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| 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
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| 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
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| 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
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| 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 |
| E-mail(s) |
nishida@lif.kyoto-u.ac.jp
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| Phone |
+81-75-753-4230
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| Organization name |
Graduate School of Biostudies, Kyoto University
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| Department |
Department of Cell and Developmental Biology
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| Street address |
Kitashirakawa, Sakyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
606-8502 |
| Country |
Japan |
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| Platforms (8)
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| 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 |
| GPL6446 |
[Mm35b_P03R] Affymetrix Mouse Tiling 2.0R Set, Array 3 |
| GPL6447 |
[Mm35b_P04R] Affymetrix Mouse Tiling 2.0R Set, Array 4 |
| GPL6448 |
[Mm35b_P05R] Affymetrix Mouse Tiling 2.0R Set, Array 5 |
| GPL6449 |
[Mm35b_P06R] Affymetrix Mouse Tiling 2.0R Set, Array 6 |
| GPL6450 |
[Mm35b_P07R] Affymetrix Mouse Tiling 2.0R Set, Array 7 |
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| Samples (59)
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| Relations |
| BioProject |
PRJNA106203 |
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