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Rpb9, a non-essential subunit of RNA polymerase H, mediates a transcription-coupled repair (TCR) sub-pathway in Saccharomyces cerevisiae. This subpathway initiates at the same upstream site as the previously identified Rad26 subpathway. However, the Rpb9 subpathway operates more effectively in the coding region than in the region upstream of the transcription start site, whereas the Rad26 subpathway operates equally in the two regions. Rpb4, another non-essential subunit of RNA polymerase II, plays a dual role in regulating the two subpathways, suppressing the Rpb9 subpathway and facilitating the Rad26 subpathway. Simultaneous deletion of RPB9 and RAD26 genes completely abolishes TCR in both the coding and upstream regions, indicating that no other TCR subpathway exists in RNA polymerase II- transcribed genes. [ABSTRACT FROM AUTHOR]

Transcription-coupled repair (TCR) and global genomic repair (GGR) are two pathways of nucleotide excision repair (NER). In Saccharomyces cerevisiae, Rad26 is important but not absolutely required for TCR. Rpb4, a nonessential RNA poly- merase II (Pol II) subunit that forms a subcomplex with Rpb7, and the Spt4-Spt5 complex, a transcription elongation factor, have been shown to suppress Rad26-independent TCR. The Pol Il-associated factor 1 complex (PafiC) has been shown to func- tion in transcription elongation, 3'-processing of mRNAs, and posttranslational modification of histones. Here we show that PafiC plays a marginal role in facilitating Rad26-dependent TCR but significantly suppresses Rad26-independent TCR. The suppression of Rad26-independent TCR is achieved by cooper- ating with Spt4-Spt5. We propose a model that, in the absence of Rad26, a lesion is "locked" in the active center of a Pol II elon- gation complex, which is stabilized by the coordinated interac- tions of Rpb4-Rpb7, Spt4-Spt5, and PafiC with each other and with the core Pol II. We also found that PafiC facilitates GGR, especially in internucleosomal linker regions. The facilitation of GGR is achieved through enabling monoubiquitination of his- tone H2B lysine 123 by Brel, which in turn permits di- and trim- ethylation of histone H3 lysine 79 by Doti. To our best knowl- edge, among the NER-modulating factors documented so far, PafiC appears to have the most diverse functions in different NER pathways or subpathways. [ABSTRACT FROM AUTHOR]