Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles.

Olga A Postnikova,Vladimir N Babenko,German Nudelman,William Samuel,T Michael Redmond,Eugenia Poliakov,Igor B Rogozin

doi:10.3390/genes10030205

Abstract

Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina. We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment. We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.

Highlights

Long non-coding RNAs are transcripts that do not encode proteins and are longer than 200 nucleotides
The low number of conserved long non-coding RNAs (lncRNAs) we found is in good agreement with current research [44,45], a greater level of conservation is expected between primates where there are important evolutionary advances such as the macular region of the primate retina
12 out of 700 studied lncRNAs are evolutionary conserved and differentially expressed in retinal pigment epithelium (RPE), this suggests that less than 5% of lncRNA genes are conserved in RPE in the human–bovine comparison

Summary

Introduction

Long non-coding RNAs (lncRNA) are transcripts that do not encode proteins and are longer than 200 nucleotides. According to GENCODEv7, the human genome has 9277 manually annotated lncRNA genes producing 14,880 transcripts [1]. LncRNAs are transcribed by polymerase II and can be polyadenylated and spliced, just as protein coding transcripts. It has been demonstrated that lncRNAs are more tissue-specific and are expressed, on average, approximately 10 times less compared to protein coding mRNAs [2]. The idea that most lncRNAs are by-products of background transcription, and “ the noise emitted by a busy machine” [10,11], may be due to the low abundance and poor evolutionary conservation of many lncRNAs compared to protein-coding sequences and small RNAs (e.g., miRNAs and snoRNAs) [12]. Some lncRNAs have strongly conserved regions [13]

Methods

Results

Conclusion