Comparative analysis of small RNA expression and RNA modification profiles of home-made and commercial orange juice

Abstract

Growing investigations suggest that diet-derived exogenous extracellular small RNA can trans-kingdom move into mammalian circulation and play important roles in gene regulation. As a widely consumed fruit juice, orange juice has been reported to have many biological benefits for human health, and this may involve the function of small RNAs. The present thesis aims to study the small RNA expression and RNA modification profiles of orange juice derived from home-made fresh squeezed orange; and two types of commercial orange juice, namely the ‘concentrate orange juice’ and the ‘not form concentrate orange juice’. The small RNA-seq results has discovered various tsRNAs, rsRNAs and miRNAs in all three types of orange juice. Interestingly, when stored in 4 °C, the small RNA expression profiles of each type of orange juice remain quite stable for as long as 28 days in this study, suggesting that the small RNAs are resilient to the chemical and enzymatic environment of the juice, this could be in part, contributed by RNA modifications. Indeed, by performing a high-throughput quantitative approach based on liquid chromatography-tandem mass spectrometry (LC-MS/MS), we efficiently detected and quantified 19 types of RNA modifications in the 30-40 nt fraction RNAs extracted from orange juice, some of them shows significant changes between different type of juice, which may reflect different manufacturing procedure and composition of juice, and thus potentially their function after consumption. The RNA modifications detected may affect RNA functions by affecting RNA structure, RNA stability, and may help RNA cross- kingdom transfer into human blood circulation, or interact with the microbiome of epithelium. Our research lays a foundation for future functional and mechanistic investigations of orange juice deriving from different sources.