title: A chromatin-based mechanism for limiting divergent noncoding transcription.
abstract: In addition to their annotated transcript, many eukaryotic mRNA promoters produce divergent noncoding transcripts. To define determinants of divergent promoter directionality, we used genomic replacement experiments. Sequences within noncoding transcripts specified their degradation pathways, and functional protein-coding transcripts could be produced in the divergent direction. To screen for mutants affecting the ratio of transcription in each direction, a bidirectional fluorescent protein reporter construct was introduced into the yeast nonessential gene deletion collection. We identified chromatin assembly as an important regulator of divergent transcription. Mutations in the CAF-I complex caused genome-wide derepression of nascent divergent noncoding transcription. In opposition to the CAF-I chromatin assembly pathway, H3K56 hyperacetylation, together with the nucleosome remodeler SWI/SNF, facilitated divergent transcription by promoting rapid nucleosome turnover. We propose that these chromatin-mediated effects control divergent transcription initiation, complementing downstream pathways linked to early termination and degradation of the noncoding RNAs.
authors.affiliation: Department of Biological Chemistry and Molecular Physiology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Marquardt
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Renan
authors.initials: R
authors.lastname: Escalante-Chong
authors.affiliation: Research Computing Group, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
authors.forename: Nam
authors.initials: N
authors.lastname: Pho
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Jue
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
authors.forename: L Stirling
authors.initials: LS
authors.lastname: Churchman
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Springer
authors.affiliation: Department of Biological Chemistry and Molecular Physiology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. Electronic address: steveb@hms.harvard.edu.
authors.forename: Stephen
authors.initials: S
authors.lastname: Buratowski
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D056504:Chromatin Assembly Factor-1 / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D015966:Gene Expression Regulation, Fungal; D009707:Nucleosomes / Q000378:metabolism; D011401:Promoter Regions, Genetic; D020871:RNA Stability; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D056504:Chromatin Assembly Factor-1; D009707:Nucleosomes; D012331:RNA, Fungal; D022661:RNA, Untranslated; D029701:Saccharomyces cerevisiae Proteins