GSE107496
Comprehensive analysis of hippocampal miRNAomes in humans and mice.
MicroRNAs (miRNAs) are small endogenous regulatory RNAs involved in hippocampal functions and lesions. Mouse has been regarded as an effective tool to explore the roles of miRNAs in hippocampus. Although the anatomical structure and physiological function across human and mouse hippocampi are highly conserved, the similarity and difference of hippocampal miRNAomes between the two species have not been well characterized. Our present study represents the first attempt to perform a systematic comparison of the miRNAomes between healthy human and mouse hippocampi using high-throughput sequencing followed by bioinformatic analyses. Contrasting between human and mouse hippocampal miRNAs shows a global similarity of expression pattern; however, the interspecific expression conservation of hippocampal miRNAs is positively associated with the interspecific sequence conservation. Although the type of the abundantly expressed hippocampal miRNAs is almost the same across the two species, only the enriched miRNAs in human hippocampus exhibit potential neuro-related activities. In addition, we also identified a novel miRNA and a species-specific miRNA in human hippocampus whose putative targets are associated with neuro-related activities. Collectively, our results can provide a framework to explore the ability of mice to model the physiological and pathological processes of human hippocampus and also aid in understanding the basis for higher order abilities of learning and memory at the miRNA level. Overall design: Total RNA from frozen hippocampi (7 humans and 7 mice) was purified using Trizol (Invitrogen, USA) protocol with no modifications. The concentration, purity and integrity were detected by Qubit 2.0 (Life Technologies, USA), Nanodrop (Thermo Scientific, USA), and Agilent 2100 bioanalyzer (Agilent Technologies, USA), respectively. One µg RNA was used to generate a small RNA sequencing library based on TruSeq Small RNA Sample Prep Kit version 2 (Illumina, USA) according to the manufacturer's instructions. In brief, T4 RNA ligase was used to ligate RNA 5' and 3' adaptors to 5' and 3' ends of RNA, respectively. Adapter-ligated RNA was reverse-transcribed using a RNA RT Primer and the resulting cDNA was amplified in an 11-cycle PCR that used RP1 (RNA PCR Primer) and indexed RP1 primers. PCR products of 140–160 bp were isolated following electrophoresis through a 6% Novex Tris-borate polyacrylamide gel (Life Technologies, USA). Quality of the generated small RNA sequencing library were confirmed using Agilent 2100 bioanalyzer (Agilent Technologies, USA). High-throughput sequencing was carried out based on an Illumina HiSeq2500 system.