Genomics

Dataset Information

19

Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: MNase-seq data


ABSTRACT: Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the "default" chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy. Overall design: Examination of MNase-digested mononucleosomal chromatin from untreated, mock-treated, and NELF-depleted Drosophila S2 cells.

INSTRUMENT(S): Illumina Genome Analyzer II (Drosophila melanogaster)

SUBMITTER: Karen Adelman   

PROVIDER: GSE22119 | GEO | 2010-10-18

SECONDARY ACCESSION(S): PRJNA127605

REPOSITORIES: GEO

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Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.

Gilchrist Daniel A DA   Dos Santos Gilberto G   Fargo David C DC   Xie Bin B   Gao Yuan Y   Li Leping L   Adelman Karen K  

Cell 20101101 4


Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter or regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a striking difference between genes that use these distinct regulatory strategies lies in the "default" chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly regulated genes whose sequences inherently disfavor nucleosome formation within the gene b  ...[more]

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