Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1

• Published in: PLoS genetics 2011-10, Vol.7 (10), p.e1002329-e1002329
• Main Authors: Creamer, Tyler J, Darby, Miranda M, Jamonnak, Nuttara, Schaughency, Paul, Hao, Haiping, Wheelan, Sarah J, Corden, Jeffry L
• Format: Article
• Language: English
• Subjects: Antisense; Base Sequence; Binding sites; Binding sites (Biochemistry); Binding Sites - genetics; Biology; Brewer's yeast; Chemical properties; Chromatin - genetics; Chromosome Mapping; Coding; Data processing; DNA helicase; DNA Helicases - genetics; DNA Helicases - metabolism; DNA-directed RNA polymerase; Experiments; Gene Expression Regulation, Fungal; Gene mapping; Genetic aspects; Genetics; Libraries; Messenger RNA; Molecular Sequence Data; mRNA; Mutation; Neurodegenerative diseases; non-coding RNA; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Peptide mapping; Physiological aspects; Poly A - genetics; Poly A - metabolism; Polyadenylation; Promoters; Proteins; RNA Helicases - genetics; RNA Helicases - metabolism; RNA polymerase; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; RNA Precursors - genetics; RNA Precursors - metabolism; RNA, Small Nucleolar - genetics; RNA, Small Nucleolar - metabolism; RNA-binding protein; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sensory systems; snoRNA; Termination factors; Transcription termination; Transcription, Genetic; Transcriptome
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1002329

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.