The complete cell atlas of an aging multicellular organism
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE208154 | GEO | 2022/08/03
REPOSITORIES: GEO
Similar Datasets
Project description:NCoR and SMRT are two paralogous vertebrate proteins that function as corepressors with unliganded nuclear receptors. Although C. elegans has a large number of nuclear receptors, orthologues of the corepressors NCoR and SMRT have not unambiguously been identified in Drosophila or C. elegans. Here, we identify GEI-8 as the closest homologue of NCoR and SMRT in C. elegans and demonstrate that GEI-8 is expressed as at least two isoforms throughout development in multiple tissues, including neurons, muscle and intestinal cells. We demonstrate that a homozygous deletion within the gei-8 coding region, which is predicted to encode a truncated protein lacking the predicted NR domain, results in severe mutant phenotypes with developmental defects, slow movement and growth, arrested gonadogenesis and defects in cholinergic neurotransmission. Whole genome expression analysis by microarrays identified sets of de-regulated genes consistent with both the observed mutant phenotypes and a role of GEI-8 in regulating transcription. Interestingly, the upregulated transcripts included a predicted mitochondrial sulfide:quinine reductase encoded by Y9C9A.16. This locus also contains non-coding, 21-U RNAs of the piRNA. Inhibition of the expression of the region coding for 21-U RNAs leads to irregular gonadogenesis in the homozygous gei-8 mutants, but not in an otherwise wild-type background, suggesting that GEI-8 may function in concert with the 21-U RNAs to regulate gonadogenesis. Our results confirm that GEI-8 is the orthologue of the vertebrate NCoR/SMRT corepressors and demonstrate important roles for this putative transcriptional corepressor in development and neuronal function.
2013-08-11 | GSE40127 | GEO
Project description:NCoR and SMRT are two paralogous vertebrate proteins that function as corepressors with unliganded nuclear receptors. Although C. elegans has a large number of nuclear receptors, orthologues of the corepressors NCoR and SMRT have not unambiguously been identified in Drosophila or C. elegans. Here, we identify GEI-8 as the closest homologue of NCoR and SMRT in C. elegans and demonstrate that GEI-8 is expressed as at least two isoforms throughout development in multiple tissues, including neurons, muscle and intestinal cells. We demonstrate that a homozygous deletion within the gei-8 coding region, which is predicted to encode a truncated protein lacking the predicted NR domain, results in severe mutant phenotypes with developmental defects, slow movement and growth, arrested gonadogenesis and defects in cholinergic neurotransmission. Whole genome expression analysis by microarrays identified sets of de-regulated genes consistent with both the observed mutant phenotypes and a role of GEI-8 in regulating transcription. Interestingly, the upregulated transcripts included a predicted mitochondrial sulfide:quinine reductase encoded by Y9C9A.16. This locus also contains non-coding, 21-U RNAs of the piRNA. Inhibition of the expression of the region coding for 21-U RNAs leads to irregular gonadogenesis in the homozygous gei-8 mutants, but not in an otherwise wild-type background, suggesting that GEI-8 may function in concert with the 21-U RNAs to regulate gonadogenesis. Our results confirm that GEI-8 is the orthologue of the vertebrate NCoR/SMRT corepressors and demonstrate important roles for this putative transcriptional corepressor in development and neuronal function. Comparison of Mutant vs. WT control with three replications per treatment group
2013-08-11 | E-GEOD-40127 | biostudies-arrayexpress
Project description:We combined in vivo expressed GFP-tagged MEG-3 (GEI-12) with label-free quantitative proteomics to identify protein-protein interactions of MEG-3 in early C. elegans embryos.
2021-07-01 | PXD012852 | Pride
Project description:During Caenorhabditis elegans oocyte meiosis, a multi-protein complex localised between homologous chromosomes, the ring complex (RC), promotes chromosome congression through the action of the chromokinesin KLP-19. While some RC components are known, the mechanism of RC assembly has remained obscure. A germline-specific screen identified KLP-19 as a SUMO substrate in vivo and we found that the SUMO E3 ligase GEI-17/PIAS is required for KLP-19 recruitment to the RC. Additionally, KLP-19 is efficiently sumoylated in vitro in a GEI-17-dependent manner. Further biochemical analysis showed that KLP-19 and GEI-17 are efficiently modified by SUMO and that GEI-17 and another RC component, the kinase BUB-1, can interact non-covalently with SUMO. While SUMO conjugation is required for RC assembly, we also provide evidence consistent with non-covalent SUMO interactions contributing to RC assembly in vivo. Our results highlight the importance of sumoylation and non-covalent SUMO interaction in regulating dynamic protein complex assembly during oocyte meiosis.
2020-10-15 | PXD005202 | Pride
Project description:Aging promotes lung function decline and susceptibility to chronic lung diseases, which are the third leading cause of death worldwide. We used single cell transcriptomics and mass spectrometry to quantify changes in cellular activity states of 30 cell types and the tissue proteome from lungs of young and old mice. Aging led to increased transcriptional noise, indicating deregulated epigenetic control. We observed highly distinct effects of aging on cell type level, uncovering increased cholesterol biosynthesis in type-2 pneumocytes and lipofibroblasts as a novel hallmark of lung aging. Proteomic profiling revealed extracellular matrix remodeling in old mice, including increased collagen IV and XVI and decreased Fraser syndrome complex proteins and Collagen XIV. Computational integration of the aging proteome and single cell transcriptomes predicted the cellular source of regulated proteins and created a first unbiased reference of the aging lung. The lung aging atlas can be accessed via an interactive user-friendly webtool at: https://theislab.github.io/LungAgingAtlas
2019-01-21 | PXD012307 | Pride
Project description:modENCODE_submission_2451 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] official name : OP179 ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene gei-11; Strain OP179(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] official name : OP179 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25795 | biostudies-arrayexpress
Project description:modENCODE_submission_3066 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2012-01-31 | E-GEOD-35276 | biostudies-arrayexpress
Project description:modENCODE_submission_3149 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37809 | biostudies-arrayexpress
Project description:modENCODE_submission_3373 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48702 | biostudies-arrayexpress
Project description:modENCODE_submission_4037 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: embryo; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48744 | biostudies-arrayexpress