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PMID: 18628398 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly.

Genes & development ·Vol. 22 ·No. 14 ·2008-07-15 ·Pages 1921-33

Gilchrist DA, Nechaev S, Lee C, Ghosh SK, Collins JB, Li L, Gilmour DS, Adelman K

Abstract

The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including Drosophila Hsp70, mammalian proto-oncogene junB, and HIV RNA. To determine the full spectrum of NELF target genes in Drosophila, we performed a microarray analysis of S2 cells depleted of NELF and discovered that NELF RNAi affects many rapidly inducible genes involved in cellular responses to stimuli. Surprisingly, only one-third of NELF target genes were, like Hsp70, up-regulated by NELF-depletion, whereas the majority of target genes showed decreased expression levels upon NELF RNAi. Our data reveal that the presence of stalled Pol II at this latter group of genes enhances gene expression by maintaining a permissive chromatin architecture around the promoter-proximal region, and that loss of Pol II stalling at these promoters is accompanied by a significant increase in nucleosome occupancy and a decrease in histone H3 Lys 4 trimethylation. These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure.

MeSH Terms
Animals Chromatin Assembly and Disassembly/physiology Chromatin Immunoprecipitation DNA Footprinting Drosophila Proteins/genetics,metabolism Drosophila melanogaster/genetics,metabolism Gene Expression Profiling Gene Expression Regulation Genes, Dominant Luciferases/metabolism Oligonucleotide Array Sequence Analysis Polymerase Chain Reaction Promoter Regions, Genetic/genetics RNA Polymerase II/genetics,metabolism Transcription Factors/antagonists & inhibitors,genetics,metabolism
Chemicals
Drosophila Proteins Transcription Factors negative elongation factor Luciferases RNA Polymerase II
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Gilchrist Daniel A
Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.
Nechaev Sergei
Lee Chanhyo
Ghosh Saikat Kumar B
Collins Jennifer B
Li Leping
Gilmour David S
Adelman Karen
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Article Info
Journal
Genes & development
Abbr.
Genes Dev
ISSN
0890-9369
DOI
10.1101/gad.1643208
Published
2008-07-15
Pages
1921-33
Language
English
Region
United States
NLM ID
8711660
PMCID
PMC2492738
Subset
IM
Grants
NIGMS NIH HHS · R01 GM047477 · United States
Intramural NIH HHS · Z01 ES101987 · United States
NIGMS NIH HHS · GM47477 · United States
External Links
PubMed source DOI: 10.1101/gad.1643208 PMC Full Text View journal details
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