title: Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing.
abstract: Pausing of RNA polymerase II (Pol II) 20-60 bp downstream of transcription start sites is a major checkpoint during transcription in animal cells. Mechanisms that control pausing are largely unknown. We developed permanganate-ChIP-seq to evaluate the state of Pol II at promoters throughout the Drosophila genome, and a biochemical system that reconstitutes promoter-proximal pausing to define pausing mechanisms. Stable open complexes of Pol II are largely absent from the transcription start sites of most mRNA genes but are present at snRNA genes and the highly transcribed heat shock genes following their induction. The location of the pause is influenced by the timing between when NELF loads onto Pol II and how fast Pol II escapes the promoter region. Our biochemical analysis reveals that the sequence-specific transcription factor, GAF, orchestrates efficient pausing by recruiting NELF to promoters before transcription initiation and by assisting in loading NELF onto Pol II after initiation.
authors.affiliation: Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: Yingyun
authors.initials: Y
authors.lastname: Liu
authors.forename: Ho Sung
authors.initials: HS
authors.lastname: Rhee
authors.forename: Saikat Kumar B
authors.initials: SK
authors.lastname: Ghosh
authors.forename: Lu
authors.initials: L
authors.lastname: Bai
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
authors.forename: David S
authors.initials: DS
authors.lastname: Gilmour
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics*; D049750:Genome, Insect; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D007700:Kinetics; D017895:Manganese Compounds / Q000737:chemistry; D010087:Oxides / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012342:RNA, Small Nuclear; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D018840:HSP70 Heat-Shock Proteins; D017895:Manganese Compounds; D010087:Oxides; D012342:RNA, Small Nuclear; D014157:Transcription Factors; C063460:Trl protein, Drosophila; C118437:negative elongation factor; C048856:permanganic acid; D012319:RNA Polymerase II