title: A comprehensive survey of non-canonical splice sites in the human transcriptome.
abstract: We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein identified U2/U12-like non-canonical splice site events and successfully validated 9 of them via reverse transcriptase-polymerase chain reaction and Sanger sequencing. Analyses of the 184 U2/U12-like non-canonical splice sites indicate that 51% of them are not annotated in GENCODE. In addition, 28% of them are conserved in mouse and 76% are involved in alternative splicing events, some of them with tissue-specific alternative splicing patterns. Interestingly, our analysis identified some U2/U12-like non-canonical splice sites that are converted into canonical splice sites by RNA A-to-I editing. Moreover, the U2/U12-like non-canonical splice sites have a differential distribution of splicing regulatory sequences, which may contribute to their recognition and regulation. Our analysis provides a high-confidence group of U2/U12-like non-canonical splice sites, which exhibit distinctive features among the total human splice sites.
authors.affiliation: Nucleus Millennium in Stress and Addiction, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
authors.forename: Guillermo E
authors.initials: GE
authors.lastname: Parada
authors.affiliation: Nucleus Millennium in Stress and Addiction, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile rnmunita@uc.cl.
authors.forename: Roberto
authors.initials: R
authors.lastname: Munita
authors.affiliation: Nucleus Millennium in Stress and Addiction, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
authors.forename: Cledi A
authors.initials: CA
authors.lastname: Cerda
authors.affiliation: Nucleus Millennium in Stress and Addiction, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile kgysling@bio.puc.cl.
authors.forename: Katia
authors.initials: K
authors.lastname: Gysling
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D016477:Artifacts; D001483:Base Sequence; D002460:Cell Line; D016384:Consensus Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D006801:Humans; D007438:Introns; D051379:Mice; D058977:Molecular Sequence Annotation; D017393:RNA Editing; D022821:RNA Splice Sites; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA; D017381:Spliceosomes / Q000378:metabolism; D059467:Transcriptome
chemical_list: D022821:RNA Splice Sites; D038621:Regulatory Sequences, Ribonucleic Acid