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Transcription coupled nucleotide excision repair (TC-NER) is believed to be triggered by an RNA polymerase stalled at a lesion in the transcribed strand of actively transcribed genes. Rad26, a DNA-dependent ATPase in the family of SWI2/SNF2 chromatin remodeling proteins, plays an important role in TC-NER in Saccharomyces cerevisiae. However, Rad26 is not solely responsible for TC-NER and Rpb9, a nonessential subunit of RNA polymerase II (RNAP II), is largely responsible for Rad26-independent TC-NER. The Rad26-dependent and Rpb9-dependent TC-NER have different efficiencies in genes with different transcription levels and in different regions of a gene. Rad26 becomes entirely or partially dispensable for TC-NER in the absence of Rpb4, another nonessential subunit of RNAP II, or a number of transcription elongation factors (Spt4, Spt5 and the RNAP II associated factor complex). Rad26 may not be a true transcription-repair coupling factor that recruits the repair machinery to the damaged sites where RNAP II stalls. Rather, Rad26 may facilitate TC-NER indirectly, by antagonizing the action of TC-NER repressors that normally promote transcription elongation. The underlying mechanism of how Rad26 functions in TC-NER remains to be elucidated. [ABSTRACT FROM AUTHOR]

Abstract: Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting DNA lesions. Rad26, a member of the Swi2/Snf2 superfamily of proteins, has been shown to be involved in a specialized NER process called transcription coupled NER. Rad16, another member of the same protein superfamily, has been shown to be required for genome-wide NER. Here we show that Rad16 and Rad26 play different roles in repairing repressed and actively transcribed genes in yeast. Rad16 is partially dispensable, and Rad26 plays a significant role in repairing certain regions of the repressed GAL1-10, PHO5 and ADH2 genes, especially in the core DNA of well-positioned nucleosomes. Simultaneous elimination of Rad16 and Rad26 results in no detectable repair in these regions of the repressed genes. Transcriptional induction of the GAL1-10 genes abolishes the role of Rad26, but does not affect the role of Rad16 in repairing the nontranscribed strand of the genes. Interestingly, when the transcription activator Gal4 is eliminated from the cells, Rad16 becomes partially dispensable and Rad26 plays a significant role in repairing both strands of the GAL1-10 genes even under inducing conditions. Our results suggest that Rad16 and Rad26 play different and, to some extent, complementary roles in repairing both strands of repressed genes, although the relative contributions of the two proteins can be different from gene to gene, and from region to region of a gene. However, Rad16 is solely responsible for repairing the nontranscribed strand of actively transcribed genes. [Copyright &y& Elsevier]

Abstract: Transcription coupled repair (TCR) is a nucleotide excision repair (NER) pathway that is dedicated to repair in the transcribed strand of an active gene. The genome overall NER is called global genomic repair (GGR). Elc1, the yeast homolog of the mammalian elongation factor elongin C, has been shown to be a component of a ubiquitin ligase complex that contains Rad7 and Rad16, two factors that are specifically required for GGR. Elc1 has also been suggested to be present in another ubiquitin ligase complex that lacks Rad7 and Rad16 and is involved in UV-induced ubiquitylation and subsequent degradation of RNA polymerase II. Here we show that elc1 deletion increases UV sensitivity of TCR-deficient cells but does not affect the UV sensitivity of otherwise wild type and GGR-deficient cells. Cells deleted for elc1 show normal NER in the transcribed strand of an active gene but have no detectable NER in the non-transcribed strand. Elc1 does not affect UV-induced mutagenesis when TCR is operative, but plays an important role in preventing the mutagenesis if TCR is defective. Furthermore, the levels of Rad7 and Rad16 proteins are not significantly decreased in elc1 cells, and overexpression of Rad7 and Rad16 individually or simultaneously in elc1 cells does not restore repair in the non-transcribed strand of an active gene. Our results suggest that Elc1 has no function in TCR but plays an important role in GGR. Furthermore, the role of Elc1 in GGR may not be subsidiary to that of Rad7 and Rad16. [Copyright &y& Elsevier]

Abstract: Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting DNA lesions. A specialized NER pathway, called transcription coupled NER (TC-NER), refers to preferential repair in the transcribed strand of an actively transcribed gene. To be distinguished from TCR-NER, the genome-wide NER process is termed as global genomic NER (GG-NER). In Saccharomyces cerevisiae, GG-NER is dependent on Rad7, whereas TC-NER is mediated by Rad26, the homolog of the human Cockayne syndrome group B protein, and by Rpb9, a non-essential subunit of RNA polymerase II. Tfb5, the tenth subunit of the transcription/repair factor TFIIH, is implicated in one group of the human syndrome trichothiodystrophy. Here, we show that Tfb5 plays different roles in different NER pathways in yeast. No repair takes place in the non-transcribed strand of a gene in tfb5 cells, or in both strands of a gene in rad26 rpb9 tfb5 cells, indicating that Tfb5 is essential for GG-NER. However, residual repair occurs in the transcribed strand of a gene in tfb5 cells, suggesting that Tfb5 is important, but not absolutely required for TC-NER. Interestingly, substantial repair occurs in the transcribed strand of a gene in rad7 tfb5 and rad7 rpb9 tfb5 cells, indicating that, in the absence of GG-NER, Tfb5 is largely dispensable for Rad26 mediated TC-NER. Furthermore, we show that no repair takes place in the transcribed strand of a gene in rad7 rad26 tfb5 cells, suggesting that Tfb5 is required for Rpb9 mediated TC-NER. Taken together, our results indicate that Tfb5 is partially dispensable for Rad26 mediated TC-NER, especially in GG-NER deficient cells. However, this TFIIH subunit is required for other NER pathways. [Copyright &y& Elsevier]