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

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

PROVIDER: PRJNA745577 | ENA |

REPOSITORIES: ENA

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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.

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 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 chromatin localization patterns [ChIP-seq]

Project description: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 transcription elongation [PRO-seq]

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

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

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Chromatin and transcriptional mechanisms regulated by TFIIS N-terminal domains (TNDs) and TND-interacting motifs (TIMs)

Project description:Chromatin and transcriptional mechanisms regulated by TFIIS N-terminal domains (TNDs) and TND-interacting motifs (TIMs)

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Human VAPome Analysis Reveals MOSPD1 and MOSPD3 as Membrane Contact Site Proteins Interacting with FFAT-Related FFNT Motifs

Project description:Membrane contact sites (MCS) are intracellular regions where two organelles come closer to exchange information and material. The majority of the endoplasmic reticulum (ER) MCS are attributed to the ER-localized tether proteins VAPA, VAPB, and MOSPD2. These recruit other proteins to the ER by interacting with their FFAT motifs. Here, we describe MOSPD1 and MOSPD3 as ER-localized tethers interacting with FFAT motif-containing proteins. Using BioID, we identify proteins interacting with VAP and MOSPD proteins and find that MOSPD1 and MOSPD3 prefer unconventional FFAT-related FFNT (two phenylalanines [FF] in a neutral tract) motifs. Moreover, VAPA/VAPB/MOSPD2 and MOSPD1/MOSPD3 assemble into two separate ER-resident complexes to interact with FFAT and FFNT motifs, respectively. Because of their ability to interact with FFNT motifs, MOSPD1 and MOSPD3 could form MCS between the ER and other organelles. Collectively, these findings expand the VAP family of proteins and highlight two separate complexes in control of interactions between intracellular compartments.

2023-06-29 | PXD043399 | Pride

Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and C53-mediated autophagy

Project description:UFMylation mediates the covalent modification of substrate proteins with UFM1 (Ubiquitin- fold modifier 1) and regulates the selective degradation of endoplasmic reticulum (ER) via autophagy (ER-phagy) to maintain ER homeostasis. Specifically, collisions of the ER-bound ribosomes trigger ribosome UFMylation, which in turn activates C53-mediated autophagy that clears the toxic incomplete polypeptides. C53 has evolved non-canonical shuffled ATG8 interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. Why these non-canonical motifs were selected during evolution, instead of canonical ATG8 interacting motifs remains unknown. Here, using a phylogenomics approach, we show that UFMylation is conserved across the eukaryotes and secondarily lost in fungi and some other species. Further biochemical assays have confirmed those results and showed that the unicellular algae, Chlamydomonas reinhardtii has a functional UFMylation machinery, overturning the assumption that this process is linked to multicellularity. Our conservation analysis also revealed that UFM1 co-evolves with the sAIMs in C53, reflecting a functional link between UFM1 and the sAIMs. Using biochemical and structural approaches, we confirmed the interaction of UFM1 with the C53 sAIMs and found that UFM1 and ATG8 bound to the sAIMs in a different mode. Conversion of sAIMs into canonical AIMs prevented binding of UFM1 to C53, while strengthening ATG8 interaction. This led to the autoactivation of the C53 pathway and sensitized Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral toggle switch embodied in the sAIMs that regulates C53- mediated autophagy to maintain ER homeostasis.

2022-11-22 | PXD038157 | Pride

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