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Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination

ABSTRACT: Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination

PROVIDER: PRJNA691345 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13405474_1.fastq.gz	Fastqsanger.gz
	SRR13405474_2.fastq.gz	Fastqsanger.gz
	SRR13405475_1.fastq.gz	Fastqsanger.gz
	SRR13405475_2.fastq.gz	Fastqsanger.gz
	SRR13405476_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination.

Project description:Expression of fission yeast Pho1 acid phosphatase is repressed under phosphate-replete conditions by transcription of an upstream prt lncRNA that interferes with the pho1 mRNA promoter. lncRNA control of pho1 mRNA synthesis is influenced by inositol pyrophosphate (IPP) kinase Asp1, deletion of which results in pho1 hyper-repression. A forward genetic screen for ADS (Asp1 Deletion Suppressor) mutations identified the 14-3-3 protein Rad24 as a governor of phosphate homeostasis. Production of full-length interfering prt lncRNA was squelched in rad24Δ cells, concomitant with increased production of pho1 mRNA and increased Pho1 activity, while shorter precociously terminated non-interfering prt transcripts persisted. Epistasis analysis showed that pho1 de-repression by rad24Δ depends on: (i) 3'-processing and transcription termination factors CPF, Pin1, and Rhn1; and (ii) Threonine-4 of the Pol2 CTD. Combining rad24Δ with the IPP pyrophosphatase-dead asp1-H397A allele caused a severe synthetic growth defect that was ameliorated by loss-of-function mutations in CPF, Pin1, and Rhn1, and by CTD phospho-site mutations T4A and Y1F. Rad24 function in repressing pho1 was effaced by mutation of its phosphate-binding pocket. Our findings instate a new role for a 14-3-3 protein as an antagonist of precocious RNA 3'-processing/termination.

| S-EPMC8789043 | biostudies-literature

Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination

Project description:This RNA-Seq analysis compares gene expression of rad24∆ mutant contrasting to the WT fission yeast S. pombe

2021-12-06 | GSE164616 | GEO

Targeted protein degradation reveals direct roles of SPT6 in POL2 elongation and termination

Project description:SPT6 is both, an important histone chaperone and POL2 elongation factor but its primary role on transcription in mammalian cells remains open, as no acute depletion system is available. We used targeted protein degradation to rapidly deplete SPT6 and analyzed defects in POL2 behavior by a multi-omics approach and estimated POL2 processivity, elongation rates and termination and compared it to gene transcription. Our data indicate that SPT6 is a crucial factor for POL2 elongation. Unexpectedly, SPT6 has also a vital role in POL2 termination, as acute depletion induces POL2 read through at most protein coding genes. In contrast, acute depletion did not induce spurious intragenic initiation, while this behavior can be induced by long-term depletion of SPT6 and can therefore be attributed to its function as a histone chaperone. In conclusion, targeted protein degradation of SPT6 allows the kinetic discrimination of its function as a histone chaperone and POL2 elongation factor.

2021-06-23 | GSE162264 | GEO

Comparison of precocious and non-precocious salmon

Project description:This SuperSeries is composed of the following subset Series: GSE16720: Comparison of precocious and non-precocious salmon brain GSE16721: Comparison of gene expression in the salmon parr precocious and non-precocious testis Refer to individual Series

2010-05-16 | E-GEOD-16860 | biostudies-arrayexpress

Comparison of precocious and non-precocious salmon brain

Project description:The objective was to compare gene expression in salmon precocious and non-precocious parr brain tissue. Eight microarray hybridisations were carried out in total as part of this design. To compare brain samples total RNA from 10 individual brains (dissected of hypothalamus and pituitary) of precocious fish and 10 brains of non-precocious fish were pooled to give two pools each of five precocious (PA and PB) and non-precocious (NPA and NPB) brains. Each pool of precocious brains was compared in a dye swap experiment with each pool of non-precocious brains.

2010-05-16 | E-GEOD-16720 | biostudies-arrayexpress

Comparison of precocious and non-precocious salmon brain

Project description:The objective was to compare gene expression in salmon precocious and non-precocious parr brain tissue.

2009-12-31 | GSE16720 | GEO

Suppressors of PHO regulon hyper-repression by Pol2 CTD Thr4 mutation implicate inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination

Project description:Suppressors of PHO regulon hyper-repression by Pol2 CTD Thr4 mutation implicate inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination

| PRJNA650467 | ENA

A genetic screen for suppressors of hyper-repression of the fission yeast PHO regulon by Pol2 CTD mutation T4A implicates inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination.

Project description:Fission yeast phosphate homeostasis genes are repressed in phosphate-rich medium by transcription of upstream lncRNAs that interferes with activation of the flanking mRNA promoters. lncRNA control of PHO gene expression is influenced by the Thr4 phospho-site in the RNA polymerase II CTD and the 3' processing/termination factors CPF and Rhn1, mutations of which result in hyper-repression of the PHO regulon. Here, we performed a forward genetic screen for mutations that de-repress Pho1 acid phosphatase expression in CTD-T4A cells. Sequencing of 18 independent STF (Suppressor of Threonine Four) isolates revealed, in every case, a mutation in the C-terminal pyrophosphatase domain of Asp1, a bifunctional inositol pyrophosphate (IPP) kinase/pyrophosphatase that interconverts 5-IP7 and 1,5-IP8. Focused characterization of two STF strains identified 51 coding genes coordinately upregulated vis-à-vis the parental T4A strain, including all three PHO regulon genes (pho1, pho84, tgp1). Whereas these STF alleles-asp1-386(Stop) and asp1-493(Stop)-were lethal in a wild-type CTD background, they were viable in combination with mutations in CPF and Rhn1, in which context Pho1 was also de-repressed. Our findings implicate Asp1 pyrophosphatase in constraining 1,5-IP8 or 1-IP7 synthesis by Asp1 kinase, without which 1-IPPs can accumulate to toxic levels that elicit precocious termination by CPF/Rhn1.

| S-EPMC7641756 | biostudies-literature

PAX3-FOXO1 directs CBP/P300 via its activation domain to build RNA Pol2 clusters

Project description:Activation of oncogenic gene expression from long-range enhancers is initiated by the assembly of DNA-binding transcription factors (TF), leading to recruitment of co-activators such as CBP/p300 to modify the local genomic context and facilitate RNA-Polymerase 2 (Pol2) binding. Yet, most TF-to-coactivator recruitment relationships remain unmapped. Here, studying the oncogenic fusion TF PAX3-FOXO1 (P3F) from alveolar rhabdomyosarcoma (aRMS), we show that a single cysteine in the activation domain (AD) of PAX3-FOXO1 forms a small alpha helical hook that recruits CBP/p300 to chromatin. P3F driven transcription requires both this single cysteine, and also CBP/p300. Furthermore, we discover a profound dependence on CBP/p300 for clustering of Pol2 loops that connect P3F to its target genes. In the absence of CBP/p300, Pol2 long range enhancer loops collapse, Pol2 accumulates in CpG islands and fails to exit the gene body. These results reveal a potential novel axis for therapeutic interference with P3F in aRMS and clarify the molecular relationship of P3F and CBP/p300 in sustaining active Pol2 clusters essential for oncogenic transcription.

2023-12-25 | GSE208146 | GEO

Comparison of gene expression in the salmon parr precocious and non-precocious testis

Project description:The objective was to compare gene expression in salmon precocious and non-precocious parr testis tissue. Nine microarray hybridisations were carried out in total as part of this loop design. Total RNA from 3 pools(PG1-PG3) each of 4 precocious fish testes were compared with 3 pools (NP1-NP3) each of 10 non-precocious fish testes. There were no direct dye swaps but there was overall dye balance in the loop

2010-05-16 | E-GEOD-16721 | biostudies-arrayexpress

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