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Gemma Marfany, Alejandro Garanto, Marina Riera, Esther Pomares, Jon Permanyer, Marta de Castro-Miró, Josep F. Abril, Roser Gonzalez-Duarte; High Transcriptional Complexity of the Retinitis Pigmentosa CERKL Gene in Human and Mouse. Invest. Ophthalmol. Vis. Sci. 2011;52(14):5404.
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Evidences of different alternatively spliced isoforms of the retinitis pigmentosa (RP) CERKL gene have been reported, but a comprehensive prioritized list of the physiologically relevant transcripts is missing. Its wide tissular expression appears to be inconsistent with the tissue-restricted phenotype of CERKL mutations, as only the retina is affected. In order to shed light on the pathogenicity of the CERKL variants, we aimed to characterize its transcriptional repertoire focussing on the use of distinct promoters and alternative splicing in human and mouse tissues.
A combination of: 1) in silico genomic searches for transcription factor binding sites, 2) computational prediction of transcriptional and translational start sites based on reported and customized matrices, 3) experimental characterization of transcripts by RT-PCR, and 4) in situ hybridization assays on different human and murine tissues and cell lines, has been used to characterize the transcriptional scenario of CERKL.
The analysis of CERKL isoforms reveals a high trancriptional complexity in human and mouse tissues arising from both, the use of tissue-specific promoters and alternative splicing of the coding exons. Four transcriptional start sites plus a high variety of alternative splicing events -mainly affecting the 5’ half of the gene- generate more than 20 mRNA isoforms, with clear tissue preferences. Notably, the retina stands out as the tissue with the highest number of transcripts. Moreover, several translational start sites contribute to the final protein complexity. This high repertoire of transcript and protein isoforms suggests a distinct function of the alternatively displayed domains.
The combined approach of in silico and experimental characterization of the CERKL gene provides a comprehensive picture of the species-specific transcriptional products in the retina, underscores a highly tuned regulation of this gene in different tissues, and establishes a framework for the study of the CERKL genotype-phenotype correlations and the assessment of the severity of new mutations. Considering the high number of CERKL isoforms, undertaking accurate analysis for localization and/or functional specificity at the subcellular level remains a key challenge to understand the contribution of this gene to retinal degeneration.
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