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| Status |
Public on Nov 05, 2015 |
| Title |
Two Distinct Promoter Nucleosome Architectures at Protein-Coding Genes in Yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a more narrow, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes.
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| Overall design |
MNase-seq profiles obtained with various MNase concentrations from wild-type cells and cells depleted of different factors. ChIP-seq using anti-RNA polymerase II antibody, anti-histone H2A antibody, and anti-histone H3 antibody.
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| Contributor(s) |
Kubik S, Bruzzone MJ, Jacquet P, Falcone JL, Rougemont J, Shore D |
| Citation(s) |
26545077 |
| |
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacques Rougemont |
| E-mail(s) |
jacques.rougemont@epfl.ch
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| Organization name |
EPFL
|
| Department |
School of Life Sciences
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| Lab |
Bioinformatics and Biostatistics Core Facility
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA296702 |
| SRA |
SRP064008 |
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