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| Status |
Public on Apr 24, 2014 |
| Title |
Definition of the fibroblast SRF-mediated immediate-early transcriptional response |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
To control transcription, SRF recruits signal-regulated co-activators, the Ternary Complex Factors (TCFs) and the Myocardin-related Transcription Factors (MRTFs), which compete for a common site on its DNA-binding domain. The TCFs - SAP-1, Elk-1 and Net - are Ets proteins that link SRF activity to Ras-ERK signalling. In contrast, the two MRTFs, MRTF-A and MRTF-B, link SRF activity to Rho-actin signalling. In this novel signalling pathway, the actin-binding MRTF RPEL domain acts as a G-actin sensor, controlling MRTF nuclear accumulation in response to signal-induced depletion of the G-actin pool. Previous studies have suggested that the Ras-ERK signalling and Rho-actin pathways control specific subsets of SRF target genes. We used ChIP-seq and RNA-seq to analyse the immediate-early transcriptional response in NIH3T3 fibroblasts, using pathway-specific inhibitors to identify the contributions of Ras-ERK and Rho-actin signalling
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| Overall design |
Chromatin immunoprecipitation and sequencing (ChIP-seq) in NIH3T3 fibroblast after serum stimulation in presence or absence of LatrunculinB or U0126 drugs and using antibodies against SRF, MRTF-A, MRTF-B, SAP1, ELK1, NET, Pol II, PolII S5P, PolII S2P and total H3. Validation by ChIP-PCR. Strand specific total-RNA-seq following DSN normalisation and validation by qRT-PCR from NIH3T3 stimulated by serum or Cytochalasin D in presence or absence of LatrunculinB and/or U0126 drugs.
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| Contributor(s) |
Esnault C, Stewart A, East P, Horswell S, Matthews N, Gualdrini F, Treisman R |
| Citation(s) |
24732378 |
| Submission date |
Apr 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco Gualdrini |
| E-mail(s) |
francesco.gualdrini@crick.org.uk
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| Organization name |
Francis Crick Institute
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| Lab |
Treisman
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| Street address |
44 Lincoln's Inn Fields
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| City |
London |
| ZIP/Postal code |
WC2A 3LY |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (69)
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| Relations |
| SRA |
SRP020638 |
| BioProject |
PRJNA196820 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45888_RAW.tar |
87.5 Gb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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