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Pablo Llavona, Bernd Wissinger, Susanne Kohl, Simone Schimpf-Linzenbold; cis-eQTLs as potential modifiers for hereditary retinal dystrophies. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):5495.
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© ARVO (1962-2015); The Authors (2016-present)
Concepts such as reduced or incomplete penetrance are frequently associated with hereditary retinal dystrophies (RD). It has been already proved that depending on the gene, or the specific mutation, the severity and onset of the disease can vary. In addition, reduced penetrance with asymptomatic mutation carriers has been reported. Although literature is extensive when it comes to this terms, in most instances it remains unclear what is the cause for phenotypic variation in cases with the same genetic anomaly. Our hypothesis for such variability relies on expression quantitative trait loci (eQTL), focusing especially on cis-eQTLs. These loci are able to modulate transcription in a cis-regulatory manner, hereby altering the expression of each allele differentially and finally resulting in allelic expression imbalance (AEI).<br />
RNA-sequencing was performed on RNA extracted out of the retinas from enucleations of 3 healthy human donors. Retinal transcriptome was analyzed in order to obtained information about those RD genes undergoing AEI by filtering for heterozygous coding single nucleotide variants (cSNPs) showing allelic expression ratios higher than 1.5 or lower than 0.66, and p<0.05 after Bonferroni correction. Sanger sequencing was performed on those cSNPs showing AEI in order to confirm their heterozygosity. AEI validation of candidate cSNPs was carried out by pyrosequencing analysis of retinal RNA of additional 13 human healthy retina donors.
RNA-Seq data analysis performed on retinal transcriptomes of three healthy donors, shows that 13 cSNP belonging to 9 RD genes undergo AEI. Further pyrosequencing validation has proven that 4 of these cSNP show AEI. One of the positively validated SNPs located in KCNV2 was later excluded as another SNP within the same exon showed no AEI. However the remaining 3 positive SNPs belong to CDHR1, or more precisely to its second alternatively spliced variant. Sequence analysis for this variant resulted in a haplotype associated with samples showing AEI for CDHR1.
Our RNA-Seq results, confirmed by pyrosequencing, indicate that CDHR1 is a strong candidate to be subjected to cis-eQTL regulation. Further RNA-Seq data will be obtained in an effort to better comprehend the retinal transcriptome and thus a deeper understanding of those cis-eQTLs involved in retinal gene expression.
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