Analysis of the transcription factor CEH-60 in Caenorhabditis elegans development
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ABSTRACT:
PROVIDER: PRJNA449674 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6983670.fastq.gz | Fastqsanger.gz | |||
| SRR6983680.fastq.gz | Fastqsanger.gz | |||
| SRR6983671.fastq.gz | Fastqsanger.gz | |||
| SRR6983681.fastq.gz | Fastqsanger.gz | |||
| SRR6983672.fastq.gz | Fastqsanger.gz |
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Project description:Animals integrate metabolic, developmental, and environmental information before committing key resources to reproduction. In C. elegans, adult animals reallocate key fat stores from intestinal cells to the germline via lipoproteins to promote reproduction. I identified the evolutionarily conserved homeodomain transcription factor CEH-60/PBX as a potent regulator of lipid homeostasis, longevity, and stress response pathways. To gain a comprehensive view of CEH-60 transcriptional activity, I profiled the transcriptomes of ceh-60 mutants by mRNA-Seq and identified genome-wide CEH-60 binding sites by ChIP-Seq. These approaches revealed that several homeostatic pathways are directly controlled by the CEH-60 transcription factor. CEH-60 functions cooperatively with UNC-62/MEIS in the intestine to directly activate lipoprotein genes while simultaneously repressing genes involved in stress responses, including the innate immune and oxidative stress responses. Thus in wild-type animals, CEH-60 serves as a molecular switch that promotes reproduction (i.e., lipoproteins) while repressing stress response and longevity pathways. This study identifies a new key regulator of fat metabolism, longevity, and stress response pathways during normal C. elegans development.
2019-04-04 | GSE112979 | GEO
Project description:Animals integrate metabolic, developmental, and environmental information before committing key resources to reproduction. In C. elegans, adult animals reallocate key fat stores from intestinal cells to the germline via lipoproteins to promote reproduction. I identified the evolutionarily conserved homeodomain transcription factor CEH-60/PBX as a potent regulator of lipid homeostasis, longevity, and stress response pathways. To gain a comprehensive view of CEH-60 transcriptional activity, I profiled the transcriptomes of ceh-60 mutants by mRNA-Seq and identified genome-wide CEH-60 binding sites by ChIP-Seq. These approaches revealed that several homeostatic pathways are directly controlled by the CEH-60 transcription factor. CEH-60 functions cooperatively with UNC-62/MEIS in the intestine to directly activate lipoprotein genes while simultaneously repressing genes involved in stress responses, including the innate immune and oxidative stress responses. Thus in wild-type animals, CEH-60 serves as a molecular switch that promotes reproduction (i.e., lipoproteins) while repressing stress response and longevity pathways. This study identifies a new key regulator of fat metabolism, longevity, and stress response pathways during normal C. elegans development.
2019-04-04 | GSE112978 | GEO
Project description:The onset of sexual maturity involves dramatic changes in physiology and gene expression in many animals. A textbook example is the production of enormous amounts of yolk proteins destined for the nascent oocytes, termed vitellogenesis. We previously identified the rapidly evolving PBC-class Hox-cofactor CEH-60/PBX as necessary for abundant vit transcription in C. elegans. Differential proteomics data shows that all vitellogenin proteins are indeed drastically downregulated in ceh-60 mutant animals and suggest an additional role for CEH-60’s involvement cuticle structure, innate immunity and stress response.
2019-09-25 | PXD013584 | Pride
Project description:Genome-wide occupancy of the CEH-60 and UNC-62 Transcription Factors in Caenorhabditis elegans
| PRJNA449681 | ENA
Project description:CEH-60 binding profile by comparison of DNA methylation of a C. elegans strain expression ceh-60::dam to a control strain expressing gfp::dam. Sequencing libraries prepared using NEBNext Singleplex oligos for Illumina®. Data analysis performed with GeneDamIDseq (Sharma, Ritler, and Meister 2016).
2020-11-16 | E-MTAB-9539 | biostudies-arrayexpress
Project description:Next Generation Sequencing and Quantitative Analysis of mRNAs in Wild Type and ceh-60 Mutant Caenorhabditis elegans
| PRJNA449675 | ENA
Project description:In Caenorhabditis elegans, let-60 Ras controls many cellular processes, such as differentiation of vulval epithelial cells, function of chemosensory neurons, and meiotic progression in the germ line. Although much is known about the let-60 Ras signaling pathway, relatively little is understood about the target genes induced by let-60 Ras signaling that carry out terminal effector functions leading to morphological change. We have used DNA microarrays to identify 708 genes that change expression in response to activated let-60 Ras. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-07-22 | GSE2974 | GEO
Project description:In Caenorhabditis elegans, let-60 Ras controls many cellular processes, such as differentiation of vulval epithelial cells, function of chemosensory neurons, and meiotic progression in the germ line. Although much is known about the let-60 Ras signaling pathway, relatively little is understood about the target genes induced by let-60 Ras signaling that carry out terminal effector functions leading to morphological change. We have used DNA microarrays to identify 708 genes that change expression in response to activated let-60 Ras. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-07-22 | E-GEOD-2974 | biostudies-arrayexpress
Project description:Downstream targets of let-60 Ras in Caenorhabditis elegans
| PRJNA91919 | ENA
Project description:modENCODE_submission_3068 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: OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) 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 Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ); Developmental Stage: late embryo; Genotype: unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene ceh-26; Strain OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) 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 Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37798 | biostudies-arrayexpress