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

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.