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Review
. 2017 Aug 1;26(R1):R68-R74.
doi: 10.1093/hmg/ddx219.

RNA expression in human retina

Mingyao Li  1 , Randy J Zauhar  2 , Clare Grazal  3 , Christine A Curcio  4 , Margaret M DeAngelis  5 , Dwight Stambolian  3
Affiliations
Review

RNA expression in human retina

Mingyao Li et al. Hum Mol Genet. .

Abstract

Recent Genome-wide Association Studies (GWASs) for eye diseases/traits have delivered a number of novel findings across a diverse range of diseases, including age-related macular degeneration (AMD), glaucoma and refractive error. However, despite this astonishing rate of success, the major challenge still remains to not only confirm that the genes implicated in these studies are truly the genes conferring protection from or risk of disease but also to define the functional roles these genes play in disease. Ongoing evidence is accumulating that the single nucleotide polymorphisms (SNPs) used in GWAS and fine mapping studies have causal effects through their influence on gene expression rather than affecting protein function. The biological interpretation of SNP regulatory effects for a tissue requires knowledge of the transcriptome for that tissue. We summarize the reasons to characterize the complete retinal transcriptome as well as the evidence to include an assessment of differences in regional retinal expression.

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Figures

Figure 1
Figure 1
Alternative approach to identifying the cause of a complex disease trait. Genomic components are first characterized in the normal tissue affected by disease. These genomic characteristics are then packaged together using an array of bioinformatic programs to understand the normal interactions between DNA, RNA and proteins. Perturbations in these interactions can then be evaluated in the diseased tissue.
Figure 2
Figure 2
Distribution of calculated fold-change (log2) of differentially expressed protein coding genes with FDR ≤ 0.05, one or the other FPKM ≥ 1, and fold difference ≥ 2, based on CuffDiff analysis against HG38. Calculated fold-changes for upregulated genes are plotted in red and downregulated genes plotted in blue. Note the significant RNA overexpression in the comparison between AMD and normal macula retina. A, comparison of AMD and normal macula retina; B, comparison of AMD and normal rpe/choroid/sclera; C, comparison of AMD and normal peripheral retina; D, comparison of AMD and normal peripheral rpe/choroid/sclera.
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