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Permanganate ChIP-seq analysis of Pol II in nonheat shocked and heat shocked Drosophila S2R+ cells and nonheat shocked BG3 cells

ABSTRACT: The genomic distribution of transcriptionally engaged Pol II in control and heat shocked cells was determined by combining formaldehyde crosslinking and permanganate oxidation of transcription bubbles Cells treated in succession with formaldehyde and then permanganate, were subjected to chromatin precipitation with Rpb3 antibody, and then the pattern of permanganate modifications were mapped genome-wide

ORGANISM(S): Drosophila melanogaster

SUBMITTER: David Gilmour

PROVIDER: E-GEOD-46620 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing.

Li Jian J Liu Yingyun Y Rhee Ho Sung HS Ghosh Saikat Kumar B SK Bai Lu L Pugh B Franklin BF Gilmour David S DS

Molecular cell 20130601 5

Pausing of RNA polymerase II (Pol II) 20-60 bp downstream of transcription start sites is a major checkpoint during transcription in animal cells. Mechanisms that control pausing are largely unknown. We developed permanganate-ChIP-seq to evaluate the state of Pol II at promoters throughout the Drosophila genome, and a biochemical system that reconstitutes promoter-proximal pausing to define pausing mechanisms. Stable open complexes of Pol II are largely absent from the transcription start sites ...[more]

PMID: 23746353

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