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Genes 2017, 8(10), 283; doi:10.3390/genes8100283

Allelic Expression Imbalance in the Human Retinal Transcriptome and Potential Impact on Inherited Retinal Diseases

1
Institute for Ophthalmic Research, Centre for Ophthalmology, 72076 Tuebingen, Germany
2
Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
3
Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
4
Center for Ophthalmology, 72076 Tuebingen, Germany
5
Augenklinik Mülheim, 45468 Mülheim an der Ruhr, Germany
6
Universitäts-Augenklinik, 55131 Mainz, Germany
*
Author to whom correspondence should be addressed.
Received: 30 June 2017 / Revised: 11 October 2017 / Accepted: 16 October 2017 / Published: 20 October 2017
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Abstract

Inherited retinal diseases (IRDs) are often associated with variable clinical expressivity (VE) and incomplete penetrance (IP). Underlying mechanisms may include environmental, epigenetic, and genetic factors. Cis-acting expression quantitative trait loci (cis-eQTLs) can be implicated in the regulation of genes by favoring or hampering the expression of one allele over the other. Thus, the presence of such loci elicits allelic expression imbalance (AEI) that can be traced by massive parallel sequencing techniques. In this study, we performed an AEI analysis on RNA-sequencing (RNA-seq) data, from 52 healthy retina donors, that identified 194 imbalanced single nucleotide polymorphisms(SNPs) in 67 IRD genes. Focusing on SNPs displaying AEI at a frequency higher than 10%, we found evidence of AEI in several IRD genes regularly associated with IP and VE (BEST1, RP1, PROM1, and PRPH2). Based on these SNPs commonly undergoing AEI, we performed pyrosequencing in an independent sample set of 17 healthy retina donors in order to confirm our findings. Indeed, we were able to validate CDHR1, BEST1, and PROM1 to be subjected to cis-acting regulation. With this work, we aim to shed light on differentially expressed alleles in the human retina transcriptome that, in the context of autosomal dominant IRD cases, could help to explain IP or VE. View Full-Text
Keywords: Inherited retinal diseases; penetrance; allelic expression imbalance; retina; expressivity Inherited retinal diseases; penetrance; allelic expression imbalance; retina; expressivity
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Llavona, P.; Pinelli, M.; Mutarelli, M.; Marwah, V.S.; Schimpf-Linzenbold, S.; Thaler, S.; Yoeruek, E.; Vetter, J.; Kohl, S.; Wissinger, B. Allelic Expression Imbalance in the Human Retinal Transcriptome and Potential Impact on Inherited Retinal Diseases. Genes 2017, 8, 283.

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