title: The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons.
abstract: Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is phylogenetically and spatially conserved in introns that flank brain-enriched alternative exons from fish to man. Analysis of sequence from the mouse, rat, dog, chicken and pufferfish genomes revealed a strongly statistically significant association of UGCAUG with the proximal intron region downstream of brain-enriched alternative exons. The number, position and sequence context of intronic UGCAUG elements were highly conserved among mammals and in chicken, but more divergent in fish. Control datasets, including constitutive exons and non-tissue-specific alternative exons, exhibited a much lower incidence of closely linked UGCAUG elements. We propose that the high sequence specificity of the UGCAUG element, and its unique association with tissue-specific alternative exons, mark it as a critical component of splicing switch mechanism(s) designed to activate a limited repertoire of splicing events in cell type-specific patterns. We further speculate that highly conserved UGCAUG-binding protein(s) related to the recently described Fox-1 splicing factor play a critical role in mediating this specificity.
authors.affiliation: Life Sciences Division and Genomics Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA.
authors.forename: Simon
authors.initials: S
authors.lastname: Minovitsky
authors.forename: Sherry L
authors.initials: SL
authors.lastname: Gee
authors.forename: Shiruyeh
authors.initials: S
authors.lastname: Schokrpur
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: John G
authors.initials: JG
authors.lastname: Conboy
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D002645:Chickens / Q000235:genetics; D017124:Conserved Sequence; D004285:Dogs; D005091:Exons; D006801:Humans; D007438:Introns; D051379:Mice; D010802:Phylogeny; D051381:Rats; D038621:Regulatory Sequences, Ribonucleic Acid; D023721:Tetraodontiformes / Q000235:genetics; D014018:Tissue Distribution
chemical_list: D038621:Regulatory Sequences, Ribonucleic Acid