In Vitro Transcription Recycling Assay Identifies PAF1 as a Driver of RNA Pol II Recycling
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE133655 | GEO | 2021/10/07
REPOSITORIES: GEO
Similar Datasets
Project description:RNA Polymerase II (Pol II) transcriptional recycling is an underappreciated mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of putative RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. By combing our in vitro transcription assays with other experiments (e.g. in vivo dynamic ChIP-seq assays), we identified PAF1 complex components as drivers for transcription recycling, revealing a new layer in controlling Pol II-dependent transcription. Our findings also point to RNA Pol II transcription recycling as a mechanism that functions aberrantly in disease states such as cancer, and indicate the potential to target factors such as PAF1 that drive RNA Pol II recycling in cancer.
2021-11-03 | PXD027143 | Pride
Project description:RNA Polymerase II (Pol II) transcriptional recycling is an underappreciated mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of putative RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. By combing our in vitro transcription assays with other experiments (e.g. in vivo dynamic ChIP-seq assays), we identified PAF1 complex components and phospho-MED1 as drivers for transcription recycling, revealing a new layer in controlling Pol II-dependent transcription. Our findings also point to RNA Pol II transcription recycling as a mechanism that functions aberrantly in disease states such as cancer, and indicate the potential to target factors such as PAF1 and phospho-MED1 that drive RNA Pol II recycling in cancer.
2021-11-03 | PXD017881 | Pride
Project description:Mammalian RNA polymerase II (Pol II) initiation, elongation, termination and reinitiation are well studied, but how Pol II dynamically recycles after the transcription cycle remains unclear. By establishing in vitro and in vivo transcription recycling systems, we find that human Mediator 1 (MED1), when phosphorylated at the mammal-specific threonine 1032 by cyclin-dependent kinase 9, dynamically travels with Pol II throughout the transcribed genes to drive Pol II recycling. Mechanistically, MED1 phosphorylation leads to an increase of recycled Pol II via the molecular bridge of MED31, enhancing mRNA output during the transcription recycling process. Importantly, MED1 phosphorylation increases during prostate cancer progression to the lethal phase, and pharmacological inhibition of CDK9 decreases prostate tumor growth through decreasing MED1 phosphorylation and Pol II recycling. Our findings reveal essential mechanisms underlying Pol II recycling and suggest a neglected, yet fundamental Pol II transcription process for therapeutic intervention.
2022-04-20 | GSE127894 | GEO
Project description:In Vitro Transcription Recycling Assay Identifies PAF1 as a Driver of RNA Pol II Recycling
| PRJNA552087 | ENA
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188412 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188415 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188413 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188410 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188417 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188416 | GEO