miRNA profiling of developing rat retina in the first three postnatal weeks

Abstract

Abstract The morphogenesis of the mammalian retina depends on the precise control of gene expression during development. Small non-coding RNAs, including microRNAs play profound roles in various physiological and pathological processes via their regulation of gene expression. A systematic analysis of the expression profile of small non-coding RNAs in developing Wistar rat retinal tissues was executed using IonTorrent PGM next-generation sequencing technique in order to reveal the crucial players in the early postnatal retinogenesis. Our analysis reveals extensive regulatory potential of microRNAs during retinal development. We found a group of microRNAs that show constant high abundance (rno-mir-19, rno-mir-101; rno-mir-181, rno-mir-183, rno-mir-124 and let-7) during the development process. Others are present only in the early stages (such as rno-mir-20a, rno-mir-206, rno-mir-133, rno-mir-466, rno-mir-1247, rno-mir-3582), or at later stages (rno-mir-29, rno-mir-96, rno-mir-125, rno-mir-344 or rno-mir-664). Further 37 miRNAs were detected which are differentially expressed on consecutive time-points with FDR < 0.05. Eight miRNAs changed significantly by more than 2-fold between time-points. Finally, pathway enrichment analysis has revealed 850 predicted target genes that mainly participate in lipid-, amino acid- and glycan metabolisms. P5-P7 transition revealed the importance of glutamatergic synapse and gap junction KEGG pathways. In these pathways, among significantly down-regulated miRNAs rno-mir-30c1 and 2, rno-mir-205 and rno-mir-503 were detected to target Prkx (ENSRNOG00000003696), Adcy6 (ENSRNOG00000011587), Gnai3 (ENSRNOG00000019465) and Gja1 (ENSRNOG00000000805) genes. The dataset described here will be a valuable resource for clarifying new regulatory mechanisms for retinal development and will greatly contribute to our understanding of the divergence and function of microRNAs.