Purchase this article with an account.
Jianhuan Chen, Haoyu Chen, Shaofen Huang, Mingzhi Zhang, Chi Pui Pang; Identification of A-to-I editing sites from RNA-Seq data of mouse retina. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):5498.
Download citation file:
© ARVO (1962-2015); The Authors (2016-present)
RNA editing is the post-transcriptional modification of RNA nucleotides. The most common type of editing in mammals is deamination of Adenosine (A) into Inosine (I). We used RNA sequencing (RNA-Seq) to study the A-to-I RNA editing in the mouse retina.
Total RNA was extracted from the whole retina of 3 eyes from C56BL/6 mice, and used to construct library using the polyA method. RNA-Seq was performed on the Illumina HiSeq 2000 platform with configuration of 20 million 100 bp pair-end reads per sample. Reads were aligned to the mouse full genome (UCSC version mm10) using Bowtie and splice junctions were identified by using TopHat2. Variants were called using Samtools and VarScan. We focused on known A-to-I editing sites, and potential editing sites was identified using annotation from RADAR database, and were filtered against dbSNP to remove polymorphisms. Sites with editing level ≥ 1% in all three samples were kept. Analysis of gene ontology (GO) enrichment and KEGG pathway was performed using DAVID bioinformatics resources. Gene network was constructed using GeneMANIA.
In total 28 A-to-I editing sites in 19 protein-encoding genes were identified from the RNA-Seq data. Among these genes, five genes (26.3%) including Rpa1, Psma3, Gria2, Ebna1bp2 and Uvssa were found to have more than one editing sites in the same transcript. Three (15.8%) of these edited genes including Wdr31, Gria2 and Snhg11 had tissue-specific expression in the retina according to the DAVID annotation. GO analysis showed that gene network of the protein coding genes with RNA editing was mainly involved in vesicle-mediated transport and response to light stimulus.
In the current study, RNA-Seq analysis identified A-to-I RNA-editing in the mouse retina. Our results warrantied further study on the potential role of RNA-editing in the retina and related eye-diseases.
This PDF is available to Subscribers Only