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| Status |
Public on Jun 12, 2012 |
| Title |
CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.
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| Overall design |
Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.
Sonicated genomic DNA has been sequenced to quantify and exclude sequencing bias in the largest CGIs regions studied in this article.
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| Contributor(s) |
Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, Andrau J |
| Citation(s) |
23100115 |
| Submission date |
Jun 07, 2012 |
| Last update date |
Mar 08, 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 (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE38577 |
CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters |
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| Relations |
| BioProject |
PRJNA168376 |
