Hsp90 RNAi in C. elegans
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ABSTRACT:
PROVIDER: PRJNA414444 | ENA |
REPOSITORIES: ENA
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Project description:Hsp90 is a molecular chaperone involved in the regulation and maturation of kinases and transcription factors. In Caenorhabditis elegans, it contributes to the development of fertility, maintenance of muscle structure, the regulation of heat-shock response and dauer state. To understand the consequences of Hsp90-depletion, we studied Hsp90 RNAi-treated nematodes by DNA microarrays and mass spectrometry. We find that upon development of phenotypes the levels of chaperones and Hsp90 cofactors are increased, while specific proteins related to the innate immune response are depleted. In microarrays, we further find many differentially expressed genes related to gonad and larval development. These genes form an expression cluster that is regulated independently from the immune response implying separate pathways of Hsp90-involvement. Using fluorescent reporter strains for the differentially expressed immune response genes skr-5, dod-24 and clec-60 we observe that their activity in intestinal tissues is influenced by Hsp90-depletion. Instead, effects on the development are evident in both gonad arms. After Hsp90-depletion, changes can be observed in early embryos and adults containing fluorescence-tagged versions of SEPA-1, CAV-1 or PUD-1, all of which are downregulated after Hsp90-depletion. Our observations identify molecular events for Hsp90-RNAi induced phenotypes during development and immune responses, which may help to separately investigate independent Hsp90-influenced processes that are relevant during the nematode’s life and development. We used microarrays to detail the global programme of gene expression after RNAi-mediated Hsp90 knock-down.
2017-10-17 | GSE105030 | GEO
Project description:A SWATH-based worflow has been developed for C. elegans proteome profiling, including sample preparation, SWATH spectral library generation and downstream data treatment. The influence of mrps-5 RNAi treatment on C. elegans total proteome were studied.
2019-12-11 | PXD009223 | Pride
Project description:Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in C. elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4. The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1. Together, our results identify additional components of the RNAi inheritance machinery whose sequence conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.
2017-06-20 | GSE92840 | GEO
Project description:The molecular chaperone HSP90 aids the maturation of a diverse but select set of metastable protein clients, many of which are key to a variety of signal transduction pathways. HSP90 function has been best investigated in animal and fungal systems, where inhibition of the chaperone has exceptionally diverse effects, ranging from reversing oncogenic transformation to facilitating the acquisition of drug resistance. Inhibition of HSP90 in the model plant Arabidopsis thaliana uncovers novel morphologies dependent on normally cryptic genetic variation and increases stochastic variation inherent to developmental processes. The biochemical activity of HSP90 is strictly conserved between animals and plants. However, the substrates and pathways dependent on HSP90 in plants are poorly understood. Progress has been impeded by reliance on light-sensitive HSP90 inhibitors due to redundancy in the A. thaliana HSP90 gene family. Here we present phenotypic and genome-wide expression analyses of A. thaliana with constitutively reduced HSP90 levels achieved by RNAi targeting. HSP90 reduction affects a variety of quantitative life-history traits, including flowering time and total seed set, and decreases developmental stability. Further, by quantitative analysis of morphological phenotypes, we demonstrate that HSP90-reduction increases phenotypic diversity in both seedlings and adult plants. Several morphologies are synergistically affected by HSP90 and growth temperature. Genome-wide expression analyses also suggest a central role for HSP90 in the genesis and maintenance of plastic responses. The expression results are substantiated by examination of the response of HSP90-reduced plants to attack by caterpillars of the generalist herbivore Trichoplusia ni. HSP90 reduction potentiates a more robust herbivore defense response. In sum, we propose that HSP90 exerts global effects on the environmental responsiveness of plants to many different stimuli. The comprehensive set of HSP90-reduced lines described here is a vital instrument to further examine the role of HSP90 as a central interface between organism, development, and environment. Experiment Overall Design: Three differerent experiments were performed. One experiment included lines RNAi-A1, RNAi-A3, and Control-2, with two biological replicates and one technical replicate per line. The second included lines RNAi-A2, RNAi-B1, RNAi-C1, Control-1, and Control-3, with three biological replicates per line. The third included the three single-isoform T-DNA insertion lines, along with the Col-0 control, with three biological replicates per line. See Sangster et al. "Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels" for details of construct construction and further experimental rationale.
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2020-04-03 | PXD009256 | Pride
Project description:Comparison of gene expression profiles from C. elegans mutant strain CF1038 treated with L4440 and K02A4.1 RNAi and C. elegans mutant strain TU3311 treated with L4440 and B0412.2 RNAi for 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110840 | GEO
Project description:Gene expression was compared from adult C. elegans after RNAi
2015-08-27 | GSE70692 | GEO
Project description:This project includes 20 samples after immunoprecipitation of C. elegans myosin heavy chain B (MHC B/UNC-54/F11C3.3, UniProt P02566 with a Gly387Arg mutation) in 4 replicates of 4 conditions. Lysates from a myosin-misfolding C. elegans strain (unc-54(e1301) with a Gly387Arg substitution in MHC B) grown on (A) control RNAi, (B) RNAi against nhl-1 (F54G8.4), (C) RNAi against F40A3.6, and (D) RNAi against nhl-1 and F40A3.6 together were used for immunoprecipitation. Samples from groups A, B, C and D were incubated over night at 4°C with 1 µg of a mouse monoclonal hybridoma antibody against MHC B (mAb 5-8 from the Developmental Studies Hybridoma Bank, DSHB), while 4 lysate samples from unc-54(e1301) worms on control RNAi (Z) were incubated WITHOUT antibody addition. The next day, co-immunoprecipitated proteins were collected on magnetic Dynabeads Protein A for 2 h at 4°C, washed, on-bead digested, and subjected to identification by mass spectrometry.
2024-07-16 | PXD045076 | Pride
Project description:The molecular mechanisms for target mRNA degradation in C. elegans undergoing RNA interference (RNAi) are not fully understood. Using a combination of genetic, proteomic and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. The RDE-10/RDE-11 complex acts in parallel of nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a 5-fold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and micro-RNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans.
2012-04-26 | GSE36494 | GEO
Project description:This dataset addresses two phenomena affected by reference strain bias in model organism research, specifically in the nematode C. elegans. I) C. elegans is the leading system for research into RNA interference (RNAi); this research has been conducted exclusively in the reference strain. However, sensitivity to RNAi is remarkably diverse across wild-type strains. Here, we used RNA sequencing to evaluate the transcriptional response of the reference strain and four other strains to RNAi by transcriptionally profiling these strains in three conditions: exogenous RNAi targeting germline-expressed genes 1) par-1 and 2) pos-1, and 3) the control condition. II) Gene expression quantification in non-reference strains relies on successful alignment of DNA reads to the reference genome, but high sequence divergence can lead to mapping failure. Here, we used this RNA-seq dataset to characterize the extent to which poor DNA genome assembly limits expression quantification inferences.
2023-03-23 | GSE190803 | GEO