title: Common genomic elements promote transcriptional and DNA replication roadblocks.
abstract: RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable noncoding RNAs and the control of pervasive transcription in Saccharomyces cerevisiae To uncover determinants of NNS termination, we mapped the 3'-ends of NNS-terminated transcripts genome-wide. We found that nucleosomes and specific DNA-binding proteins, including the general regulatory factors (GRFs) Reb1p, Rap1p, and Abf1p, and Pol III transcription factors enhance the efficiency of NNS termination by physically blocking Pol II progression. The same DNA-bound factors that promote NNS termination were shown previously to define the 3'-ends of Okazaki fragments synthesized by Pol δ during DNA replication. Reduced binding of these factors results in defective NNS termination and Pol II readthrough. Furthermore, inactivating NNS enables Pol II elongation through these roadblocks, demonstrating that effective Pol II termination depends on a synergy between the NNS machinery and obstacles in chromatin. Consistent with this finding, loci exhibiting Pol II readthrough at GRF binding sites are depleted for upstream NNS signals. Overall, these results underscore how RNA termination signals influence the behavior of Pol II at chromatin obstacles, and establish that common genomic elements define boundaries for both DNA and RNA synthesis machineries.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Roy
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Gabunilas
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
authors.forename: Abigail
authors.initials: A
authors.lastname: Gillespie
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
authors.forename: Duy
authors.initials: D
authors.lastname: Ngo
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, USA.
authors.forename: Guillaume F
authors.identifier: 0000-0002-2505-1950
authors.initials: GF
authors.lastname: Chanfreau
mesh_terms: D004247:DNA / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism; D004257:DNA Polymerase II / Q000235:genetics / Q000378:metabolism; D004258:DNA Polymerase III / Q000235:genetics / Q000378:metabolism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000235:genetics / Q000378:metabolism; D061805:Transcription Elongation, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D061806:Transcription Termination, Genetic
chemical_list: C061886:ABF1 protein, S cerevisiae; D004268:DNA-Binding Proteins; C090564:NAB3 protein, S cerevisiae; C491211:NRD1 protein, S cerevisiae; D009687:Nuclear Proteins; C022262:Okazaki fragments; C440829:RAP1 protein, S cerevisiae; C065681:REB1 protein, S cerevisiae; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D014157:Transcription Factors; D004247:DNA; D004257:DNA Polymerase II; D004258:DNA Polymerase III; C542347:SEN1 protein, S cerevisiae; D004265:DNA Helicases; D020365:RNA Helicases