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PMID: 18332113 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

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

Molecular and cellular biology ·Vol. 28 ·No. 10 ·2008-05-00 ·Pages 3290-300

Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS

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.

MeSH Terms
Animals Base Sequence Binding Sites/genetics Chromatin Immunoprecipitation DNA/genetics,metabolism DNA-Binding Proteins/metabolism Drosophila Proteins/metabolism Drosophila melanogaster/genetics,metabolism Gene Expression Genes, Insect HSP70 Heat-Shock Proteins/genetics Models, Biological Promoter Regions, Genetic RNA Polymerase II/metabolism RNA-Binding Proteins/metabolism Transcription Factor TFIID/metabolism Transcription Factors/metabolism
Chemicals
DNA-Binding Proteins Drosophila Proteins HSP70 Heat-Shock Proteins RNA-Binding Proteins Transcription Factor TFIID Transcription Factors Trl protein, Drosophila negative elongation factor DNA RNA Polymerase II
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Lee Chanhyo
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Li Xiaoyong
Hechmer Aaron
Eisen Michael
Biggin Mark D
Venters Bryan J
Jiang Cizhong
Li Jian
Pugh B Franklin
Gilmour David S
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Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
1098-5549
DOI
10.1128/MCB.02224-07
Published
2008-05-00
Epub
2008-00-10
Pages
3290-300
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC2423147
Subset
IM
Grants
NHGRI NIH HHS · HG004160 · United States
NIGMS NIH HHS · R01 GM047477 · United States
NIGMS NIH HHS · GM47477 · United States
NIGMS NIH HHS · R01 GM070444 · United States
NIGMS NIH HHS · GM704403 · United States
NHGRI NIH HHS · R01 HG004160 · United States
External Links
PubMed source DOI: 10.1128/MCB.02224-07 PMC Full Text View journal details
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