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ABSTRACT:
PROVIDER: PRJNA641212 | ENA |
REPOSITORIES: ENA
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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
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: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:Population genomics of fig wasp (Agaonidae) using genome-wide sequence data
| PRJDB5116 | ENA
Project description:To elucidate the transcriptional and epigenetic alterations underlying the neurogenic defects of FA-NSCs, we conducted gene expression microarray analysis and global DNA methylation profiling. The gene expression pattern of gene-corrected NSCs (C-FA-NSCs) resembled that of control-NSCs but clustered distantly from FA-NSCs (Fig. 6F and Table S1). Hierarchical clustering based on DNA methylation levels in the promoter region (+/-1.5kb from TSS) of genes whose expression levels were rescued in C-FA-NSCs, placed C-FA-NSCs closer to control-NSCs and away from FA-NSCs (Fig. 6G), although this pattern was not seen at the whole genome level (Fig. S4C). This suggests that FANCA gene correction leads to specific methylation changes in a subset of promoters. Examination of the methylomes of NSCs derived from Fanconi Anemia iPSCs before and after gene correction by targeted bisulfite sequencing with padlock probes
2014-05-15 | E-GEOD-57685 | biostudies-arrayexpress
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:Wiskott-Aldrich syndrome (WAS) is characterized by X-linked thrombocytopenia, eczema, immunodeficiency, recurrent infections and increased risk of autoimmunity and malignancies. WAS is caused by mutations in the WAS gene, which encodes the exclusively hematopoietic WAS protein (WASp) that is classically characterized as aν actin nucleator. However, disruption of F-actin polymerization by WAS mutations can not account for many aspects of WAS pathogenesis. Ignorance of other functions of WASP precludes in-depth understanding of the pathogenic effects of mutant WASP, and therefore hampers development of effective therapy. Here we generated induced pluripotent stem cells (iPSCs) from WAS patients (WAS-iPSC) bearing different mutations and corresponding isogenic iPSCs in which the pathogenic mutations had been corrected by targeted genome editing. Hematopoietic cells differentiated from WAS-iPSCs not only recapitulated known disease phenotypes, but also revealed novel defects of WASP deficient cells. WASP co-localized with nuclear pores, nucleoli, nuclear speckles and PML bodies by immunocytochemistry and/or serial block face scanning microscopy (SBF-SEM). MudPIT (multi-dimensional protein identification technology) analysis revealed that WASP physically interacted with nuclear body components, nuclear structural proteins, chromatin modifying complexes, and many RNA-binding proteins including major components of the spliceosome. Next-generation sequencing captured a dramatic global change of alternative splicing in WAS patient cells. WAS mutation impacted splicing of multiple genes frequently mutated in myelodysplastic syndrome and other cancers. RNA sequencing showed that WAS-iPSC derived immune cells misregulated many cell cycle regulators, tumor suppressors, immune function genes and splicing factors, and activated gene networks that drive cancer development and inflammatory diseases. Together these data uncovered previously unappreciated functions of the WASP and provided a mechanistic understanding of the pathogenesis of malignancy and autoimmunity in the most severe form of WAS. These new knowledge could help develop targeted therapy for WAS in the future. Human WAS-iPSCs (p.Phe35*) and gene corrected WAS-iPSCs (cWAS-iPSC) were differentiated into macrophages. WAS patient derived B-lymphocyte line ID00003 (p.Glu133Lys) and a wile-type B-lymphocyte line GM11518 were cultured using standard protocol. Total RNAs were extracted and been analyzed by RASL-seq.
2016-03-31 | E-GEOD-77253 | biostudies-arrayexpress