Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells.
Allele-specific splicing is the production of different RNA isoforms from different alleles of a gene. Altered splicing patterns such as exon skipping can have a dramatic effect on the final protein product yet have traditionally proven difficult to predict. We investigated the splicing effects of a set of nine single nucleotide polymorphisms (SNPs) which are predicted to have a direct impact on mRNA splicing, each in a different gene. Predictions were based on SNP location relative to splice junctions and intronic/exonic splicing elements, combined with an analysis of splice isoform expression data from public sources. Of the nine genes tested, six SNPs led to direct impacts on mRNA splicing as determined by the splicing reporter minigene assay and RT-PCR in human HeLa cells, of which four were allele-specific effects. These included previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1. Notably, the SNP in ZNF419, a transcription factor, leads to the deletion of a DNA-binding domain from the protein and is associated with an expression QTL, while the SNP in DKKL1 leads to shortened transcripts predicted to produce a truncated protein. We conclude that the impact of SNP mutations on mRNA splicing, and its biological relevance, can be predicted by integrating SNP position with available data on relative isoform abundance in human cell lines.
Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
Grace
G
Martin
Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
S Duygu
SD
Selcuklu
Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
Katherine
K
Schouest
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch, 7700 Cape Town, South Africa.
Victoria
V
Nembaware
Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
Peter C
PC
McKeown
School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland.
Cathal
C
Seoighe
Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland. Electronic address: charles.spillane@nuigalway.ie.
Charles
C
Spillane
D000483:Alleles; D017398:Alternative Splicing; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005091:Exons; D006367:HeLa Cells; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics* / Q000378:metabolism; D007438:Introns; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
C577596:DKKL1 protein, human; D004268:DNA-Binding Proteins; D036341:Intercellular Signaling Peptides and Proteins; D020033:Protein Isoforms; D022821:RNA Splice Sites; D012333:RNA, Messenger; D014157:Transcription Factors; C000613800:ZNF419 protein, human
Allele-specific; Alternative splicing; Minigene splicing reporter assay; Single nucleotide polymorphisms