HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Andreas Rechtsteiner
PROVIDER: E-GEOD-85445 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the location of RNA Pol II in sig-7(RNAi) embryos to the localization in L4440/RNAi control embryos to examine the global effect of loss of sig-7 on RNA Pol II regulation and its distribution within gene bodies anti-AMA-1 ChIP in 2 replicates each of sig-7(RNAi) and RNAi control early stage embryos
2016-08-10 | E-GEOD-85441 | biostudies-arrayexpress
Project description:RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the transcript levels in sig-7(RNAi) embryos to those of L4440/RNAi control embryos to examine the global transcriptional effect caused by of loss of sig-7 function Examination of RNA levels using RNAseq in 2 replicate samples each of early embryos from sig-7(RNAi) and RNAi controls
2016-08-10 | E-GEOD-85442 | biostudies-arrayexpress
Project description:Ecosystems are chronically exposed to ionizing radiations. But environmental risk assessment of chronic exposure suffers from a lack of knowledge. Extrapolation of data from acute to chronic exposure is not always relevant, and can lead to uncertainties. In fact, effects could be different between the two irradiation modes, especially regarding reproduction endpoint, which is an ecologically relevant parameter . The free living nematode Caenorhabditis elegans is a particularly appropriate model organism to address this proteomic issues. With its fully sequenced genome and its short life cycle, C. elegans has been successfully used to study acute and chronic irradiation effects and their consequences on germline development and hatching. Results showed that a decrease of the number of progeny associated with a decrease of hatching success occurred from and above 30 Gy of acute irradiation.. In the present study, we decided to refine the understanding of molecular mechanisms of acute and chronic irradiation by a global proteome analysis. To do so, C. elegans were exposed to 3 common cumulated doses between acute and chronic exposure. These 3 doses, lower than the doses for which an effect on the reproduction was shown, were susceptible to allow us to find early and sensitive biomarkers of a reproduction decline. After exposure, global modification of the proteome expression was studied using a label free LC-MS/MS proteomic approach. Our objectives were to test the following hypotheses: (1) whether or not proteome expression varied with the dose, and with the irradiation mode; (2) if proteome expression modification was associated with effects on reproduction, with potential direct implications for ecological risk assessment.
2020-10-15 | PXD011731 | Pride
Project description:In animals with germ plasm, specification of the germline involves “germ granules”, cytoplasmic condensates that enrich maternal transcripts in the germline founder cells. In C. elegans embryos, P granules enrich maternal transcripts, but surprisingly P granules are not essential for germ cell fate specification. Here we have described a second condensate in the C. elegans germ plasm. Like canonical P-bodies found in somatic cells, “germline P-bodies” contain regulators of mRNA decapping and deadenylation and, in addition, the intrinsically-disordered proteins MEG-1 and MEG-2 and the TIS11-family RNA-binding protein POS-1. Embryos lacking meg-1 and meg-2 do not stabilize P-body components, miss-regulate POS-1 targets, miss-specify the germline founder cell, and do not develop a germline. Our findings suggest that specification of the germ line involves at least two distinct condensates that independently enrich and regulate maternal mRNAs in the germline founder cells.
2022-10-05 | PXD036610 | Pride
Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.
2015-11-02 | PXD002525 | Pride
Project description:Higher order structure of interphase chromosomes and their spatial organization within the nucleus can have profound effects on regulation of gene expression. We show how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina can affect gene expression during C. elegans dosage compensation. In this organism, the dosage compensation complex (DCC) binds both X chromosomes of hermaphrodites to repress gene expression two-fold, thus balancing gene expression between XX hermaphrodites and XO males. X chromosome structure is disrupted by mutations in DCC subunits. We found that X chromosome structure and subnuclear localization are also disrupted when the mechanisms that anchor heterochromatin to the nuclear lamina are defective. Strikingly, the heterochromatic left end of the X chromosome is less affected than the gene-rich middle region which lacks heterochromatic anchors. Our results suggest a model in which tethers at the left of the chromosome nucleate formation of a compact structure, which, by the action of the DCC, is propagated to the rest of the chromosome. These changes in X chromosome structure and subnuclear localization are accompanied by small, but significant levels of derepression of X-linked genes, without any observable defects in DCC localization and DCC-mediated changes in histone modification. RNA-seq profiles of C. elegans L1 wild type hermaphrodites, cec-4, met-2 set-25, and DPY-27 RNAi. RNA-seq profiles or C. elegans. Strains are N2 Bristol strain (wild type), RB2301 cec-4(ok3124) IV, and EKM99 met-2(n4256) set-25(n5021) III. Biological replicates for each strain/stage listed separately.
2016-03-25 | E-GEOD-79597 | biostudies-arrayexpress
Project description:The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.* Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs. Male and female RNA seq data was then generated and used to determine sex-biased expression. For both DNA and RNA experiments, 50bp paired-end (DNA) or single-end (RNA) reads were generated on the Illumina HiSeq 2500. Sequencing lanes were multiplexed. Genomic DNA was isolated from 50-100 hand-picked young adult worms. At least two replicates for each sex were prepared. DNA was sheared via sonication and 350-500 bp sequencing libraries were prepared following the Illumina protocol. Total RNA was isolated from at least 1000 hand-picked L4/young adult worms (*C. **elegans, *N2) or J4/young adult worms (*P. pacificus, *PS312*). *PolyA beads were used to enrich for mRNA. Stranded RNAseq libraries were prepared via incorporation of dUTPs during cDNA synthesis, following the protocol detailed in Parkhomchuk et al, 2009. DNAseq and RNAseq reads were aligned to the appropriate WS228 reference genomes. DNA sequencing data (2-3 replicates) from male and female YA worms are included along with RNAseq data from C.elegans YA hermaphrodites and P.pacificus YA males and hermaphrodites.
2014-04-17 | E-GEOD-53144 | biostudies-arrayexpress
Project description:In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. Here, we analyzed dosage compensation of the X chromosome between sexes, and the roles of dpy-27 (condensin subunit), dpy-21 (non-condensin DCC member), set-1 (H4K20 monomethylase) and set-4 (H4K20 di-/tri-methylase) in X chromosome repression using mRNA-seq and ChIP-seq analyses across several developmental time points. We found that the DCC starts repressing the X chromosomes by the 40-cell stage, but X-linked transcript levels remain significantly higher in hermaphrodites compared to males through the comma stage of embryogenesis. Dpy-27 and dpy-21 are required for X chromosome repression throughout development, but particularly in early embryos dpy-27 and dpy-21 mutations produced distinct expression changes, suggesting a DCC independent role for dpy-21. We previously hypothesized that the DCC increases H4K20me1 by reducing set-4 activity on the X chromosomes. Accordingly, in the set-4 mutant, H4K20me1 increased more from the autosomes compared to the X, equalizing H4K20me1 level between X and autosomes. H4K20me1 increase on the autosomes led to a slight repression, resulting in a relative effect of X derepression. H4K20me1 depletion in the set-1 mutant showed greater X derepression compared to equalization of H4K20me1 levels between X and autosomes in the set-4 mutant, indicating that H4K20me1 level is important, but X to autosomal balance of H4K20me1 contributes only slightly to X-repression. Thus H4K20me1 by itself is not a downstream effector of the DCC. In summary, X chromosome dosage compensation starts in early embryos as the DCC localizes to the X, and is strengthened in later embryogenesis by H4K20me1. RNA-Seq profiles of C. elegans wild type hermaphrodite, mixed sex, at 5 time points and dpy-27, set-4, dpy-21, set-1 and RNAi at 2-3 time points with 3-4 replicates each. RNA-Seq profiles of C. elegans. Strains are N2 (wild type), BS553 fog-2(oz40) V, CB428 dpy-21(e428) V, MK4 dpy-27(y56) III, MT14911 set-4 (n4600) II, SS1075 set-1(tm1821)/hT2g[bli-4(e937) let-?(q782) qIs48] (I;III). Set-1 collections made as heterozygotes and dpy-27(y56) homozygotes. Spike in RNA-seq libraries have AF16 wild type C. briggsae L1s added at a 1:10 ratio. Timepoints are early embryos (synchronized collection, <40 cells), comma embryos (synchronized early embryos aged for 4 hours), mixed embryos (mixed stage embryos from unsynchronized population), L1 (synchronized L1 larvae), L3 (synchronized L3 larvae), and YA (synchronized young adults, collected before embryos present in hermaphrodite gonad). Biological replicates for each strain/stage listed separately. ChIP-seq profiles of C. elegans DCC subunit dpy-27, H4K20me1 histone modification and RNA pol II large subunit ama-1 in 3-6 replicates from mixed stage (unsynchronized) embryos and synchronized L3 larvae. Corresponding inputs are labelled with "Input_" plus ChIP name.
2015-11-09 | E-GEOD-67650 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE28561: Genome-wide maps of HLH-1 binding in muscle-enriched embryos. GSE28562: Genome-wide RNA expression in muscle-enriched embryos across different mutations. Refer to individual Series
2012-06-21 | E-GEOD-28563 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-08-15 | E-GEOD-50488 | biostudies-arrayexpress