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| Status |
Public on Jul 27, 2021 |
| Title |
RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription [nascent RNA-Seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. Depletion of RSC increased divergent noncoding and decreased protein coding transcription of promoters with strong directionality. Consistent with RSC’s role in regulating chromatin, RSC depletion negatively impacts nucleosome positions upstream of the nucleosome depleted region where divergent transcription initiates, suggesting that nucleosome positioning upstream in promoters physically blocks the recruitment of transcription machinery. Likewise, divergent transcription can be suppressed by targeting GRFs and TFs or the bulky dCas9 protein to transcriptional initiation sites. We propose that RSC mediated nucleosome positioning, GRFs including TFs form the physical barriers in promoters for limiting of divergent transcription, thereby controlling promoter directionality.
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| Overall design |
Nascent RNA-Seq analysis of Saccharomyces cerevisiae. Rap1, Sth1 or Sth1/Rap1 (co) depleted cells were used for RNA-Seq libraries, respectively.
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| Contributor(s) |
Wu A, Vivori C, Patel H, Sideri T, van Werven F |
| Citation(s) |
36114005 |
| Submission date |
Jul 01, 2021 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Folkert van Werven |
| E-mail(s) |
Folkert.vanWerven@crick.ac.uk
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| Organization name |
Francis Crick Institute
|
| Street address |
1 Midland Road
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| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL21656 |
Illumina HiSeq 4000 (Saccharomyces cerevisiae) |
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| Samples (21)
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| GSM5412599 |
Wild-type nascent RNA-Seq biological replicate 1 |
| GSM5412600 |
Wild-type nascent RNA-Seq biological replicate 2 |
| GSM5412601 |
Wild-type nascent RNA-Seq biological replicate 3 |
| GSM5412602 |
Sth1-AID degron no induction nascent RNA-Seq biological replicate 1 |
| GSM5412603 |
Sth1-AID degron no induction nascent RNA-Seq biological replicate 2 |
| GSM5412604 |
Sth1-AID degron no induction nascent RNA-Seq biological replicate 3 |
| GSM5412605 |
Sth1-AID degron induction nascent RNA-Seq biological replicate 1 |
| GSM5412606 |
Sth1-AID degron induction nascent RNA-Seq biological replicate 2 |
| GSM5412607 |
Sth1-AID degron induction nascent RNA-Seq biological replicate 3 |
| GSM5412608 |
Rap1-AID degron no induction nascent RNA-Seq biological replicate 1 |
| GSM5412609 |
Rap1-AID degron no induction nascent RNA-Seq biological replicate 2 |
| GSM5412610 |
Rap1-AID degron no induction nascent RNA-Seq biological replicate 3 |
| GSM5412611 |
Rap1-AID degron induction nascent RNA-Seq biological replicate 1 |
| GSM5412612 |
Rap1-AID degron induction nascent RNA-Seq biological replicate 2 |
| GSM5412613 |
Rap1-AID degron induction nascent RNA-Seq biological replicate 3 |
| GSM5412614 |
Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 1 |
| GSM5412615 |
Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 2 |
| GSM5412616 |
Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 3 |
| GSM5412617 |
Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 1 |
| GSM5412618 |
Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 2 |
| GSM5412619 |
Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE179256 |
RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription |
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| Relations |
| BioProject |
PRJNA743012 |
| SRA |
SRP326472 |
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