Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1.
RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA-binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein-RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3' antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3' end of most pre-mRNA transcripts, suggesting an extensive role in mRNA 3' end formation and/or termination.
Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Tyler J
TJ
Creamer
Miranda M
MM
Darby
Nuttara
N
Jamonnak
Paul
P
Schaughency
Haiping
H
Hao
Sarah J
SJ
Wheelan
Jeffry L
JL
Corden
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000235:genetics*; D002874:Chromosome Mapping; D004265:DNA Helicases / Q000235:genetics* / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011061:Poly A / Q000235:genetics / Q000378:metabolism; D020365:RNA Helicases / Q000235:genetics* / Q000378:metabolism*; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome
D002843:Chromatin; C090564:NAB3 protein, S cerevisiae; C491211:NRD1 protein, S cerevisiae; D009687:Nuclear Proteins; D012322:RNA Precursors; D020537:RNA, Small Nucleolar; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D011061:Poly A; D012319:RNA Polymerase II; C542347:SEN1 protein, S cerevisiae; D004265:DNA Helicases; D020365:RNA Helicases