A germline PAF1 paralog complex ensures cell type-specific gene expression
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ABSTRACT:
PROVIDER: PRJNA1100457 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28681900.fastq.gz | Fastqsanger.gz | |||
| SRR28681901.fastq.gz | Fastqsanger.gz | |||
| SRR28681902.fastq.gz | Fastqsanger.gz | |||
| SRR28681903.fastq.gz | Fastqsanger.gz | |||
| SRR28681904.fastq.gz | Fastqsanger.gz |
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Project description:Animal germline development and fertility rely on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream of such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here we show that efficient termination of tTAF-activated transcription requires a testis-specific Polymerase Associated Factor 1 Complex (tPAF) composed of paralogs of canonical Polymerase Associated Factor 1 Complex (PAF1C) proteins. Defective transcription termination in tPAF mutants causes aberrant expression of hundreds of downstream genes due to read-in transcription, compromising cell type-specific gene expression in spermatocytes. Consistently, tPAF is required for the segregation of meiotic chromosomes, sperm individualisation, and male fertility. Comparative in vivo proximity labeling assays of tPAF and PAF1C showed tPAF-specific association with tTAF as well as connections to central RNA polymerase II termination factors. Our study uncovers transcription termination as a developmentally regulated process required for cell type-specific gene expression.
2024-04-16 | GSE263955 | GEO
Project description:Animal germline development and fertility relies on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream of such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here we show that efficient termination of tTAF-activated transcription requires a testis-specific Polymerase Associated Factor 1 Complex (tPAF) composed of paralogs of canonical Polymerase Associated Factor 1 Complex (PAF1C) proteins. Defective transcription termination in tPAF mutants causes aberrant expression of hundreds of downstream genes due to read-in transcription, compromising cell type-specific gene expression in spermatocytes. Consistently, tPAF is required for the segregation of meiotic chromosomes, sperm individualisation, and male fertility. Comparative in vivo proximity labeling assays of tPAF and PAF1C showed tPAF-specific association with tTAF as well as connections to central RNA polymerase II termination factors. Our study uncovers transcription termination as a developmentally regulated process required for cell type-specific gene expression.
2024-04-13 | PXD049375 | Pride
Project description:Animal germline development and fertility relies on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream of such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here we show that efficient termination of tTAF-activated transcription requires a testis-specific Polymerase Associated Factor 1 Complex (tPAF) composed of paralogs of canonical Polymerase Associated Factor 1 Complex (PAF1C) proteins. Defective transcription termination in tPAF mutants causes aberrant expression of hundreds of downstream genes due to read-in transcription, compromising cell type-specific gene expression in spermatocytes. Consistently, tPAF is required for the segregation of meiotic chromosomes, sperm individualisation, and male fertility. Comparative in vivo proximity labeling assays of tPAF and PAF1C showed tPAF-specific association with tTAF as well as connections to central RNA polymerase II termination factors. Our study uncovers transcription termination as a developmentally regulated process required for cell type-specific gene expression.
2024-04-13 | PXD049360 | Pride
Project description:Animal germline development and fertility rely on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream from such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here, we show that efficient termination of tTAF-activated transcription relies on testis-specific paralogs of canonical polymerase-associated factor 1 complex (PAF1C) proteins, which form a testis-specific PAF1C (tPAF). Consequently, tPAF mutants show aberrant expression of hundreds of downstream genes due to read-in transcription. Furthermore, tPAF facilitates expression of Y-linked male fertility factor genes and thus serves to maintain spermatocyte-specific gene expression. Consistently, tPAF is required for the segregation of meiotic chromosomes and male fertility. Supported by comparative in vivo protein interaction assays, we provide a mechanistic model for the functional divergence of tPAF and the PAF1C and identify transcription termination as a developmentally regulated process required for germline-specific gene expression.
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Project description:To identify the direct targets of the Paf1/RNA polymerase II complex we compared expression profiles of isogenic wild type and paf1 and ctr9 mutant strains. We also created a Tet-regulated form of Paf1 and monitored expression patterns after shut off of Paf1. Samples were isolated at one hour intervals from 1 to 8 hours after shut off. Experiment Overall Design: Transcripts were compared on Affymetrix microarrays using standard protocols.
2007-09-19 | E-GEOD-3200 | biostudies-arrayexpress
Project description:Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of Paf1, Leo1 and Cdc73 subunits of the Paf1 complex in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the significant decrease of Paf1 complex binding to its targets in ESCs.
2016-08-31 | GSE73445 | GEO
Project description:In this study, we found that the ARF tumor suppressor directly binds the PAF1 subunit to block the assembly of PAF1 complex (PAF1c) and its interaction with RNAPII, thereby dampening PAF1c-dependent transcription in vitro and in cells. To investigate whether ARF regulates RNAPII and PAF1c occupancy at putative target genes identified through RNA-seq, we performed ChIP-seq (RNAPII, PAF1, and CTR9) in ARF (shARF) vs. control (shNT) knockdown MEFs. Our data show that loss of ARF increases RNAPII, PAF1, and CTR9 occupancy on upregulated genes, consistent with ARF-mediated gene-specific repression. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA polymerase subunit RPB3 and PAF1 complex subunits PAF1 and CTR9 in mouse embryonic fibroblasts.
2024-10-10 | GSE217765 | GEO
Project description:Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory.
2015-03-25 | GSE59170 | GEO
Project description:Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory.
2015-03-25 | GSE59169 | 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