seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT. RNA from rat’s retina was extracted using the RNeasy Lipid Tissue Mini Kit. Two retinal samples were sequenced: a sample subjected to ischemia-reperfusion (IR) injury and collected 12 hours after the reperfusion (IR12) and a control sample (CTRL) subjected to a sham-procedure. 350ng of total RNA samples was used for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina). Single-end 150 bp reads were generated on a NextSeq 550 sequencer.