Abstract
Long intervening non-coding RNAs (lincRNAs) are increasingly being implicated as important factors in many aspects of cellular development, function, and disease, but remain poorly understood. In this study, we examine the human retinal pigment epithelium (RPE) lincRNA transcriptome using RNA-Seq data generated from human fetal RPE (fRPE), RPE derived from human induced pluripotent stem cells (iPS-RPE), and undifferentiated iPS (iPS). In addition, we determine the suitability of iPS-RPE, from a transcriptome standpoint, as a model for use in future studies of lincRNA structure and function. A comparison of gene and isoform expression across the whole transcriptome shows only minimal differences between all sample types, though fRPE and iPS-RPE show higher concordance than either shows with iPS. Notably, RPE signature genes show the highest degree of fRPE to iPS-RPE concordance, indicating that iPS-RPE cells provide a suitable model for use in future studies. An analysis of lincRNAs demonstrates high concordance between fRPE and iPS-RPE, but low concordance between either RPE and iPS. While most lincRNAs are expressed at low levels (RPKM < 10), there is a high degree of concordance among replicates within each sample type, suggesting the expression is consistent, even at levels subject to high variability. Finally, we identified and annotated 180 putative novel genes in the fRPE samples, a majority of which are also expressed in the iPS-RPE. Overall, this study represents the first characterization of lincRNA expression in the human RPE, and provides a model for studying the role lincRNAs play in RPE development, function, and disease.
Highlights
The retinal pigment epithelium (RPE), a single cell layer in the posterior eye, is integral for maintaining visual function [1]
An important consideration for transcriptome studies of the RPE derived from whole eyes is contamination from surrounding cell types, such as photoreceptors and choroid [49].To determine the extent to which our fetal RPE (fRPE) samples were contaminated with these other cell types, we looked at expression of protein-coding genes that are expressed more highly in choroid and photoreceptors relative to RPE
The goal of this study was two-fold: to characterize lincRNA expression in the human fetal RPE, and to determine if iPS-RPE can serve as a suitable model for future studies of the role lincRNAs play in RPE function
Summary
The retinal pigment epithelium (RPE), a single cell layer in the posterior eye, is integral for maintaining visual function [1]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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