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Influence of IWS1 TND-interacting motifs (TIMs) on transcription elongation [PRO-seq]

ABSTRACT: To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we prepared PRO-seq libraries from these samples and examined elongation profiles. Analysis of elongation profiles revealed that TIM3 disruption induces pervasive defects of transcription elongation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179916 | GEO | 2021/11/26

REPOSITORIES: GEO

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Influence of IWS1 TND-interacting motifs (TIMs) on gene expression patterns [RNA-seq]

Project description:To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we prepared mRNA from these samples and performed expression profiling using RNA-seq. Analysis of differential gene expression provided markers that are differentially regulated by TIM3 of IWS1.

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Influence of IWS1 TND-interacting motifs (TIMs) on chromatin localization patterns [ChIP-seq]

Project description:To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we performed ChIP using anti-FLAG antibodies from these samples and performed chromatin occupancy profiling using ChIP-seq. Analysis of locations reveal that both WT and M3 samples are highly enriched in at transcribed gene bodies.

2021-11-26 | GSE179909 | GEO

Influence of IWS1 TND-interacting motifs (TIMs) on transcription elongation [PRO-seq]

Project description:Influence of IWS1 TND-interacting motifs (TIMs) on transcription elongation [PRO-seq]

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Influence of IWS1 TND-interacting motifs (TIMs) on chromatin localization patterns [ChIP-seq]

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Influence of IWS1 TND-interacting motifs (TIMs) on gene expression patterns [RNA-seq]

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Toxoplasma IWS1 determines fitness in interferon-γ-activated host cells and mice by regulating ROP18 mRNA expression

Project description:Toxoplasma gondii secretes various virulence effector molecules into host cells to disrupt host interferon-γ (IFN-γ)-dependent immunity. Among the effectors, ROP18 directly phosphorylates and inactivates IFN-inducible GTPases, such as immunity-related GTPases (IRGs) and guanylate-binding proteins (GBPs), leading to subversion of IFN-inducible GTPase-induced cell-autonomous immunity. The modes of action of ROP18 have been studied extensively; however, little is known about the molecular mechanism of how ROP18 is produced in the parasite itself. Here, we report a role of T. gondii transcription factor IWS1 in ROP18 mRNA expression in the parasite. Compared with wild-type virulent type I T. gondii, IWS1-deficient parasites showed dramatically increased loading of IRGs and GBPs onto the parasitophorous vacuole membrane (PVM). Moreover, IWS1-deficient parasites displayed decreased virulence in wild-type mice but retained normal virulence in mice lacking the IFN-γ receptor. Furthermore, IWS1-deficient parasites showed severely decreased ROP18 mRNA expression. Ectopic expression of ROP18 in IWS1-deficient parasites restored the decreased loading of effectors onto the PVM and in vivo virulence in wild-type mice. Taken together, these data demonstrate that T. gondii IWS1 regulates ROP18 mRNA expression to determine fitness in IFN-γ-activated host cells and mice.

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Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae

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2022-05-16 | GSE202590 | GEO

Comparison of the transcriptomes of tfIIs vs Col-0

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Widespread backtracking by RNA pol II is a major effector of gene activation, 5’ pause release, termination and transcription elongation rate

Project description:In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. We identified backtracking sites using mNET-seq in human cells expressing dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3’ flanking regions where termination is enhanced by TFIISDN. Inhibition of the rescue from backtracked pol II by TFIISDN impaired the escape from 5’ pause sites, the completion of long transcripts, and activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half as measured by sequencing nascent transcripts pulse labeled with Bromouridine (Bru-seq) and by anti-pol II ChIP-seq at time points after release of a DRB block. These results suggest that rescue of backtracked pol II by TFIIS is a major stimulus of elongation.

2018-11-30 | GSE120201 | GEO

NDF Is a Transcription Factor that Stimulates Elongation by RNA Polymerase II

Project description:RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we find that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than does transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II-binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.

2022-03-10 | GSE185464 | GEO

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