ArticlePLoS genetics2007
Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 103 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
103 citing papers in PubMed, 159 citations in OpenAlex.
- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
- Autoregulation of three yeast ribosomal protein genes by splicing inhibition.G3 (Bethesda, Md.) · 2026Article
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- An ultraconserved pseudo 5' splice site fine-tunes development by regulating alternative splicing within TOR-related pathways.Nature communications · 2026Article
- A homozygous synonymous variant in SMG5, encoding a nonsense-mediated mRNA decay factor, causes developmental delay with growth retardation and relative macrocephaly.Human genetics · 2026Article
- Splicing regulation and intron evolution in the short-intron ciliate model of endosymbiosis Paramecium bursaria.Nucleic acids research · 2026Article
- Ancestral intronic splicing regulatory elements in the SCNbioRxiv : the preprint server for biology · 2026Article
- Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4.Nature structural & molecular biology · 2025Article
- Interactions Between Monocarboxylate TransporterGenes · 2025Article
- Autoregulation of RPL7B by inhibition of a structural splicing enhancer.Nucleic acids research · 2025Article
- Single Antisense Oligonucleotides Correct Diverse Splicing Mutations in Hotspot Exons.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing.Molecular cell · 2024Article
- Development and validation of AI/ML derived splice-switching oligonucleotides.Molecular systems biology · 2024Article
- Article
- Hypoplastic Left Heart Syndrome: Signaling & Molecular Perspectives, and the Road Ahead.International journal of molecular sciences · 2023Review
- MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.Briefings in bioinformatics · 2023Article
- Minor Intron Splicing from Basic Science to Disease.International journal of molecular sciences · 2021Review
- Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies.PLoS genetics · 2020Article
- Next-generation sequencing and recombinant expression characterized aberrant splicing mechanisms and provided correction strategies in factor VII deficiency.Haematologica · 2020Article
- Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms.The pharmacogenomics journal · 2019Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issuedNostrand, Eric L Van [corrected to Van Nostrand, Eric L]
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our approach yielded 314 ISREs, and insertions of ~70 ISREs between competing splice sites demonstrated that 84% of ISREs altered 5' and 94% altered 3' splice site choice in human cells. Consistent with our experiments, comparisons of ISREs to known splicing regulatory elements revealed that 40%-45% of ISREs might have dual roles as exonic splicing silencers. Supporting a role for ISREs in alternative splicing, we found that 30%-50% of ISREs were enriched near alternatively spliced (AS) exons, and included almost all known binding sites of tissue-specific alternative splicing factors. Further, we observed that genes harboring ISRE-proximal exons have biases for tissue expression and molecular functions that are ISRE-specific. Finally, we discovered that for Nova1, neuronal PTB, hnRNP C, and FOX1, the most frequently occurring ISRE proximal to an alternative conserved exon in the splicing factor strongly resembled its own known RNA binding site, suggesting a novel application of ISRE density and the propensity for splicing factors to auto-regulate to associate RNA binding sites to splicing factors. Our results demonstrate that ISREs are crucial building blocks in understanding general and tissue-specific AS regulation and the biological pathways and functions regulated by these AS events.
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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.