NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila

Chanhyo Lee, Xiaoyong Li, Aaron Hechmer, Michael Eisen, Mark D. Biggin, Bryan J. Venters, Cizhong Jiang, Jian Li, Benjamin Franklin Pugh, David Scott Gilmour

Research output: Contribution to journalArticle

146 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)3290-3300
Number of pages11
JournalMolecular and cellular biology
Volume28
Issue number10
DOIs
StatePublished - May 1 2008

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Drosophila
Genes
Conserved Sequence
Chromatin Immunoprecipitation
Transcription Factor TFIID
RNA Polymerase II
Transcription Initiation Site
Microarray Analysis
Drosophila melanogaster
DNA Sequence Analysis
Genetic Promoter Regions
Nucleotides
Genome
RNA
Gene Expression

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Lee, Chanhyo ; Li, Xiaoyong ; Hechmer, Aaron ; Eisen, Michael ; Biggin, Mark D. ; Venters, Bryan J. ; Jiang, Cizhong ; Li, Jian ; Pugh, Benjamin Franklin ; Gilmour, David Scott. / NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. In: Molecular and cellular biology. 2008 ; Vol. 28, No. 10. pp. 3290-3300.
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Lee, C, Li, X, Hechmer, A, Eisen, M, Biggin, MD, Venters, BJ, Jiang, C, Li, J, Pugh, BF & Gilmour, DS 2008, 'NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila', Molecular and cellular biology, vol. 28, no. 10, pp. 3290-3300. https://doi.org/10.1128/MCB.02224-07

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. / Lee, Chanhyo; Li, Xiaoyong; Hechmer, Aaron; Eisen, Michael; Biggin, Mark D.; Venters, Bryan J.; Jiang, Cizhong; Li, Jian; Pugh, Benjamin Franklin; Gilmour, David Scott.

In: Molecular and cellular biology, Vol. 28, No. 10, 01.05.2008, p. 3290-3300.

Research output: Contribution to journalArticle

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