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Lina Zelinger, Gökhan Karakülah, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew Brooks, Anand Swaroop; De-novo assembly of mouse photoreceptor transcriptome identifies un-annotated lncRNAs regulated by NRL. Invest. Ophthalmol. Vis. Sci. 2017;58(8):2488. doi: https://doi.org/.
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© ARVO (1962-2015); The Authors (2016-present)
Our goal is to provide a detailed picture of the photoreceptor transcriptomic landscape that will serve as a basis to study gene regulatory networks underlying development and disease. This study focuses on identifying and cataloging un-annotated lncRNAs in developing rod photoreceptors.
Wild type (Nrlp-GFP) rods and S-cone like (Nrlp-GFP;Nrl-/-) photoreceptors were purified from mice retina using fluorescence-activated cell sorting. RNA-seq profiles of sorted cells were generated from 6 stages of differentiation. Genome guided de novo transcriptome assembly was performed using TopHat2 v2.0.11 and Cufflinks v2.2.1. Previously un-annotated lncRNAs were examined for their coding potential using TransDecoder v1. Selected un-annotated lncRNAs were validated by in situ hybridization (ISH).
We identified 586 known photoreceptor-expressed lncRNAs and 1037 previously un-annotated lncRNAs. LncRNA expression profiles revealed specific signatures and co-expression clusters during rod development, consistent with milestones of morphogenesis as observed in coding genes. In the absence of rod differentiation factor NRL, 23% (239/1037) lncRNAs demonstrated differential expression, and 33% (80/239) of these included NRL binding sites in their promoter region. Weighted correlation network analysis linked 74 un-annotated lncRNAs to proteins associated with “visual perception”, and 10 of these are putative direct targets of NRL. A number of un-annotated lncRNAs showed cell specific expression in photoreceptors and were undetceted in eight other adult mouse tissues. We prioritized un-annotated lncRNAs for validation based on expression pattern, NRL regulation, and protein co-expression. ISH analysis validated the expression of 12 lncRNAs that were selected; of these, 11 showed cell specific expression.
We identified and validated un-annotated lncRNAs expressed in the rod photoreceptors and potentially regulated by NRL. Our analysis suggests that coding and non-coding transcriptomes are under similar regulatory constraints. We also propose possible roles of lncRNAs by relating them to genes of known function and to developmental milestones. Our study provides the framework for deciphering the function of lncRNAs during photoreceptor development.
This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.
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