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Series GSE11576 Query DataSets for GSE11576
Status Public on Jul 01, 2008
Title RNA mapping and ChIP with tiling arrays in FGF-stimulated NIH3T3 cells
Organism Mus musculus
Experiment type Expression profiling by genome tiling array
Genome binding/occupancy profiling by genome tiling array
Summary Transcription initiation in mammals is assumed to be independently controlled among nearby genes. On the other hand, recent large-scale transcriptome analyses have shown that the genome is pervasively transcribed, such that the majority of its DNA gives rise to RNAs. A simple question therefore arises: is it possible to pinpoint and activate a particular locus without perturbing numerous neighboring transcripts? Here we show that intensive transcription of immediate-early genes (IEGs) in response to growth factor stimulation is often accompanied by co-upregulation of their neighboring genes. Profiling primary transcripts in the nucleus with whole-genome tiling arrays delineated simultaneous activation of transcription centered on IEGs. Even in surrounding intergenic regions, which lack annotated protein-coding genes, transcriptional upregulation took place at the same time. We further found that acetylation levels of histone H3 and H4 are elevated along with the IEG induction and neighbouring co-upregulation, and that inhibition of the mitogen-activated protein kinase (MAPK) pathway or the transcription factor SRF suppresses all these transcriptional upregulation. These results suggest that transcriptional activation has a ripple effect, and causes a substantial fluctuation in multiple intragenic and intergenic transcripts.

Keywords: Time course and ChIP-chip
Overall design The following RNA mapping and ChIP experiments were performed using tiling arrays in FGF-stimulated NIH3T3 cells. 1) Expression time course of nuclear RNA 2) Expression time course of total RNA 3) Effect of the MEK inhibitor U0126 4) ChIP-chip with anti-acetylated histone H3 antibody 5) ChIP-chip with anti-SRF antibody
Contributor(s) Ebisuya M, Yamamoto T, Nakajima M, Nishida E
Citation(s) 19160492
Submission date May 28, 2008
Last update date Mar 21, 2017
Contact name Eisuke Nishida
Phone +81-75-753-4230
Organization name Graduate School of Biostudies, Kyoto University
Department Department of Cell and Developmental Biology
Street address Kitashirakawa, Sakyo-ku
City Kyoto
ZIP/Postal code 606-8502
Country Japan
Platforms (8)
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
GPL6444 [Mm35b_P01R] Affymetrix Mouse Tiling 2.0R Set, Array 1
GPL6445 [Mm35b_P02R] Affymetrix Mouse Tiling 2.0R Set, Array 2
Samples (59)
GSM291463 NuclearRNA_0min_A
GSM291464 NuclearRNA_0min_B
GSM291465 NuclearRNA_0min_C
BioProject PRJNA106203

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11576_RAW.tar 2.3 Gb (http)(custom) TAR (of BAR, BED, CEL)
Processed data provided as supplementary file

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