ArticleNucleic acids research2013
Computational identification of functional introns: high positional conservation of introns that harbor RNA genes.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Intron size minimisation in teleosts.BMC genomics · 2022Article
- The evolution of hemocyanin genes in Tectipleura: a multitude of conserved introns in highly diverse gastropods.BMC ecology and evolution · 2021Article
- Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences.Evolutionary bioinformatics online · 2020Article
- Deep intronic mutations and human disease.Human genetics · 2017Review
- Particulate matter-induced epigenetic changes and lung cancer.The clinical respiratory journal · 2017Review
- Identification of introns harboring functional sequence elements through positional conservation.Scientific reports · 2017Article
- The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.Scientific reports · 2016Article
- Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae.Genetics · 2016Article
- JuncDB: an exon-exon junction database.Nucleic acids research · 2016Article
- Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint.Life (Basel, Switzerland) · 2015Article
- LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.PloS one · 2015Article
- Deciphering the RNA landscape by RNAome sequencing.RNA biology · 2015Article
- Intron evolution in Saccharomycetaceae.Genome biology and evolution · 2014Article
- Origin of spliceosomal introns and alternative splicing.Cold Spring Harbor perspectives in biology · 2014Article
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Authors and funding
2 authors.
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Abstract
An appreciable fraction of introns is thought to have some function, but there is no obvious way to predict which specific intron is likely to be functional. We hypothesize that functional introns experience a different selection regime than non-functional ones and will therefore show distinct evolutionary histories. In particular, we expect functional introns to be more resistant to loss, and that this would be reflected in high conservation of their position with respect to the coding sequence. To test this hypothesis, we focused on introns whose function comes about from microRNAs and snoRNAs that are embedded within their sequence. We built a data set of orthologous genes across 28 eukaryotic species, reconstructed the evolutionary histories of their introns and compared functional introns with the rest of the introns. We found that, indeed, the position of microRNA- and snoRNA-bearing introns is significantly more conserved. In addition, we found that both families of RNA genes settled within introns early during metazoan evolution. We identified several easily computable intronic properties that can be used to detect functional introns in general, thereby suggesting a new strategy to pinpoint non-coding cellular functions.
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