title: NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.
abstract: Recent analyses of RNA polymerase II (Pol II) revealed that Pol II is concentrated at the promoters of many active and inactive genes. NELF causes Pol II to pause in the promoter-proximal region of the hsp70 gene in Drosophila melanogaster. In this study, genome-wide location analysis (chromatin immunoprecipitation-microarray chip [ChIP-chip] analysis) revealed that NELF is concentrated at the 5' ends of 2,111 genes in Drosophila cells. Permanganate genomic footprinting was used to determine if paused Pol II colocalized with NELF. Forty-six of 56 genes with NELF were found to have paused Pol II. Pol II pauses 30 to 50 nucleotides downstream from transcription start sites. Analysis of DNA sequences in the vicinity of paused Pol II identified a conserved DNA sequence that probably associates with TFIID but detected no evidence of RNA secondary structures or other conserved sequences that might directly control elongation. ChIP-chip experiments indicate that GAGA factor associates with 39% of the genes that have NELF. Surprisingly, NELF associates with almost one-half of the most highly expressed genes, indicating that NELF is not necessarily a repressor of gene expression. NELF-associated pausing of Pol II might be an obligatory but sometimes transient checkpoint during the transcription cycle.
authors.affiliation: Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Chanhyo
authors.initials: C
authors.lastname: Lee
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Li
authors.forename: Aaron
authors.initials: A
authors.lastname: Hechmer
authors.forename: Michael
authors.initials: M
authors.lastname: Eisen
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Venters
authors.forename: Cizhong
authors.initials: C
authors.lastname: Jiang
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
authors.forename: David S
authors.initials: DS
authors.lastname: Gilmour
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism*; D015870:Gene Expression; D017344:Genes, Insect; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D008954:Models, Biological; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D035362:Transcription Factor TFIID / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D018840:HSP70 Heat-Shock Proteins; D016601:RNA-Binding Proteins; D035362:Transcription Factor TFIID; D014157:Transcription Factors; C063460:Trl protein, Drosophila; C118437:negative elongation factor; D004247:DNA; D012319:RNA Polymerase II