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Abstract:
The RNA polymerase II (RNApII) C-terminal domain (CTD)-
interacting domain (CID) proteins are involved in two distinct
RNApII termination pathways and recognize different phosphorylated
forms of CTD. To investigate the role of differential
CTD-CID interactions in the choice of termination pathway, we
altered the CTD-binding specificity of Nrd1 by domain swapping.
Nrd1 with the CID from Rtt103 (Nrd1(CIDRtt103)) causes
read-through transcription at many genes, but can also trigger
termination where multiple Nrd1/Nab3-binding sites and the
Ser(P)-2 CTD co-exist. Therefore, CTD-CID interactions target
specific termination complexes to help choose an RNApII termination
pathway. Interactions of Nrd1 with bothCTDand nascent
transcripts contribute to efficient termination by the Nrd1
complex. Surprisingly, replacing the Nrd1 CID with that from
Rtt103 reduces binding to Rrp6/Trf4, and RNA transcripts terminated
by Nrd1(CIDRtt103) are predominantly processed by
core exosome. Thus, the Nrd1 CID couples Ser(P)-5 CTD not only to termination, but also to RNA processing by the nuclear
exosome.