Identify The Regulatory Network Of LncRNA HAR1A In Neurological Development By RNA-Sequencing And Bioinformatics Analysis

Background:HAR1(Human accelerated region 1)is a 118 bp segment of chromosome 20 located in the two overlapping long non-coding RNA(lnc RNA)genes,HAR1 A and HAR1 B.It has been conserved through vertebrate evolution but has 18 mutations between humans and chimpanzees.Mutations of HAR1 lead to a different secondary structure of lnc RNA HAR1 A in both humans and chimps.Methods:We cloned HAR1 into the EF-1α promoter vector to make transgenic mice.Morris water maze(MWM)tests and step-down passive avoidance tests were conducted to observe the changes in memory and cognitive ability of mice.RNA-seq analysis was performed to identify the differentially expressed genes(DEGs)of the experimental and control groups.Systematic bioinformatic analysis was used to confirm the pathways and functions that the DEGs were involved in.523 human gene expression datasets were downloaded from The Cancer Genome Atlas(TCGA)for co-expression analysis to obtain the Protein-Protein Interaction Network(PPI-Net)and enrichment pathways of lnc RNA HAR1A’s co-expression genes.Results:The memory and cognitive ability of transgenic mice were both significantly improved.The results of Gene Ontology(GO)analysis showed that Neuron differentiation,Dentate gyrus development,Nervous system development,Cerebral cortex neuron differentiation,Cerebral cortex development,Cerebral cortex development and Neurogenesis are all significant GO terms related to brain development.The DEGs enriched in these terms included Lhx2,Emx2,Foxg1,Nr2e1 and Emx1.These genes all play an important role in the regulation of the functioning of Cajal–Retzius cells(CRs)."Cellular response to calcium ions" exhibited the second highest Rich factor in the(GO)analysis.The core genes in the PPI-Net were SNAP25,GRIN1,SYN1,DLG4,CAMK2 A.SNAP25,and SYN1,which are related to synaptic function,and GRIN1,DLG4,and CAMK2 A,related to synapse formation.GO and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis of DEGs and lnc RNA HAR1 A ’s co-expressed genes in humans showed that the interaction between synapses,axon guidance,synaptic signaling and ligand-receptors was significant.Conclusions:Overexpression of HAR1 lead to improvements in memory and cognitive abilities of transgene mice.The possible mechanism for this was that lnc RNA HAR1 A affected brain development by regulating the function of CRs.Moreover,lnc RNA HAR1 A may be involved in ligand-receptor interaction,axon guidance,and synapse formation,all of which are important in brain development and evolution.Furthermore,cellular response to calcium may also play an important role in those process.