ArticleGenome biology2008
Exon creation and establishment in human genes.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Unproductive alternative splicing of ATM exon 7: mapping of critical regulatory elements and identification of 34 spliceogenic variants.Journal of molecular medicine (Berlin, Germany) · 2025Article
- Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies.Frontiers in immunology · 2024Review
- Recursive splicing discovery using lariats in total RNA sequencing.Life science alliance · 2023Article
- Transcriptome innovations in primates revealed by single-molecule long-read sequencing.Genome research · 2022Article
- Growth Hormone Receptor (GHR) 6Ω Pseudoexon Activation: a Novel Cause of Severe Growth Hormone Insensitivity.The Journal of clinical endocrinology and metabolism · 2021Article
- Exon size and sequence conservation improves identification of splice-altering nucleotides.RNA (New York, N.Y.) · 2019Article
- Article
- Deep intronic mutations and human disease.Human genetics · 2017Review
- Lessons from non-canonical splicing.Nature reviews. Genetics · 2016Review
- The contribution of Alu exons to the human proteome.Genome biology · 2016Article
- Gain of a New Exon by a Lineage-Specific Alu Element-Integration Event in the BCS1L Gene during Primate Evolution.Molecules and cells · 2015Article
- Species-specific exon loss in human transcriptomes.Molecular biology and evolution · 2015Article
- Novel kinin B₁ receptor splice variant and 5'UTR regulatory elements are responsible for cell specific B₁ receptor expression.PloS one · 2014Article
- Reverse transcriptase and intron number evolution.Stem cell investigation · 2014Article
- Exon-phase symmetry and intrinsic structural disorder promote modular evolution in the human genome.Nucleic acids research · 2013Article
- Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing.Nucleic acids research · 2013Article
- Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence.BMC bioinformatics · 2012Article
- Splice variant PRKC-ζ(-PrC) is a novel biomarker of human prostate cancer.British journal of cancer · 2012Article
- Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.Genome research · 2012Article
- Posttraining ablation of adult-generated neurons degrades previously acquired memories.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. Despite many recent studies, it is still unclear which are the splicing regulatory requirements for de novo exonization and how splicing regulation changes throughout an exon's lifespan.
resultsUsing comparative genomics, we have defined sets of exons with different evolutionary ages. Younger exons have weaker splice-sites and lower absolute values for the relative abundance of putative splicing regulators between exonic and adjacent intronic regions, indicating a less consolidated splicing regulation. This relative abundance is shown to increase with exon age, leading to higher exon inclusion. We show that this local difference in the density of regulators might be of biological significance, as it outperforms other measures in real exon versus pseudo-exon classification. We apply this new measure to the specific case of the exonization of anti-sense Alu elements and show that they are characterized by a general lack of exonic splicing silencers.
conclusionsOur results suggest that specific sequence environments are required for exonization and that these can change with time. We propose a model of exon creation and establishment in human genes, in which splicing decisions depend on the relative local abundance of regulatory motifs. Using this model, we provide further explanation as to why Alu elements serve as a major substrate for exon creation in primates. Finally, we discuss the benefits of integrating such information in gene prediction.
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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.