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Lina Zelinger, Jung-Woong Kim, Hyun-Jin Yang, Matthew Brooks, Anand Swaroop; A possible role for lnc-RNA in mouse and human retina. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):2602.
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The protein-coding genome is estimated to be about 2%, yet the actual transcribed genome is much larger and includes several families of non-coding RNAs with a wide range of potential functions. The goal of this study is to examine the presence and function of long non-coding RNAs (lncRNA) in the retina.<br />
Photoreceptors were purified from Nrl-GFP and Nrl-knock out (KO)-GFP mice by fluorescence activated cell sorting. We carried out a transcriptome analysis of developing mouse retina and human retina using RNA-seq. Data annotated using the ENSMBL annotation. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was done to validate the RNA-seq results.<br />
Of 44154 non-coding transcripts identified in Nrl-GFP and Nrl-KO-GFP photoreceptors, 130 transcripts were exclusively expressed in the Nrl-KO cells. Expression pattern analysis based on six time points (postnatal days 2, 4, 6, 10, 14 and 28) showed a subset of 8 transcripts with a pattern of elevated expression after day 10. At this time point during mouse retina development, we see a significant formation of photoreceptor outer segments. The retina of Nrl-KO mouse contains only cone like photoreceptors. Hence we suspected that the 8 RNAs might have a role in the formation of cone outer segment (COS). To further establish the involvement of these RNAs in COS formation, RNA-seq data from CRX-KO mice was used. Photoreceptors of CRX-KO mice form very short or no outer segment. 5 out of the 8 transcripts show low to no expression in the CRX-KO RNA-seq data. The correlating human lncRNAs (2/5 loci) were present in the RNA-seq data obtained from human retina. One of these transcripts lies within a previously reported cone-rod dystrophy locus on chromosome 17, CORD4. We have validated the expression of both mouse and human transcripts using qRT-PCR. Additional analysis is currently on the way to shed light on the function of these lncRNAs in the retina, including their interaction with other RNA species and proteins.
Using a combination of bioinformatic tools and approaches, we have identified a small subset of lncRNAs that are predicted to be involved in COS formation. Further studies are currently underway to verify these results and define their exact role in the photoreceptors.
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