ArticleGenome research2013
The transcription start site landscape of C. elegans.
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 40 papers.
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Who cites it
40 citing papers in PubMed.
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- A high-throughput, streamlined cloning protocol to generate guide RNAs for CRISPR activation.Frontiers in genome editing · 2026Article
- 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 GATA factor radiation inbioRxiv : the preprint server for biology · 2025Article
- Binding profiles for 961Genome research · 2024Article
- The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction.GeroScience · 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
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events inbioRxiv : the preprint server for biology · 2024Article
- Pre-piRNA trimming safeguards piRNAs against erroneous targeting by RNA-dependent RNA polymerase.Cell reports · 2024Article
- Binding profiles for 954 Drosophila andbioRxiv : the preprint server for biology · 2024Article
- Transcript accumulation rates in the earlyScience advances · 2023Article
- LAFITE Reveals the Complexity of Transcript Isoforms in Subcellular Fractions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- A somatic proteoglycan controls Notch-directed germ cell fate.Nature communications · 2021Article
- Article
- Distinctive regulatory architectures of germline-active and somatic genes inGenome research · 2020Article
- Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons.PLoS neglected tropical diseases · 2020Article
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.
Funding
Abstract
More than half of Caenorhabditis elegans pre-mRNAs lose their original 5' ends in a process termed "trans-splicing" in which the RNA extending from the transcription start site (TSS) to the site of trans-splicing of the primary transcript, termed the "outron," is replaced with a 22-nt spliced leader. This complicates the mapping of TSSs, leading to a lack of available TSS mapping data for these genes. We used growth at low temperature and nuclear isolation to enrich for transcripts still containing outrons, applying a modified SAGE capture procedure and high-throughput sequencing to characterize 5' termini in this transcript population. We report from this data both a landscape of 5'-end utilization for C. elegans and a representative collection of TSSs for 7351 trans-spliced genes. TSS distributions for individual genes were often dispersed, with a greater average number of TSSs for trans-spliced genes, suggesting that trans-splicing may remove selective pressure for a single TSS. Upstream of newly defined TSSs, we observed well-known motifs (including TATAA-box and SP1) as well as novel motifs. Several of these motifs showed association with tissue-specific expression and/or conservation among six worm species. Comparing TSS features between trans-spliced and non-trans-spliced genes, we found stronger signals among outron TSSs for preferentially positioning of flanking nucleosomes and for downstream Pol II enrichment. Our data provide an enabling resource for both experimental and theoretical analysis of gene structure and function in C. elegans.
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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.