Identification of key miRNAs and genes for mouse retinal development using a linear model.

Abstract

MicroRNAs (miRNAs) are upstream regulators of gene expression and are involved in several biological processes. The purpose of the present study was to obtain a detailed spatiotemporal miRNA expression profile in mouse retina, to identify one or more miRNAs that are key to mouse retinal development and to investigate the roles and mechanisms of these miRNAs. The miRNA expression pattern of the developing mouse retina was acquired from Locked Nucleic Acid microarrays. Data were processed to identify differentially expressed miRNAs (DE-miRNAs) using the linear model in Python 3.6. Following bioinformatics analysis and reverse transcription-quantitative polymerase chain reaction validation, 8 miRNAs (miR-9-5p, miR-130a-3p, miR-92a-3p, miR-20a-5p, miR-93-5p, miR-9-3p, miR-709 and miR-124) were identified as key DE-miRNAs with low variability during mouse retinal development. Gene Ontology analysis revealed that the target genes of the DE-miRNAs were enriched in cellular metabolic processes. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that the target genes of the DE-miRNAs were significantly enriched in PI3K/AKT/mTOR, class O of forkhead box transcription factors, mitogen-activated protein kinase (MAPK), neurotrophin and transforming growth factor (TGF)-β signaling, as well as focal adhesion and the axon guidance pathway. PI3K, AKT, PTEN, MAPK1, Son of Sevenless, sphingosine-1-phosphate receptor 1, BCL-2L11, TGF-β receptor type 1/2 and integrin α (ITGA)/ITGAB, which are key components of the aforementioned pathways and were revealed to be target genes of several of the DE-miRNAs. The present study used a linear model to identify several DE-miRNAs, as well as their target genes and associated pathways, which may serve crucial roles in mouse retinal development. Therefore, the results obtained in the present study may provide the groundwork for further experiments.