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

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

PROVIDER: PRJNA745686 | ENA |

REPOSITORIES: ENA

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Influence of IWS1 TND-interacting motifs (TIMs) on transcription elongation [PRO-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 PRO-seq libraries from these samples and examined elongation profiles. Analysis of elongation profiles revealed that TIM3 disruption induces pervasive defects of transcription elongation.

2021-11-26 | GSE179916 | GEO

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.

2021-11-26 | GSE179911 | GEO

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 chromatin localization patterns [ChIP-seq]

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

| PRJNA745575 | ENA

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

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

| PRJNA745577 | ENA

Glucose regulates cotton fiber elongation by interacting with brassinosteroid

Project description:Glucose regulates cotton fiber elongation by interacting with brassinosteroid

| PRJNA701442 | ENA

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.

2023-01-30 | GSE204926 | GEO

RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins

Project description:RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins

| PRJNA417119 | ENA

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

Project description:Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications as an integral member of the RNA polymerase II elongation complex. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated eight suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA co-activator complex, Sgf73. The identification of these distinct groups and their analysis suggests that there are multiple mechanisms by which Spn1 bypass can occur, including changes in histone acetylation and alterations of other histone chaperones. Thus, Spn1 may participate in multiple functions during transcription. Our results suggest that bypass of a subset of these functions allows viability in the absence of Spn1.

2022-05-16 | GSE202590 | GEO

Glucose regulates cotton fiber elongation by interacting with brassinosteroid

Project description:Our study provides evidence for the mechanism of Glc regulation of cotton fiber elongation, indicating that Glc not only serves as a nutrient, but also serves as a signal to regulate cotton fiber elongation. We also provided evidence that there is crosstalk between Glc and BR, and that the BR signal is located downstream of the Glc signal in the regulation of cotton fiber elongation

2022-02-01 | GSE166628 | GEO

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