Transcriptomics

Dataset Information

63

RNA polymerase is poised for activation across the genome


ABSTRACT: Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter, followed by initiation of RNA synthesis and the transition to productive elongation. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of gene. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region. To determine the importance of polymerase stalling for transcription regulation, we performed a genome-wide search for Drosophila genes with promoter-proximally stalled Pol II. Our data reveal that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals, indicating a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues. Keywords: gene expression, ChIP-chip, transcriptional regulation Drosophila Schneider cells (S2) were untreated or treated with dsRNA against LacZ or NELF for 96 hours. RNA isolation and immunoprecipitations (IPs) were performed for each of the test samples. Each treatment group (untreated, dsRNA-LacZ, dsRNA-NELF) was cultured in duplicate. Each RNA sample was amplified according to Affymetrix Eukaryotic One-cycle Protocol and hybridized to an Affymetrix Drosophila Genome 2.0 array, resulting in two biological replicates for each treatment group. Immunoprecipitations were performed either in the presence of Pol II Rpb3 or Ser2P Pol II CTD antibody or mock-immunoprecipitated with Protein-A agarose in the absence of antibody. Each IP was paired with a genomic DNA sample obtained at the time of the experiment. A separate labeling reaction was completed for each array type on which the IP/genomic DNA comparison was made (Agilent Dm3, Dm7 and Whole Drosophila Genome 2 chip set) and each of the two biological replicates were assayed.

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Joel Parker   Ginger W Muse  NIEHS Microarray Core  Karen Adelman  Sergei Nechaev  Ruchir Shau  Julia Zeitlinger  Daniel A Gilchrist  Sherry F Grissom 

PROVIDER: E-GEOD-6714 | ArrayExpress | 2007-11-11

SECONDARY ACCESSION(S): GSE6714PRJNA99039

REPOSITORIES: GEO, ArrayExpress

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Publications

RNA polymerase is poised for activation across the genome.

Muse Ginger W GW   Gilchrist Daniel A DA   Nechaev Sergei S   Shah Ruchir R   Parker Joel S JS   Grissom Sherry F SF   Zeitlinger Julia J   Adelman Karen K  

Nature genetics 20071111 12


Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter, followed by initiation of RNA synthesis and the transition to productive elongation. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-onc  ...[more]

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