Interactions of Sen1/Nrd1/Nab3 with Multiple Phosphorylated Forms of the Rpb1 C-terminal Domain in Saccharomyces cerevisiae.

Laboratory of Genetics.

The Saccharomyces cerevisiae SEN1 gene codes for a nuclear, ATP-dependent helicase which is embedded in a complex network of protein-protein interactions. Pleiotropic phenotypes of mutations in SEN1 suggest that Sen1 functions in many nuclear processes including transcription termination, DNA repair, and RNA processing. Sen1, along with termination factors Nrd1 and Nab3, is required for termination of non-coding RNA transcripts, but Sen1 is associated during transcription with coding and non-coding genes. Sen1 and Nrd1 both interact directly with Nab3, as well as with the C-terminal domain (CTD) of Rpb1, the largest subunit of RNA polymerase II. It has been proposed that Sen1, Nab3, and Nrd1 form a complex that associates with Rpb1 through an interaction between Nrd1 and the Ser(5)-phosphorylated CTD. To further study the relationship between the termination factors and Rpb1, we used two-hybrid analysis and immunoprecipitation to characterize sen1-R302W, a mutation that impairs an interaction between Sen1 and the Ser(2)-phosphorylated CTD. Chromatin immunoprecipitation indicates that impairment of the interaction between Sen1 and Ser(2)-P causes reduced occupancy of mutant Sen1 across the entire length of non-coding genes. For protein-coding genes, mutant Sen1 occupancy is reduced early and late in transcription but is similar to wild-type across most of the coding region. The combined data suggest a “handoff” model in which proteins differentially transfer from the Ser(5)- to the Ser(2)-phosphorylated CTD to promote termination of non-coding transcripts or other co-transcriptional events for protein-coding genes.