Screening, identification and functional analysis of differential expression genes in rat visual cortex after monocular deprivation by RNA-Seq technique

To screen differentially expressed genes (DEGs) in rat visual cortex after monocular deprivation by RNA sequencing technology, and to analyze the function of the DEGs.

Methods

Eighteen 14-day-old SD rats were randomly divided into blank control group and monocular deprivation model group according to random number table method, with 9 rats in each group.The monocular deprivation model was established through lid suture of the right eye for 14 days.Patten visual evoked potential (PVEP) in the right eyes of the rats was recorded before and 14 days after modeling, respectively.Bilateral visual cortex tissues of the rats were dissected from the two groups, and specific genes associated with the pathogenesis of amblyopia were screened out for RNA-seq analysis.The biological functions of differentially expressed genes were evaluated by Gene Ontology (GO) enrichment analysis, and metabolic pathways involved were analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.The use and care of the animals complied with ARVO statement.This study protocol was approved by an Ethics Committee of Gansu University of Chinese Medicine (No.2016-58).

Results

Compared with blank control group, the latency of P₁₀₀ wave was significantly prolonged, and the amplitude was reduced in the eyes of monocular deprivation model group (both at P<0.05). Forty DEGs in the left visual cortex and 63 DEGs in the right visual cortex were determined, among which 9 genes were overlapped.GO analysis indicated that the DEGs were mainly involved in biological processes, such as DNA-templated transcription, glutamate secretion, transcriptional regulation of RNA polymerase Ⅱ promoter, protein phosphorylation etc., as well as molecular functions, such as DNA binding, ATP binding, protein serine/threonine kinase activity, calcium ion binding, zinc ion binding, phospholipase A₂ activity, nucleic acid binding and cell components involved in the formation of intracellular and membrane of endoplasmic reticulum.The abnormal expressions of Grm2 and Pla2g2a genes might be closely associated with visual function impairment.Grm2 gene was mainly involved in visual signaling pathway processes including glutamate synapse, long-term potentiation (LTP), long-term depression (LTD) etc.Pla2g2a gene was mainly involved in α-linolenic acid metabolism and arachidonic acid pathway.

Conclusions

There are abnormal expressions of genes in the bilateral visual cortices of monocular deprivation rats in the sensitive period of visual development, mainly leading to the disorder of visual signal transduction pathway.Metabolic pathway changes based on specific response gene regulation may be one of the important molecular biological mechanisms in the pathogenesis of amblyopia.

RNA-Seq; Models, animal/rats; Evoked potentials, visual/pattern; Form-eprivation; Bioinformatics