ArticleProceedings of the National Academy of Sciences of the United States of America2008
RNA landscape of evolution for optimal exon and intron discrimination.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 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
61 citing papers in PubMed, 107 citations in OpenAlex.
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- Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell genomics · 2024Article
- CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.Nature communications · 2024Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Deep screening of proximal and distal splicing-regulatory elements in a native sequence context.bioRxiv : the preprint server for biology · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture.Microorganisms · 2022Article
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- Genetically programmed alternative splicing of NEMO mediates an autoinflammatory disease phenotype.The Journal of clinical investigation · 2022Article
- Spliceator: multi-species splice site prediction using convolutional neural networks.BMC bioinformatics · 2021Article
- F5-Atlanta: A novel mutation in F5 associated with enhanced East Texas splicing and FV-short production.Journal of thrombosis and haemostasis : JTH · 2021Article
- Article
- Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition.International journal of molecular sciences · 2020Article
- Delivery of oligonucleotides to bone marrow to modulate ferrochelatase splicing in a mouse model of erythropoietic protoporphyria.Nucleic acids research · 2020Article
- Predicting gene structure changes resulting from genetic variants via exon definition features.Bioinformatics (Oxford, England) · 2018Article
- Mis-splicing of the GALNS gene resulting from deep intronic mutations as a cause of Morquio a disease.BMC medical genetics · 2018Article
- Splicing mutations in human genetic disorders: examples, detection, and confirmation.Journal of applied genetics · 2018Review
- The synonymous nucleotide substitution RHD 1056C>G alters mRNA splicing associated with serologically weak D phenotype.Journal of clinical laboratory analysis · 2018Article
- Normal and altered pre-mRNA processing in the DMD gene.Human genetics · 2017Review
- Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics?International journal of molecular sciences · 2017Review
1 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
4 authors at 2 institutions in 1 country.
Funding
Abstract
Accurate pre-mRNA splicing requires primary splicing signals, including the splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs). The SREs include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs), which are typically located near the splice sites. However, it is unclear to what extent splicing-driven selective pressure constrains exonic and intronic sequences, especially those distant from the splice sites. Here, we studied the distribution of SREs in human genes in terms of DNA strand-asymmetry patterns. Under a neutral evolution model, each mononucleotide or oligonucleotide should have a symmetric (Chargaff's second parity rule), or weakly asymmetric yet uniform, distribution throughout a pre-mRNA transcript. However, we found that large sets of unbiased, experimentally determined SREs show a distinct strand-asymmetry pattern that is inconsistent with the neutral evolution model, and reflects their functional roles in splicing. ESEs are selected in exons and depleted in introns and vice versa for ESSs. Surprisingly, this trend extends into deep intronic sequences, accounting for one third of the genome. Selection is detectable even at the mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of ESEs and ESSs. We developed a method that effectively predicts SREs based on strand asymmetry, expanding the current catalog of SREs. Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution.
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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.