Next‐generation sequencing analysis of rat heart left ventricle: novel microRNAs, novel isomiRs and transmural distribution of microRNA expression

Abstract

MicroRNAs (miRNAs) have a significant role in regulating gene expression in heart disease. They can exist as isoforms (isomiRs) that are potentially (patho)physiologically important. The heterogeneity of cardiomyocyte physiology across the left ventricular wall has an important influence on heart (patho)physiology, and may well be affected by transmural miRNA expression gradients. With the aims of determining rat heart isomiR profiles and left ventricular transmural miRNA expression we investigated epi/midmyo/endocardial tissue samples using Illumina next‐generation sequencing. We detected significant quantities of 146 known rat miRNAs and 68 novel orthologs of known miRNAs. Many novel isomiRs were detected at a higher frequency than the corresponding mature sequence, and have predicted targets different from those of the corresponding canonical miRNA. We identified a novel rat miR‐1 analogue from a second miR‐1 gene and a novel rat miRNA similar to miR‐676. We also cloned and sequenced the rat miR‐486 gene. Several important cardiac intracellular signalling pathways are predicted targets of the most highly detected miRNAs. Most miRNAs are not expressed in a gradient across the ventricular wall; the exceptions include miR‐10b, miR‐21, miR‐99b and miR‐486. These findings suggest new mechanisms of cardiac gene regulation in health and disease. Funded by British Heart Foundation PG110/039/28365.