ArticleGenome research2015
Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- Quantitative RNA-seq meta-analysis of alternative exon usage inGenome research · 2017Pooled it
- Genome-wide modulation of alternative splicing by a predicted alpha helix in U2AF2.Nucleic acids research · 2025Article
- Alternative splicing ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs.Nucleic acids research · 2024Article
- Alternative splicing ofbioRxiv : the preprint server for biology · 2024Article
- Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.RNA (New York, N.Y.) · 2024Article
- Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice.Genomics, proteomics & bioinformatics · 2023Article
- A forward genetic screen in C. elegans identifies conserved residues of spliceosomal proteins PRP8 and SNRNP200/BRR2 with a role in maintaining 5' splice site identity.Nucleic acids research · 2022Article
- A genetic screen in C. elegans reveals roles for KIN17 and PRCC in maintaining 5' splice site identity.PLoS genetics · 2022Article
- An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.PLoS computational biology · 2021Article
- Global regulatory features of alternative splicing across tissues and within the nervous system ofGenome research · 2020Article
- Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition inGenetics · 2020Article
- mRNA Editing, Processing and Quality Control inGenetics · 2020Review
- Direct full-length RNA sequencing reveals unexpected transcriptome complexity duringGenome research · 2020Article
- On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes.Genome biology and evolution · 2019Article
- CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing.PLoS genetics · 2019Article
- Prp8 impacts cryptic but not alternative splicing frequency.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- SNRP-27, theRNA (New York, N.Y.) · 2018Article
- N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Reveals an Intronic Residue Critical for Caenorhabditis elegans 3' Splice Site Function in Vivo.G3 (Bethesda, Md.) · 2016Article
- Systematic transcriptome analysis associated with physiological and chronological aging inGenome researchArticle
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Adjacent alternative 3' splice sites, those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron's 3' end depends upon sequence elements that define the branchpoint, polypyrimidine tract, and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched Caenorhabditis elegans samples, we identify hundreds of introns with adjacent alternative 3' splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is monodirectional, with somatic cells preferring to splice at the distal 3' splice site (furthest from the 5' end of the intron) and germline cells showing a distinct shift toward usage of the adjacent proximal 3' splice site (closer to the 5' end of the intron). Splicing patterns in somatic cells follow C. elegans consensus rules of 3' splice site definition; a short stretch of pyrimidines preceding an AG dinucleotide. Splicing in germline cells occurs at proximal 3' splice sites that lack a preceding polypyrimidine tract, and in three instances the germline-specific site lacks the AG dinucleotide. We provide evidence that use of germline-specific proximal 3' splice sites is conserved across Caenorhabditis species. We propose that there are differences between germline and somatic cells in the way that the basal splicing machinery functions to determine the intron terminus.
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