Abstract
The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).
Highlights
The retina is the specialized region of the central nervous system that transduces light stimuli into neural signals
On average 79% of the reads were successfully mapped to the human genome reference version hg19 (Supplementary Figure S4 and Table S4)
We generated a UCSC genome browser track to report the average coverage (AC) across the genomic sequence by counting the number of mapped reads per 100 bp averaged across the 50 samples
Summary
The retina is the specialized region of the central nervous system that transduces light stimuli into neural signals. It is formed by a concentric structure of three cell layers externally surrounded by the retinal pigment epithelium (RPE), composed of tightly connected cells that form the bloodretina barrier [1]. Primary genetic defects of photoreceptor cells cause inherited retinal diseases (IRDs) that are characterized by broad clinical manifestations, ranging from isolated defects of the peripheral or central retina to reduced acuity in low-light condition to complete blindness [2]. Several families affected by such conditions lack a conclusive genetic diagnosis [3,4,5] suggesting the presence of additional, yet to be identified, causative genes
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