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Extensive functional analyses of RHD splice site variants: Insights into the potential role of splicing in the physiology of Rh
Author(s) -
Fichou Yann,
Gehannin Pierre,
Corre Ma,
Le Guern Alice,
Le Maréchal Cédric,
Le Gac Gérald,
Férec Claude
Publication year - 2015
Publication title -
transfusion
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.045
H-Index - 132
eISSN - 1537-2995
pISSN - 0041-1132
DOI - 10.1111/trf.13083
Subject(s) - minigene , rna splicing , exon , intron , biology , phenotype , genetics , alternative splicing , gene , allele , exon skipping , splice , computational biology , rna
BACKGROUND Among more than 300 mutated alleles identified so far within the RHD gene, almost 40 are assumed to alter cellular splicing and therefore may have a direct effect on Rh phenotype both at the quantitative and at the qualitative levels. Functional data are, however, mostly unavailable to assess the direct involvement of splicing defect in the underlying physiology. STUDY DESIGN AND METHODS We generated plasmid constructs to carry out an exhaustive investigation of 38 RHD variants located within or in the vicinity of exon–intron junctions by a minigene splicing assay, further characterized the transcript structures by sequencing, and identified cryptic sites activated by the genetic defect. Bioinformatics predictions were carried out in parallel and compared with the functional data. RESULTS For the first time we demonstrate that a product including the full‐length Exon 9 is transcribed in the presence of the c.1227G>A substitution frequently carried by Asians with DEL phenotype and confirmed that splicing is altered in the RHD*weak D Type 2 allele, a rare variant most commonly found in Caucasians. CONCLUSION Overall we 1) show significant correlation between functional analyses, bioinformatics predictions, and phenotypes, when available, especially for variants in close proximity of the consensus splice sites; 2) classify the variations as splicing or nonsplicing variants; and 3) provide functional data to further improve bioinformatics splicing tools. Conversely assessment of seven silent exonic variants was mainly inconclusive.