Non-coding RNAs in fish physiology and development : miRNAs as a cornerstone in gene networks

Abstract

Non-coding RNAs (ncRNAs) play a central role in the complex and tightly regulated processes sustaining life, from gene transcription to post-transcriptional regulation, including DNA methylation. Among the different ncRNAs, microRNAs (miRNAs) are the most extensively studied and characterized. Here, we will briefly describe their biogenesis and mechanisms of action. A broad range of methodological approaches have been applied to identify, quantify and functionally characterize miRNAs in different biological processes. Among them, high-throughput sequencing as well as the development of computational tools to predict the mRNA targets have been the most powerful approaches to determine in which biological processes miRNAs are involved and to infer the molecular pathways specifically regulated. The implementation of these methodologies in studies with different fish species have provided the first evidence of miRNAs controlling fish development, reproduction, immunocompetence, adaptation to environmental conditions and fish nutrition. Additionally, miRNAs are also potentially responsible for fish diversity. The development of different in vitro and in vivo biotechnological tools allowed researchers to go in depth and achieving their functional characterization. While an overview of all the available methodologies is here provided at a glance, the main steps of a general small RNA sequencing (RNA-Seq) protocol will be dissected as one of the most extensively used methodologies to identify and quantify miRNAs. Finally, the most recent progress on the use of these methodologies for biomarker discovery and future perspectives on the field of miRNAs will be discussed. Certainly, while knowledge gained during the last two decades increased our understanding of how miRNAs exert a key role in fish development and physiology, future efforts are needed to translate it in the use of miRNAs as more ethical and integrative biomarkers of fish physiological status and/or innovative therapies to solve important industrial bottlenecks in fish farming.

Non-coding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks