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H. Vastinsalo, J. Isosomppi, A. Dinculescu, W. W. Hauswirth, S. Geller, J. Flannery, E.-M. Sankila; Alternative Splice Variants of the Usher Syndrome Type 3 (USH3) Gene Clarin 1 (CLRN1). Invest. Ophthalmol. Vis. Sci. 2007;48(13):3791.
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© ARVO (1962-2015); The Authors (2016-present)
To further characterize the structure of human and murine clarin 1 (CLRN1) genes responsible for autosomal recessive Usher syndrome type 3 (progressive retinitis pigmentosa and sensorineural hearing loss), by searching for alternative splice variants including previously uncharacterized exons, determining expression patterns of splice variants in different tissues, and analyzing the promoter(s) of the gene.
Human and mouse cDNA libraries from various tissues were used to amplify CLRN1 transcripts using several different primer combinations. The amplified products were cloned using TOPO TA cloning kit and subsequently sequenced. The expression patterns of alternatively spliced variants were studied in mouse retina and cochlea by in situ hybridization. Function of mouse and human CLRN1 promoter regions was studied by in silico analyses and by using luciferase reporter assays in combination with varying promoter region constructs.
The main splice variant of CLRN1 is considered to contain exons: 0, 2 and 3. Other exons present in known alternative splice variants are 1, 1b, and 4. We have found splicing variants with new combinations of known exons, and also new sequences that are incorporated into CLRN1 mRNA presenting previously unknown exons. The studies show that the promoter region upstream of exon 0 is conserved whereas the hypothetical promoter region upstream of exon 1 is less conserved. Results from in silico studies suggest possible dual promoter for CLRN1.
CLRN1 has several alternative splice variants and it has two possible promoter regions upstream of exons 0, and 1, respectively. Observed differences in CLRN1 splice variants and promoter region conservation between mouse and human may indicate that CLRN1 has functional differences between mouse and human. CLRN1 may well have two classes of splice variants: ubiquitously expressed ones and tissue specific ones with functional differences. Knowing the structure and function of the CLRN1 gene is a prerequisite for the understanding of the pathophysiology of Usher syndrome type 3, and for developing therapies for the disease.
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