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Myc binding to target sites in S2 cells (ChIPseq) in response to knockdown of Myc or the PAF1 complex component Atu/Leo1

ABSTRACT: Myc binding to target sites in S2 cells (ChIPseq) in response to knockdown of Myc or the PAF1 complex component Atu/Leo1

PROVIDER: PRJEB22853 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2146860.fastq.gz	Fastqsanger.gz
	ERR2146861.fastq.gz	Fastqsanger.gz
	ERR2146862.fastq.gz	Fastqsanger.gz

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Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast [ChIP-exo]

Project description:Maintenance of open and repressed chromatin states is crucial for regulation of gene expression. To study the genes involved in maintaining chromatin states we generated a random mutant library using the Hermes transposon mutagenesis system in fission yeast Schizosacchromyces pombe. The silencing of reporter genes inserted in the euchromatic region adjacent to the heterochromatic mating type locus was monitored. We identified Leo1-Paf1, a subcomplex of the RNA Polymerase II Associated Factor 1 Complex (Paf1C), required to prevent spreading of heterochromatin into euchromatin. Through high-resolution genome-wide ChIP (ChIP-exo) we mapped the heterochromatin mark H3K9me2 in leo1∆ cells. Loss of Leo1-Paf1 led to increased heterochromatin stability at several facultative heterochromatin loci. The RNAi machinery is the major pathway for heterochromatin formation in S. pombe. However, small RNA sequencing showed that heterochromatin assembly in leo1∆ cells was RNAi-independent. By examining histone turnover rate in leo1∆ cells, we showed that deletion of Leo1 decreased nucleosome turnover, which led to heterochromatin spreading. Our data revealed that Leo1-Paf1 promotes chromatin state fluctuations by enhancing histone turnover.

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Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast [ncRNA-Seq]

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Myc binding to target sites in S2 cells (ChIPseq) in response to knockdown of Myc or the PAF1 complex component Atu/Leo1

Project description:S2 cells were left untreated or incubated for 48 hours with dsRNA directed against Myc or Atu. Subsequently, chromatin was processed for chromatin immunoprecipitation with a rabbit polyclonal antibody agains Myc.

2017-10-02 | E-MTAB-5471 | biostudies-arrayexpress

Transcriptome of S2 cells after depletion of the PAF1 complex component Atu/Leo1

Project description:Transcriptome of S2 cells after depletion of the PAF1 complex component Atu/Leo1

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PAF1 complex component Leo1 helps recruit <i>Drosophila</i> Myc to promoters.

Project description:The Myc oncogene is a transcription factor with a powerful grip on cellular growth and proliferation. The physical interaction of Myc with the E-box DNA motif has been extensively characterized, but it is less clear whether this sequence-specific interaction is sufficient for Myc's binding to its transcriptional targets. Here we identify the PAF1 complex, and specifically its component Leo1, as a factor that helps recruit Myc to target genes. Since the PAF1 complex is typically associated with active genes, this interaction with Leo1 contributes to Myc targeting to open promoters.

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Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast [ChIPseq]

Project description:Project Abstract : Trimethylation of histone H3 lysine 4 (H3K4me3) is predominantly associated with transcriptional start sites (TSSs) and is believed to facilitate transcription initiation. Furthermore, H3K4me3 plays a role in defining cell fate and specific cellular functions. Nevertheless, the precise function of H3K4me3 in transcription activation remains a topic of ongoing debate. The Polymerase-associated factor 1 complex (Paf1C), which is integral to various transcription-related cellular processes, consists of five highly conserved subunits: Paf1, Ctr9, Rtf1, Cdc73, and Leo1. While all subunits of Paf1C are indispensable for the maintenance of H3K4 methylation levels, it is noteworthy that strains lacking Leo1 exhibited unaltered levels of H3K4me3. To elucidate the role of H3K4me3, we conducted a transcriptome analysis coupled with ChIP-sequencing of H3K4me3 in cells lacking Leo1. Our research uncovers a distinctive role of Leo1 in yeast, whereby it plays a pivotal role in maintaining sterol homeostasis through the suppression of Upc2 expression. Importantly, this role stands apart from the functions of other Paf1C subunits. H3K4me3 is essential for promoting the expression of sterol uptake genes that are Upc2-dependent when Leo1 is absent. Additionally, Set1 contributes to sterol homeostasis by regulating iron metabolism and mitochondrial functions rather than directly suppressing Upc2 expression. Therefore, our findings reveal a novel role for Leo1 in sterol homeostasis and highlight the importance of H3K4me3 in promoting transcription of response genes required for sterol uptake.

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Project description:Cyclin-dependent kinase 12 (CDK12) interacts with Cyclin K to form a functional nuclear kinase that promotes processive transcription elongation through phosphorylation of the RNA polymerase II (Pol II) C-terminal domain (CTD). To gain a broader understanding of CDK12 cellular function, we used chemical-genetic and phosphoproteomic screening to identify a landscape of nuclear human CDK12 substrates, including regulators of transcription, chromatin organization, and RNA splicing. We further validated LEO1, a subunit of the PAF1 complex (PAF1C), as a bona fide cellular substrate of CDK12. Acute depletion of LEO1, or substituting LEO1 phosphorylation sites with alanine, attenuated PAF1C association with elongating Pol II and impaired processive transcription elongation. We also found that LEO1 interacts with, and is dephosphorylated by, the Integrator-PP2A complex (INTAC) and that INTAC promotes the association of PAF1C with Pol II. Together, this study reveals a previously unknown role for CDK12 and INTAC in regulating LEO1 phosphorylation for transcriptional regulation, providing important insights into gene transcription and its regulation.

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Characterization of Paf1 complex occupancy in mouse myoblasts and myotubes under control conditions or Phf5a knockdown

Project description:Phf5a regulates occupancy of Paf1 complex in mouse myotubes. In this study we assayed for genome-wide localization of Leo1 subunit of the Paf1 complex in mouse myoblasts or myotubes under conditions of shControl or shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in significant decrease of Leo1 binding to its targets in myotubes.

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Characterization of Paf1 complex occupancy in mouse embryonic stem cells under control conditions or Phf5a knockdown

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.

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