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Phenotypic consequences of branch point substitutions
Author(s) -
Královičová Jana,
Lei Haixin,
Vořechovský Igor
Publication year - 2006
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20362
Subject(s) - biology , rna splicing , intron , genetics , exon , spliceosome , point mutation , gene , splice site mutation , polypyrimidine tract , splice , exonic splicing enhancer , exon skipping , mutation , microbiology and biotechnology , rna
The branch point sequence (BPS) is a conserved splicing signal important for spliceosome assembly and lariat intron formation. BPS mutations may result in aberrant pre‐mRNA splicing and genetic disorders, but their phenotypic consequences have been difficult to predict, largely due to a highly degenerate nature of the BPS consensus. Here, we have examined the splicing pattern of nine reporter pre‐mRNAs that have previously been shown to give rise to human hereditary diseases as a result of single‐nucleotide substitutions in the predicted BPS. Increased exon skipping and intron retention observed in vivo were recapitulated for each mutated pre‐mRNA, but the reproducibility of cryptic splice site activation was lower. BP mutations in reporter pre‐mRNAs frequently induced aberrant 3′ splice sites and also activated a cryptic 5′ splice site. Systematic mutagenesis of BP adenosines showed that in most pre‐mRNAs, the expression of canonical transcripts was lower for BP transitions than BP transversions. Differential splicing outcome for transitions vs. transversions was abrogated or reduced if introns were truncated to 200 nt or less, suggesting that the nature of the BP residue is less critical for interactions across very short introns. Together, these results improve prediction of phenotypic consequences of point mutations upstream of splice acceptor sites and suggest that the overrepresentation of disease‐causing adenosine‐to‐guanosine BP substitutions observed in Mendelian disorders is due to more profound defects of gene expression at the level of pre‐mRNA splicing. Hum Mutat 27(8), 803–813, 2006. © 2006 WileyLiss, Inc.