Rpb9, a non-essential subunit of RNA polymerase II, mediates a transcription-coupled repair (TCR) subpathway 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.