title: The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome.
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(CID(Rtt103))) 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 both CTD and 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(CID(Rtt103)) 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.
authors.affiliation: From the Center for RNA Research, Institute for Basic Science and.
authors.forename: Dong-hyuk
authors.initials: DH
authors.lastname: Heo
authors.forename: Inhea
authors.initials: I
authors.lastname: Yoo
authors.forename: Jiwon
authors.initials: J
authors.lastname: Kong
authors.forename: Michael
authors.initials: M
authors.lastname: Lidschreiber
authors.forename: Andreas
authors.initials: A
authors.lastname: Mayer
authors.forename: Byung-Yi
authors.initials: BY
authors.lastname: Choi
authors.forename: Yoonsoo
authors.initials: Y
authors.lastname: Hahn
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
authors.forename: Stephen
authors.initials: S
authors.lastname: Buratowski
authors.forename: Minkyu
authors.initials: M
authors.lastname: Kim
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002467:Cell Nucleus / Q000378:metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012319:RNA Polymerase II / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D061806:Transcription Termination, Genetic
chemical_list: C090564:NAB3 protein, S cerevisiae; C491211:NRD1 protein, S cerevisiae; D009687:Nuclear Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C553428:Rtt103 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C516801:ADH1 protein, S cerevisiae; D000426:Alcohol Dehydrogenase; D012319:RNA Polymerase II; D063326:Exosome Multienzyme Ribonuclease Complex; C112610:RRP6 protein, S cerevisiae
keywords: C-terminal Domain; Nrd1; RNA Polymerase II; RNA Processing; Small Nucleolar RNA (snoRNA); Transcription Termination; mRNA