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| Status |
Public on Dec 20, 2018 |
| Title |
Identification of non-coding transcripts regulated by the transcription factor Rap1 by RNA-Seq analysis |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.
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| Overall design |
RNA-Seq analysis of Saccharomyces cerevisiae S288C strains transformed with OsTIR1 ligase and auxin-inducible degron (IAA7) tagged Rap1, or wild-type control strains. 3 biological replicates for each sample type and condition are analyzed. For each biological replicate, cells were grown overnight in YPD media, diluted, and treated with DMSO or 500 μM 3-indole-acetic acid (3-IAA, auxin). UNINDUCED samples were taken 30 minutes after treatment, and INDUCED samples were taken 30 minutes or 2 hours after treatment. For WT controls, samples were taken in mid-logarithmic growth. RNA was either subjected to rRNA depletion or polyA RNA purification to generate POLYA and TOTAL RNA-Seq libraries, respectively.
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| Contributor(s) |
Wu A, Patel H, Chia M, Moretto F, Frith D, Snijders AP, van Werven FJ |
| Citation(s) |
30576656 |
| |
| Submission date |
Dec 07, 2017 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Folkert van Werven |
| E-mail(s) |
Folkert.vanWerven@crick.ac.uk
|
| Organization name |
Francis Crick Institute
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (18)
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| GSM2879618 |
Wild-type total RNA-Seq biological replicate 1 |
| GSM2879619 |
Wild-type total RNA-Seq biological replicate 2 |
| GSM2879620 |
Wild-type total RNA-Seq biological replicate 3 |
| GSM2879621 |
Rap1-AID degron no induction total RNA-Seq biological replicate 1 |
| GSM2879622 |
Rap1-AID degron no induction total RNA-Seq biological replicate 2 |
| GSM2879623 |
Rap1-AID degron no induction total RNA-Seq biological replicate 3 |
| GSM2879624 |
Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 1 |
| GSM2879625 |
Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 2 |
| GSM2879626 |
Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 3 |
| GSM2879627 |
Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 1 |
| GSM2879628 |
Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 2 |
| GSM2879629 |
Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 3 |
| GSM2879630 |
Rap1-AID degron no induction polyA RNA-Seq biological replicate 1 |
| GSM2879631 |
Rap1-AID degron no induction polyA RNA-Seq biological replicate 2 |
| GSM2879632 |
Rap1-AID degron no induction polyA RNA-Seq biological replicate 3 |
| GSM2879633 |
Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 1 |
| GSM2879634 |
Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 2 |
| GSM2879635 |
Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE110004 |
Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor |
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| Relations |
| BioProject |
PRJNA421472 |
| SRA |
SRP126328 |
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