The Alu insertion in the CLCN5 gene of a patient with Dent's disease leads to exon 11 skipping.
Alu sequences are short, interspersed elements that have generated more than one million copies in the human genome. They propagate by transcription followed by reverse transcription and integration, causing mutations, recombination, and changes in pre-mRNA splicing. We have recently identified a 345-bp long Alu Ya5 element inserted in codon 650 within exon 11 of the chloride channel ClC-5 gene (CLCN5) of a patient with Dent's disease. A microsatellite pedigree analysis indicated that the insertion occurred in the germline of the maternal grandfather. Dent's disease is an X-linked renal tubular disorder characterized by low-molecular-weight proteinuria, hypercalciuria, nephrolithiasis, and nephrocalcinosis. Here, we found, by RT-PCR amplification of RNA extracted from the patient's blood and subsequent DNA sequencing, that the Alu insertion led to an aberrant splicing of the CLCN5 pre-mRNA that skipped exon 11. Using the ESE finder and RESCUE-ESE Web interfaces, we identified two high-score exonic splicing enhancer (ESE) sequences in the site of insertion. The functional significance of these ESE motifs is suggested by our observation that these sequences are highly conserved among mammal CLCN5 genes. Therefore, we suggest that the Alu insertion causes exon skipping by interfering with splicing regulatory elements. The altered splicing would predict a truncated ClC-5 protein that lacks critical domains for sorting and chloride channel function.
Claverie-Martín
Félix
F
Unidad de Investigación, Asociada al Centro de Investigaciones Biológicas, CSIC, Hospital Universitario Nuestra Señora de Candelaria, 38010, Santa Cruz de Tenerife, Spain. fclamar@gobiernodecanarias.org.
Flores
Carlos
C
Unidad de Investigación, Asociada al Centro de Investigaciones Biológicas, CSIC, Hospital Universitario Nuestra Señora de Candelaria, 38010, Santa Cruz de Tenerife, Spain.
Antón-Gamero
Montserrat
M
Unidad de Nefrología Pediátrica, Hospital Universitario Reina Sofia, Córdoba, Spain.
González-Acosta
Hilaria
H
Unidad de Investigación, Asociada al Centro de Investigaciones Biológicas, CSIC, Hospital Universitario Nuestra Señora de Candelaria, 38010, Santa Cruz de Tenerife, Spain.
García-Nieto
Víctor
V
Unidad de Nefrología Pediátrica, Hospital Universitario Nuestra Señora de Candelaria, 38010, Santa Cruz de Tenerife, Spain.
D017398:Alternative Splicing / Q000235:genetics*; D020087:Alu Elements / Q000235:genetics*; D001483:Base Sequence; D002648:Child; D018118:Chloride Channels / Q000235:genetics*; D017931:DNA Primers; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005091:Exons / Q000235:genetics; D006801:Humans; D007674:Kidney Diseases / Q000235:genetics*; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010375:Pedigree; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017421:Sequence Analysis; D017422:Sequence Analysis, DNA
C097503:CLC-5 chloride channel; D018118:Chloride Channels; D017931:DNA Primers