Comprehensive splice-site analysis using comparative genomics
By Nihar U. Sheth, Xavier Roca, M. Hastings, T. Roeder, Adrian R. Krainer, Ravi Sachidanandam. Nucleic Acids Research, 2006
401 citations recorded by the source corpus.
We have collected over half a million splice sites from five species—Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana—and classified them into four subtypes: U2-type GT–AG and GC–AG and U12-type GT–AG and AT–AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT–AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3′ splice sites (3′ss) and (iv) distinct evolutionary histories of 5′ and 3′ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8cf39bd0e7c348eb07650f59e2d7869fc75a6713
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In Molecular Biology
Citations in the corpus
- Spinal Muscular Atrophy: Why do low levels of SMN make motor neurons sick? (2009, background): “This would suggest that some of the approximately 700 genes that use the minor U12- and U11-dependent splicing pathway would be disrupte”
- Mechanisms and pathways of growth failure in primordial dwarfism. (2011, background): “However, the effect on transcript splicing is selective (Pessa et al. 2010; Edery et al. 2011; He et al. 2011), and it is quite possible that specific impairment of one of the U12-type intron-containing genes involved in cell cycle control (Sheth et al. 2006) causes the growth failure.”
- Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis (2012, methodology): “We have evaluated the splice sites using the procedure and PWMs described by Sheth et al. (2006).”