ArticleGenome research2013
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed, 108 citations in OpenAlex.
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- WDR-5 exhibits H3K4 methylation-independent activity during embryonic development in C. elegans.Epigenetics & chromatin · 2026Article
- Transcriptomic and chromatin accessibility profiling unveils new regulators of heat hormesis in Caenorhabditis elegans.PLoS biology · 2026Article
- Harnessing microbial tools: Escherichia coli as a vehicle for neuropeptide functional analysis in Caenorhabditis elegans.Genetics · 2026Article
- An intrinsically disordered region of Drosha selectively promotes miRNA biogenesis independent of tissue-specific Microprocessor condensates.Genes & development · 2026Article
- A high-throughput, streamlined cloning protocol to generate guide RNAs for CRISPR activation.Frontiers in genome editing · 2026Article
- Chromatin context shapes DNA damage formation and nucleotide excision repair dynamics in Caenorhabditis elegans.Nucleic acids research · 2025Article
- A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
- Parameters that influence bipartite reporter system expression in Caenorhabditis elegans.Genetics · 2025Article
- A transcription coupling model for how enhancers communicate with their target genes.Nature structural & molecular biology · 2025Review
- Cell type-dependent directional transcription at enhancers.NAR genomics and bioinformatics · 2025Article
- Evolutionary changes of noncoding elements associated with transition of sexual mode inScience advances · 2024Article
- A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs.Nucleic acids research · 2024Article
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans.PLoS genetics · 2024Article
- Assembling the RNA therapeutics toolbox.Medical review (2021) · 2024Review
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events inbioRxiv : the preprint server for biology · 2024Article
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- Emerging insights into enhancer biology and function.Transcription · 2023Review
- Transcript accumulation rates in the earlyScience advances · 2023Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. The initial 5' end of most protein-coding transcripts is removed by trans-splicing, and noncoding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is frequent, with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. Our results provide a new resource to investigate transcription regulation in metazoans.
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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.