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| Status |
Public on Feb 25, 2019 |
| Title |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination (zebrafish 3' mRNA-seq) |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including: mNET-seq, 3’ mRNA-seq, chromatin RNA-seq and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and downstream gene silencing. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript, and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination.
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| Overall design |
3' mRNA-seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild-type (wt, +/+), heterozygous (het, +/-) and homozygous mutant (hom, -/-) embryos were analyzed. Wild-type and heterozygous animals were phenotypically indistinguishable.
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| Contributor(s) |
Kamieniarz-Gdula K, Gdula MR, Panser K, Pauli A, Proudfoot N |
| Citation(s) |
30819644 |
| |
| Submission date |
Jan 02, 2019 |
| Last update date |
May 02, 2019 |
| Contact name |
Kinga Kamieniarz-Gdula |
| Organization name |
University of Oxford
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| Department |
Sir William Dunn School of Pathology
|
| Street address |
South Parks Road
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| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (28)
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| This SubSeries is part of SuperSeries: |
| GSE123105 |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination |
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| Relations |
| BioProject |
PRJNA512489 |
| SRA |
SRP175015 |
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