than NER and therefore was the predominant repair pathway. Active genes were faster repaired by photolyase than were silenced genes providing evidence for an open chromatin structure during repair. The transcribed strands of active genes, but not of inactive genes, were slightly faster repaired by NER providing evidence for transcriptioncoupled repair by RNAP-I. There was no pronounced inhibition of photoreactivation by RNAP-I in the transcribed strand, which is in contrast to genes transcribed by RNAP-II and suggests different stabilities of RNAP-I and RNAP-II stalled at CPDs.

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“…NER preferentially repairs the transcribed strand of genes transcribed by RNA polymerase II, which is referred to as transcription-coupled repair (15,18). Photolyase, on the other hand, is inhibited by RNA polymerases stalled at CPDs, which leads to slow repair of the transcribed strand (1,24,53). Hence, the modulation of repair allows conclusions to be drawn on the accessibility of DNA in chromatin (the repair footprint).…”

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confidence: 99%

Kinetochores Prevent Repair of UV Damage in Saccharomyces cerevisiae Centromeres

Capiaghi

Thoma

2004

Molecular and Cellular Biology

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Centromeres form specialized chromatin structures termed kinetochores which are required for accurate segregation of chromosomes. DNA lesions might disrupt protein-DNA interactions, thereby compromising segregation and genome stability. We show that yeast centromeres are heavily resistant to removal of UVinduced DNA lesions by two different repair systems, photolyase and nucleotide excision repair. Repair resistance persists in G 1 -and G 2 /M-arrested cells. Efficient repair was obtained only by disruption of the kinetochore structure in a ndc10-1 mutant, but not in cse4-1 and cbf1⌬ mutants. Moreover, UV photofootprinting and DNA repair footprinting showed that centromere proteins cover about 120 bp of the centromere elements CDEII and CDEIII, including 20 bp of flanking CDEIII. Thus, DNA lesions do not appear to disrupt protein-DNA interactions in the centromere. Maintaining a stable kinetochore structure seems to be more important for the cell than immediate removal of DNA lesions. It is conceivable that centromeres are repaired by postreplication repair pathways.

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Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase III-transcribed genes in Saccharomyces cerevisiae

Cited by 28 publications

References 48 publications

Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

Repair of Active and Silenced rDNA in Yeast

Kinetochores Prevent Repair of UV Damage in Saccharomyces cerevisiae Centromeres

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