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RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

ABSTRACT: RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

PROVIDER: PRJNA785637 | ENA |

REPOSITORIES: ENA

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RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

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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.

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

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Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation

Project description:The Piwi-interacting RNA (piRNA) pathway plays a crucial role in protecting animal germ cells by repressing transposons. However, the mechanism behind this RNA-mediated epigenetic regulation that leads to heterochromatin formation is not yet fully understood. Through RNA interference screens, we discovered Pcf11 and PNUTS, two conserved termination factors of RNA polymerase II (Pol II), as essential for piRNA-guided silencing. When Pcf11 is artificially tethered to a reporter, it leads to co-transcriptional repression and Pol II stalling, both of which are dependent on an alpha-helical region of Pcf11 capable of forming condensates when triggered by the C-terminal repeat domain (CTD) of Pol II. Interestingly, an intrinsically disordered region (IDR) derived from the Plant FCA can substitute for the alpha-helical region of Pcf11 in its silencing capacity and support animal development, demonstrating a causal relationship between phase separation and Pcf11’s function. Further exploration into how Pcf11 causes Pol II stalling revealed a direct interaction between Pcf11’s CTD-interaction domain (CID) and a CTR region of Spt5. The dephosphorylation of Spt5-CTR by PP1/PNUTS is essential for Pcf11’s recruitment during Pol II termination. It appears that the phosphorylated state of CTR inhibits Pcf11 condensate formation, while the phosphorylation of Pol II CTD at Threonine 4 enhances Pcf11’s ability to undergo phase separation. In conclusion, we propose a model in which Pcf11 regulates transcriptional termination by slowing down Pol II elongation, a process that is aided by phase separation with the unphosphorylated Spt5. The ability of Pcf11 to stall Pol II, utilized by the piRNA pathway to initiate heterochromatin formation, might represent a universal strategy for nascent RNA-mediated epigenetic control.

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