ArticleGenome research2011
A spatial and temporal map of C. elegans gene expression.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers.
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Who cites it
189 citing papers in PubMed.
- Repeated mutation of a GT92 glycosyltransferase gene confers antiviral resistance in two Caenorhabditis species.Molecular biology and evolution · 2026Article
- Multilevel transcriptional regulation of embryonic sex determination and dosage compensation by the X-signal element sex-1.Genetics · 2026Article
- Lysosome-related organelles employ divergent mechanisms to modulate cytosolic zinc homeostasis.PLoS genetics · 2026Article
- Repeated mutation of a GT92 glycosyltransferase gene confers antiviral resistance in twobioRxiv : the preprint server for biology · 2026Article
- Whole-organism spatial transcriptomics at single-cell resolution inbioRxiv : the preprint server for biology · 2026Article
- Integrating MACSPI and SILAC for Neuron Type-specific Proteomics in Caenorhabditis elegans.Molecular & cellular proteomics : MCP · 2026Article
- Single-nucleus neuronal transcriptional profiling of male C. elegans uncovers regulators of sex-specific and sex-shared behaviors.Cell reports · 2025Article
- Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.Nature communications · 2025Article
- Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Article
- GExplore 1.5: a comprehensive Caenorhabditis elegans database for the analysis of gene function with a new user-friendly web interface.Database : the journal of biological databases and curation · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- Multi-level transcriptional regulation of embryonic sex determination and dosage compensation by the X-signal elementbioRxiv : the preprint server for biology · 2024Article
- Functional Optimization in Distinct Tissues and Conditions Constrains the Rate of Protein Evolution.Molecular biology and evolution · 2024Article
- XOL-1 regulates developmental timing by modulating the H3K9 landscape in C. elegans early embryos.PLoS genetics · 2024Article
- Mutations in nucleotide metabolism genes bypass proteasome defects in png-1/NGLY1-deficient Caenorhabditis elegans.PLoS biology · 2024Article
- Transcriptomic Analysis of the Spatiotemporal Axis of Oogenesis and Fertilization inbioRxiv : the preprint server for biology · 2024Article
- Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans.Nature communications · 2024Article
- The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerantmSystems · 2024Article
- The effect of developmental variation on expression QTLs in a multi parental Caenorhabditis elegans population.G3 (Bethesda, Md.) · 2024Article
129 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning-based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor- and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.