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Transcriptome analysis of hpl-2(tm1489) vs wild-type worms at mixed embryonic and third larval stages

ABSTRACT: Epigenetic factors guide cell fate decisions and can stabilize development by buffering environmental variation. HP1 proteins have a well-characterized role in heterochromatin packaging and gene regulation, while their function in organismal development is less well understood. Here we used genome-wide expression profiling to assess novel functions of the C. elegans HP1 homologue HPL-2 at specific developmental stages

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE33700 | GEO | 2011/11/30

SECONDARY ACCESSION(S): PRJNA148283

REPOSITORIES: GEO

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Transcriptome analysis of hpl-2(tm1489) vs wild-type worms at mixed embryonic and third larval stages

Project description:Epigenetic factors guide cell fate decisions and can stabilize development by buffering environmental variation. HP1 proteins have a well-characterized role in heterochromatin packaging and gene regulation, while their function in organismal development is less well understood. Here we used genome-wide expression profiling to assess novel functions of the C. elegans HP1 homologue HPL-2 at specific developmental stages RNA was extracted from either mixed-stage embryos or from third larval stage worms for both wild-type N2 (Bristol) and hpl-2(tm1489) strains.

2011-11-30 | E-GEOD-33700 | biostudies-arrayexpress

HPL-2 in PFR40 (hpl-2) early embryo

Project description:ChIP-chip of HPL-2 in hpl-2 C. elegans early embryo

2014-10-11 | GSE58763 | GEO

The C. elegans ortholog of TDP-43 regulates the chromatin localization of the heterochromatin protein 1 homolog, HPL-2

Project description:TDP-1 is the C. elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced transcriptional gene silencing leading to increased sensitivity to heritable RNA interference (RNAi). As heritable RNAi in C. elegans depends on chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We find that TDP-1 and HPL-2 interact directly, and loss of TDP-1 dramatically alters the chromatin association of HPL-2. We have shown previously that deletion of the tdp-1 gene results in transcriptional alterations and the accumulation of double-stranded (ds) RNA. These molecular changes are replicated in an hpl-2 deletion strain, consistent with HPL-2 acting downstream of TDP-1 to modulate these aspects of RNA metabolism. Our observations identify novel mechanisms by which HP1 homologs can be recruited to chromatin, and by which nuclear depletion of human TDP-43 could lead to disease-relevant changes in RNA metabolism.

2018-05-17 | GSE100829 | GEO

HPL-2 in PFR40 (hpl-2) early embryo

Project description:ChIP-chip of HPL-2 in hpl-2 C. elegans early embryo EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: PFR40; Developmental Stage: Early Embryo; Genotype: hpl-2(tm1489); Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 1; EXPERIMENTAL FACTORS: temperature 20

2014-10-11 | E-GEOD-58763 | biostudies-arrayexpress

Paenibacillus terrae HPL-003

Project description:Paenibacillus terrae HPL-003 Genome sequencing

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Tissue-specific chromatin binding patterns of C. elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression.

Project description:Tissue-specific chromatin binding patterns of C. elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression.

2023-01-09 | GSE222056 | GEO

HPL-2 in N2 (wild-type) early embryo

Project description:ChIP-chip of HPL-2 in N2 C. elegans early embryo

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HPL-2 in GW638 (met-2 set-25) MxEmb

Project description:ChIP-chip of HPL-2 in met-2 set-25 C. elegans mixed-stage embryo

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Expression profiling in PFR40 (hpl-2) mutant early embryo

Project description:Identification of genes significantly misregulated in hpl-2 mutant early embryo compared to wild-type early embryo

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Identification of Transcription Factor HPL-2::GFP Binding Regions in L1

Project description:modENCODE_submission_3604 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: YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene hpl-2; Strain YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius

2013-02-04 | E-GEOD-44017 | biostudies-arrayexpress

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