Detection and comparison of circular RNAs in mouse striatum and retina

Abstract

PurposeCircular RNAs (circRNAs) are a type of non‐coding RNAs (ncRNAs), and could be potential clinical biomarkers in complex disorders of the nervous system. Expression of circRNAs possess spatio‐temporal properties. Herein we used RNA sequencing (RNA‐Seq) to detect and compare circRNAs and their expression pattern in the mouse striatum and retina.MethodsWhole striatum and retina was collected from adult mice, and total RNA was extracted using TRIzol followed by phenol/chloroform processing. RNA‐Seq libraries were prepared from total RNA using the ribosomal RNA depletion method. RNA‐Seq was performed for three striatum and three retina samples on the Illumina HiSeq X10 platform with a configuration of 90 million 150 bp pair‐end reads per sample. Reads was aligned to the mouse full genome (UCSC version mm10) and splice junctions were identified by using RNA STAR version 2.5. circRNAs were detected and quantified using DCC version 0.4.4, and difference of circRNA expression between the striatum and retina was analyzed using CircTest. Functional analysis including gene ontology (GO) enrichment and KEGG pathway was performed using DAVID bioinformatics resources 6.8.ResultsIn total 781 circRNAs were detected and passed quality control in the striatum and retina, among which 342 showed significant expression difference between the two types of neural tissue. Among the differentially expressed circRNAs, 5 were only detected in the striatum and 29 only in the retina. Functional Annotation Clustering analysis using DAVID showed that a total of 70 host genes of differentially expressed circRNAs were enriched in K48‐linked ubiquitination and positive regulation of cell cycle, and 39 of these genes had a high expression level in the brain.ConclusionIn the current study, our results demonstrated remarkable difference in circRNA patterns between two types of neural tissue including the striatum and retina, suggesting the potential importance of circRNAs in development and differentiation of nerve system.Support or Funding InformationThe Natural Science Foundation of China (No. 31671311, 81371033 and 81000397), the “Six Talent Peak” Project of Jiangsu Province (SWYY‐127), the Guandong High‐level Personnel of Special Support Program, the Yangfan Plan of Talents, and the Fundamental Research Funds for the Central Universities (JUSRP51712B).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.