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| Status |
Public on May 20, 2011 |
| Title |
Transcription Initiation Platforms and GTF recruitment at tissue-specific enhancers and promoters |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Recent works have shown that RNA Polymerase (Pol) II can be recruited to, and transcribe, distal regulatory regions. Here, we analyzed transcription initiation and elongation through genome-wide localization of Pol II, General Transcription Factors (GTFs) and active chromatin in developing T-cells. We show that Pol II and GTFs are recruited to known, highly T-cell-specific enhancers. We extend this observation for the first time to many new putative enhancers, a majority of which are transcribed with or without polyadenylation. Importantly, we also identify genomic features characterized by large Pol II/GTFs recruitment and Transcriptional Initiation Platforms (TIPs) at promoters, intergenic and intragenic regions. TIPs are characterized by variable widths (0.4 to 10 kb), and correlate with high CpG content and tissue-specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important novel regulatory hallmarks of the genome.
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| Overall design |
This study is based on the analysis of 20 samples in mouse double-positive thymocytes, 15 of which cover a range of general and specific transcription factors, chromatin modifying enzymes as well as histone modifications. 2 samples were dedicated for strand-specific RNA sequencing either from the total RNA population or after a selection of Poly(A) RNA. A Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sample has been sequenced in order to isolate open chromatin regions. Finally, input and IG control samples were designed and sequenced for data processing purposes. Biological and technical replicates were processed as described in the supplementary methods.
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| Contributor(s) |
Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, Lamy de la Chapelle A, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau J |
| Citation(s) |
21765417 |
| Submission date |
May 17, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Romain Fenouil |
| Organization name |
CNRS
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| Department |
CIML
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| Lab |
CB2M
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| Street address |
Parc Scientifique et Technologique de Luminy - Case 906
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| City |
Marseille |
| State/province |
F13288 Cedex 09 |
| ZIP/Postal code |
13009 |
| Country |
France |
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| Platforms (2) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL10010 |
AB SOLiD System (Mus musculus) |
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| Samples (20)
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| Relations |
| SRA |
SRP006816 |
| BioProject |
PRJNA140193 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29362_RAW.tar |
3.0 Gb |
(http)(custom) |
TAR (of GFF, SGR, WIG) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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