ArticleGenome research2012
Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.
Article in Genome research, 2012. 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, 118 citations in OpenAlex.
- Integration of epigenetics into ecotoxicology: insights and fundamental research needs.Biological reviews of the Cambridge Philosophical Society · 2026Review
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- Genome-Wide Identification and Expression Analysis of the Aquaporin Gene Family in the Qinghai Toad-Headed Agama (Biology · 2025Article
- Genome-Wide Identification of the Glycosyl Hydrolase Family 1 Genes inPlants (Basel, Switzerland) · 2025Article
- Emerging Orchestrator of Ecological Adaptation: mMolecular ecology · 2025Review
- Global dysregulation of circular RNAs in frontal cortex and whole blood from DM1 and DM2.Human genetics · 2025Article
- DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.Nucleic acids research · 2025Article
- Expression of Truncated Products at the 5'-Terminal Region of RIPK2 and Evolutive Aspects that Support Their Biological Importance.Genome biology and evolution · 2024Article
- Non-canonical retinoid signaling in neural development, regeneration and synaptic function.Frontiers in molecular neuroscience · 2024Review
- Intronic position +9 and -9 are potentially splicing sites boundary from intronic variants analysis of whole exome sequencing data.BMC medical genomics · 2023Article
- Article
- Branch point strength controls species-specificLife science alliance · 2023Article
- Characterization of immunoglobulinFrontiers in immunology · 2023Article
- Characterization of nuclear DNA diversity in an individualFrontiers in plant science · 2023Article
- Introns: the "dark matter" of the eukaryotic genome.Frontiers in genetics · 2023Review
- Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ.Communications biology · 2022Article
- Splice site proximity influences alternative exon definition.RNA biology · 2022Article
- Alternative splicing level related to intron size and organism complexity.BMC genomics · 2021Article
- ExOrthist: a tool to infer exon orthologies at any evolutionary distance.Genome biology · 2021Article
- Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms.Communications biology · 2021Article
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
8 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exon-intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon-intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3' and 5' splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery.
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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.