Whole-organism C. elegans L2 GRH-1 ChIP-seq (experiment 1 of 2)
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE213508 | GEO | 2022/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms.
2022-12-31 | GSE213509 | GEO
Project description:We report identification of possible GRH-1 target genes in C. elegans, by analyzing changes in overall transcriptome following stable overexpression of this transcription factor.
2021-10-24 | GSE159077 | GEO
Project description:The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a major insect pest of cultivated rice in temperate Asia. GRH2-near-isogenic line (NIL) TGRH11, GRH4-NIL (TGRH16) and GRH2/GRH4-pyramided line (PYL) TGRH29 were developed by introducing the GRH2 and GRH4 from indica rice (DV85). We identified GRH-inducible genes in respective rice lines. Furthermore, we compared the gene expression levels between NILs/PYL and control plants (T65). The gene expression changes in respective rice lines were detected by comparison between GRH-infested and pre-infested plants. Seedlings at the second-leaf stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and shoots were collected at 30 h after GRH infestation. Detached-leaf blades at heading stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and samples were collected at 30 h after GRH infestation. For each treatment, two biological replicates were performed.
2016-04-02 | E-GEOD-46409 | biostudies-arrayexpress
Project description:Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. We show that deletion or ectopic expression of Grh causes loss or gain of DNA accessibility, respectively. However, while Grh binding is necessary for enhancer accessibility, it is insufficient to activate enhancers. Finally, we show that human Grh homologs, GRHL1/2/3, function similarly. We conclude that Grh binding is necessary and sufficient for the opening of epithelial enhancers, but not for their activation. Our data support the model that complex spatiotemporal expression patterns are controlled by regulatory hierarchies in which pioneer factors, such as Grh, establish tissue-specific accessible chromatin landscapes upon which other factors can act.
2018-06-04 | GSE108019 | GEO
Project description:The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a major insect pest of cultivated rice in temperate Asia. GRH2-near-isogenic line (NIL) TGRH11, GRH4-NIL (TGRH16) and GRH2/GRH4-pyramided line (PYL) TGRH29 were developed by introducing the GRH2 and GRH4 from indica rice (DV85). We identified GRH-inducible genes in respective rice lines. Furthermore, we compared the gene expression levels between NILs/PYL and control plants (T65).
2016-04-02 | GSE46409 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-31 | GSE213510 | GEO
Project description:Genome-wide expression analysis of C. elegans nematodes overexpressing the transcription factor grh-1
| PRJNA667640 | ENA
Project description:It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.
2017-02-02 | GSE83305 | GEO
Project description:Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the Latent Dirichlet Allocation algorithm, our chromatin accessibility data provide new insights into which genomic loci may be participating in cell type-specific gene regulation, with promise for better understanding of cellular differentiation and gene regulation in the worm.
2021-04-12 | GSE157017 | GEO
Project description:The nematode Caenorhabditis elegans (C. elegans) is often used as a model organism to study cell and developmental biology. Quantitative mass spectrometry has only recently been performed in C. elegans and, so far, most studies have been done on adult worm samples. Here we use quantitative mass spectrometry to characterise protein level changes across the four larval developmental stages (L1-L4) of C. elegans, in biological triplicate. In total, we identify 4,130 proteins and quantify 1,541 proteins that were identified across all four stages in all three biological repeats with at least 2 unique peptides per protein. Using hierarchical clustering and functional ontological analyses, we identify 21 protein groups containing proteins with similar protein profiles across the four stages, and highlight the most overrepresented biological functions in each of these protein clusters. In addition, we use the dataset to identify putative larval stage specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides a system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the worm development research community.
2017-12-04 | PXD006676 | Pride