Project description:NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in C. elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical coregulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa. Synchronized populations of L1 larvae were plated with two sets of HT115 bacteria, one that had been transformed with the RNAi vector only (L4440 plasmid) and another that had been transformed with a vector targeting nhr-23 (clone 5174) [Proc Natl Acad Sci USA 98 (2001) 7360-7365]. Worms were kept on 2% agarose plates for 21 hr at 20C, collected, and approximately 200ml of worms resuspended in PBS were used in each individual experiment. Total RNA was isolated from frozen pellets using a Mixer-Mill (Miller-Mill 300) following an RNeasy Mini Kit (Qiagen, Germantown, MD) according to manufacturer protocol. Aliquots of cultures used for RNA isolation were kept on nhr-23 RNAi plates to confirm the knockdown phenotypic changes occurred during subsequent molts.

2012-08-29 | E-GEOD-32031 | biostudies-arrayexpress

Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]

Project description:Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]

| PRJNA1219661 | ENA

Caenorhabditis elegans

Project description:Expression data from C. elegans wdr-23 mutants

| PRJNA296035 | ENA

Caenorhabditis elegans

Project description:Identification of Transcription Factor NHR-6v2::GFP Binding Regions in L2

| PRJNA141435 | ENA

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

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

Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]

Project description:We performed ChIP-seq to determine chromatin regions bound by transcription factor NHR-23, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms

2025-09-17 | GSE288869 | GEO

Caenorhabditis elegans

Project description:Expression data of wild-type C. elegans shifted from 23 degrees to 17 degrees

| PRJNA140687 | ENA