title: The Silent Sway of Splicing by Synonymous Substitutions.
abstract: Alternative splicing diversifies mRNA transcripts in human cells. This sequence-driven process can be influenced greatly by mutations, even those that do not change the protein coding potential of the transcript. Synonymous mutations have been shown to alter gene expression through modulation of splicing, mRNA stability, and translation. Using a synonymous position mutation library in SMN1 exon 7, we show that 23% of synonymous mutations across the exon decrease exon inclusion, suggesting that nucleotide identity across the entire exon has been evolutionarily optimized to support a particular exon inclusion level. Although phylogenetic conservation scores are insufficient to identify synonymous positions important for exon inclusion, an alignment of organisms filtered based on similar exon/intron architecture is highly successful. Although many of the splicing neutral mutations are observed to occur, none of the exon inclusion reducing mutants was found in the filtered alignment. Using the modified phylogenetic comparison as an approach to evaluate the impact on pre-mRNA splicing suggests that up to 45% of synonymous SNPs are likely to alter pre-mRNA splicing. These results demonstrate that coding and pre-mRNA splicing pressures co-evolve and that a modified phylogenetic comparison based on the exon/intron architecture is a useful tool in identifying splice altering SNPs.
authors.affiliation: From the Department of Microbiology and Molecular Genetics and.
authors.forename: William F
authors.identifier: http://orcid.org/0000-0001-9134-7648
authors.initials: WF
authors.lastname: Mueller
authors.affiliation: the Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California 92619.
authors.forename: Liza S Z
authors.initials: LS
authors.lastname: Larsen
authors.affiliation: From the Department of Microbiology and Molecular Genetics and.
authors.forename: Angela
authors.initials: A
authors.lastname: Garibaldi
authors.affiliation: From the Department of Microbiology and Molecular Genetics and the Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California 92619.
authors.forename: G Wesley
authors.initials: GW
authors.lastname: Hatfield
authors.affiliation: From the Department of Microbiology and Molecular Genetics and the Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California 92619 khertel@uci.edu.
authors.forename: Klemens J
authors.initials: KJ
authors.lastname: Hertel
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D004252:DNA Mutational Analysis; D005091:Exons; D015723:Gene Library; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D012322:RNA Precursors / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D055533:Survival of Motor Neuron 1 Protein / Q000235:genetics
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; C526471:SMN1 protein, human; D055533:Survival of Motor Neuron 1 Protein
keywords: RNA processing; RNA splicing; alternative splicing; evolution; genomics; spliceosome