Wasp metagenome
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ABSTRACT:
PROVIDER: PRJNA163505 | ENA |
REPOSITORIES: ENA
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Project description:To determine the global gene occupancy by Wiskott - Aldrich syndrome Protein (WASP) we perform ChIP-seq assay in two lymphoblastoid cell lines. We identify WASP-enriched genes, including several WASP-interaction genes previously reported; in addition, our results suggest the implication of WASP in diverse cellular process
2022-04-18 | GSE126483 | GEO
Project description:To investigate a role of nuclear WASp in T cell development we performed WASp chromatin immunoprecipitation and deep sequencing (ChIP-Seq) in thymocytes and spleen CD4+ T cells. To pre-process raw ChIP-Seq data, the total number of reads were normalized and aligned against the mouse genome. WASp was enriched at transcription start sites of a large number of protein-coding genes. Many of the WASp-enriched genes were associated with RNA Polymerase II-enriched genes and active epigenetic marks of transcription; H3K4m3, H3K9a, H3K27a, and with the epigenetic mark for active enhancers H3K4m1. To study the distribution of overactive WASpI296T in the thymocyte genome and to identify regions enriched in WASpI296T binding, we performed second round of ChIP-Seq analysis using the WASp F-8 antibody. To detect differences in gene enrichment between thymocytes expressing wildtype WASp or WASpI296T, we applied stringent conditions and subtracted common genes between the two samples. Using this approach, we identify 70 WASpI296T-enriched genes. Functional clustering of these genes revealed that WASpI296T was associated with RNA Polymerase II genes in 11 functional groups of genes.thymocytes and spleen CD4+ T cells. WASp was enriched at transcription start sites of a large number of protein-coding genes.
2017-10-05 | GSE89172 | GEO
Project description:The pleiotropic RTK Kit can provide cytoskeletal signals that define cell shape, positioning and migration, but the underlying mechanisms are less well understood. Here we provide evidence that Kit signals through WASP (Wiskott-Aldrich Syndrome Protein), the central hematopoietic actin nucleation- promoting factor and regulator of the cytoskeleton. KL-mediated gene expression in WT and WASP-deficient BMMCs was compared and revealed that approximately 30% of all Kit-induced changes were WASP-dependent. The results indicate that Kit signaling through WASP is necessary for normal Kit-mediated filopodia formation, cell survival and gene expression and provide new insight in the mechanism how WASP exerts a strong selective pressure in hematopoiesis.
2009-08-29 | E-MEXP-2282 | biostudies-arrayexpress
Project description:Phagocytosis requires the activation of a plethora of mechanisms that include the activation of the actin cytoskeleton guided by the Arp2/3 complex. These are promoted by activators such as the Wiskott Aldrich Syndrome Protein (WASP) family members. In order to further understand the molecular mechanisms involved in the early events leading the phagocytosis of the pathogenic Mycobacterium tuberculosis, we set out to examine potential roles of miRNAs in phagocytosis using genome-wide expression profiling to identify miRNAs differentially regulated following mycobacterial infection. One of the miRNAs activated upon infection of mouse macrophages with the non-pathogenic Mycobacterium smegmatis, the widely conserved miR-142-3p, was predicted and confirmed to target the Neural-WASP (N-WASP). Upregulating of miR-142-3p in mouse macrophages inversely correlated with levels of N-WASP, upon infection with live pathogenic and non-pathogenic mycobacteria, suggesting an active role of Mycobacterium tuberculosis on the regulation of phagocytosis, at the post-transcriptional level, in host cells. The reduction of N-WASP correlated with a reduced internalization of bacteria per macrophage, independently of the phagocytosis index. Furthermore, the downregulation of WASP levels accompanied those of N-WASP, at early but not at late time points, suggesting a closely regulatory mechanism among both family members, dependent on the time frame of the phagocytosis. Additionally, upregulating of miR-142-3p promoted the change in the protein levels of another predicted and confirmed target, the Cofilin2 protein, in a phagocytosis-independent fashion. Downregulation experiments promoted aberrant morphologic phenotypes in macrophages, similar to observed by others in PBMCs of humans with Wiskott Aldrich Syndrome, suggesting the strong involvement of miR-142-3p on the regulation of the actin machinery in macrophages. Altogether these results show for the first time that miRNAs are involved in the regulation of actin-mediated phagocytosis of pathogenic bacteria and that these are direct targets of Mycobacterium tuberculosis.
2013-06-16 | GSE23429 | GEO
Project description:Phagocytosis requires the activation of a plethora of mechanisms that include the activation of the actin cytoskeleton guided by the Arp2/3 complex. These are promoted by activators such as the Wiskott Aldrich Syndrome Protein (WASP) family members. In order to further understand the molecular mechanisms involved in the early events leading the phagocytosis of the pathogenic Mycobacterium tuberculosis, we set out to examine potential roles of miRNAs in phagocytosis using genome-wide expression profiling to identify miRNAs differentially regulated following mycobacterial infection. One of the miRNAs activated upon infection of mouse macrophages with the non-pathogenic Mycobacterium smegmatis, the widely conserved miR-142-3p, was predicted and confirmed to target the Neural-WASP (N-WASP). Upregulating of miR-142-3p in mouse macrophages inversely correlated with levels of N-WASP, upon infection with live pathogenic and non-pathogenic mycobacteria, suggesting an active role of Mycobacterium tuberculosis on the regulation of phagocytosis, at the post-transcriptional level, in host cells. The reduction of N-WASP correlated with a reduced internalization of bacteria per macrophage, independently of the phagocytosis index. Furthermore, the downregulation of WASP levels accompanied those of N-WASP, at early but not at late time points, suggesting a closely regulatory mechanism among both family members, dependent on the time frame of the phagocytosis. Additionally, upregulating of miR-142-3p promoted the change in the protein levels of another predicted and confirmed target, the Cofilin2 protein, in a phagocytosis-independent fashion. Downregulation experiments promoted aberrant morphologic phenotypes in macrophages, similar to observed by others in PBMCs of humans with Wiskott Aldrich Syndrome, suggesting the strong involvement of miR-142-3p on the regulation of the actin machinery in macrophages. Altogether these results show for the first time that miRNAs are involved in the regulation of actin-mediated phagocytosis of pathogenic bacteria and that these are direct targets of Mycobacterium tuberculosis. Expression analysis of mouse macrophage cell line J774A.1 in response to infection with Mycobacterium smegmatis mc2155 EGFP. Three biological replicates each for uninfected and infected samples.
2013-06-16 | E-GEOD-23429 | biostudies-arrayexpress
Project description:We knocked out Wiskott-Aldrich Syndrome protein (WASP) in an iPSC line and derived the cells to differentiate into macrophages. We found deficiency of WASP results in overexpression of splicing factors and irregulaly sized nulcear speckles. We performed DIA-MS based quantative proteome analysis for WASP wild-type and deficient macrophages.
2022-04-21 | PXD033326 | Pride
Project description:Total RNA was extracted from primary T cell lymphoma that spontaneously developed in either NPM-ALK or NPM-ALK/WASP-deficent transgenic mice
2018-11-08 | GSE102889 | GEO
Project description:A striking property of the ancient and obligate mutualism between figs and their pollinating wasps is that fig wasps consistently oviposit in the inner flowers of the fig syconium (gall flowers, which develop into galls that house developing larvae), but typically do not use the outer ring of flowers (seed flowers, which develop into seeds). To better understand differences between gall and seed flowers that might influence oviposition choices, and the unknown mechanisms underlying gall formation, we used a metatranscriptomic approach to analyze eukaryotic gene expression within fig flowers at the time of oviposition choice and early gall development. Consistent with the unbeatable seed hypothesis, which posits that only a portion of fig flowers are physiologically capable of responding to gall induction or supporting larval development, we found significant differences in gene expression assigned to defense and metabolism between gall- and seed flowers in receptive syconia. Transcripts assigned to flavonoids and defense were especially prevalent in receptive gall flowers, and carbohydrate metabolism was significantly up-regulated relative to seed flowers. In turn, high expression of the venom gene icarapin during wasp embryogenesis within galled flowers distinguishes it as a candidate gene for gall initiation. In response to galling, the fig significantly up-regulates the expression of chalcone synthase, which previously has been connected to gall formation in other plants. This study simultaneously evaluates the gene expression profile of both mutualistic partners in a plant-insect mutualism and provides evidence for a stability mechanism in the ancient fig-fig wasp association. We examined two different Ficus flower types at two different time points. Each sample contained a pool of hundreds of individual flowers from multiple sycomia.
2015-03-05 | E-GEOD-55700 | biostudies-arrayexpress
Project description:A striking property of the ancient and obligate mutualism between figs and their pollinating wasps is that fig wasps consistently oviposit in the inner flowers of the fig syconium (gall flowers, which develop into galls that house developing larvae), but typically do not use the outer ring of flowers (seed flowers, which develop into seeds). To better understand differences between gall and seed flowers that might influence oviposition choices, and the unknown mechanisms underlying gall formation, we used a metatranscriptomic approach to analyze eukaryotic gene expression within fig flowers at the time of oviposition choice and early gall development. Consistent with the unbeatable seed hypothesis, which posits that only a portion of fig flowers are physiologically capable of responding to gall induction or supporting larval development, we found significant differences in gene expression assigned to defense and metabolism between gall- and seed flowers in receptive syconia. Transcripts assigned to flavonoids and defense were especially prevalent in receptive gall flowers, and carbohydrate metabolism was significantly up-regulated relative to seed flowers. In turn, high expression of the venom gene icarapin during wasp embryogenesis within galled flowers distinguishes it as a candidate gene for gall initiation. In response to galling, the fig significantly up-regulates the expression of chalcone synthase, which previously has been connected to gall formation in other plants. This study simultaneously evaluates the gene expression profile of both mutualistic partners in a plant-insect mutualism and provides evidence for a stability mechanism in the ancient fig-fig wasp association.
2015-03-05 | GSE55700 | GEO