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Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

ABSTRACT: Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

PROVIDER: PRJNA785631 | ENA |

REPOSITORIES: ENA

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RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

| PRJNA785637 | ENA

RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:High Throughput bulk-sample ChIP-seq data targeted to RNA-polymerase II was collected for duplicate samples of two distinct mutations of Pcf11 and a matched wildtype w303 samples under standard growth conditions. The overall goal was quantification of changes in transcriptional activity in response to these mutations.

2023-11-01 | GSE190049 | GEO

DRS expression and polyA site measurement of Pcf11 mutations in yeast

Project description:DRS expression and polyA site measurement of Pcf11 mutations in yeast

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DRS expression and polyA site measurement of Pcf11 mutations in yeast

Project description:Direct-RNA Sequencing expression data, quantifying both abundance and 3'-processing (cleavage and polyadenylation) site was obtained for two distinct mutations of Pcf11 and matched wildtype w303 samples under both standard growth conditions, as well as under growth in a caffeine-supplemented medium, since these mutations have been shown to increase susceptiblity to caffeine-related phenotypes. The overall goal was quantification of expression and pre-mRNA processing changes in response to these mutations.

2023-11-01 | GSE190050 | GEO

Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-01 | GSE190052 | GEO

RNA-seq expression analysis of Pcf11 mutations Pcf11-13 and Pcf11-DNL

Project description:RNA-seq expression analysis of Pcf11 mutations Pcf11-13 and Pcf11-DNL

| PRJNA785635 | ENA

RNA-seq expression analysis of Pcf11 mutations Pcf11-13 and Pcf11-DNL

Project description:High Throughput bulk-sample RNA-sequencing expression data, was collected for triplicate samples of two distinct mutations of Pcf11 and a matched wildtype w303 samples under standard growth conditions. The overall goal was quantification of expression abundance and pre-mRNA processing changes in response to these mutations.

2023-11-01 | GSE190051 | GEO

Selective roles of vertebrate PCF11 in premature and full-length transcript termination (ChIP-seq)

Project description: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.

2019-02-28 | GSE127256 | GEO

Selective roles of vertebrate PCF11 in premature and full-length transcript termination (mNET-seq)

2019-02-25 | GSE123104 | GEO

m6Am sequesters PCF11 to promote full-length transcription [m6ACE]

Project description:RNA modifications regulate how RNAs metabolize and function to impact development and diseases. N6,2’-O-dimethyladenosine (m6Am) is one such modification and despite being abundant, m6Am function remains unclear. Here, we identified cleavage and polyadenylation factor, PCF11 as a m6Am-specific binding protein. Direct quantification of mature versus nascent RNAs revealed that m6Am does not regulate mRNA stability but promotes transcription of nascent RNAs. m6Am caused RNA Polymerase II (Pol II) to be more processive when transcribing m6Am-modified RNAs. Rather than PCF11 regulating m6Am-modified RNA, m6Am sequesters PCF11 away from proximal Pol II, suppressing premature dissociation of elongating Pol II and promoting Pol II full-length transcription of m6Am-modified RNAs. This establishes a mechanism through which an RNA modification regulates transcription.

2024-10-31 | GSE254149 | GEO

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