Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus.

Setu Chakraborty,Matthew L Rise,Rune Andreassen,Javier Santander,Tina Visnovska,Nardos T Woldemariam,Danny Boyce

doi:10.3390/biology11010130

Abstract

Simple SummaryLumpfish (Cyclopterus lumpus) is an emergent aquaculture species, and its miRNA repertoire is still unknown. miRNAs are critical post-transcriptional modulators of teleost gene expression. Therefore, a lumpfish reference miRNAome was characterized by small RNA sequencing and miRDeep analysis of samples from different organs and developmental stages. The resulting miRNAome, an essential reference for future expression analyses, consists of 443 unique mature miRNAs from 391 conserved and eight novel miRNA genes. Enrichment of specific miRNAs in particular organs and developmental stages indicates that some conserved lumpfish miRNAs regulate organ and developmental stage-specific functions reported in other teleosts.MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies.

Highlights

The discovery of microRNAs in 1993 in Caenorhabditis elegans and further identification in humans and many other animals significantly alters the longstanding dogmas that defined gene regulation [1]
Small RNA libraries were successfully generated for 16 samples
Together this resulted in a miRNAome consisting of 443 unique mature miRNAs that were used as lumpfish miRNA reference for analysis of high-throughput sequencing (HTS) data and primer design (RT-qPCR analysis) of single miRNAs

Summary

Introduction

The discovery of microRNAs (miRNAs) in 1993 in Caenorhabditis elegans and further identification in humans and many other animals significantly alters the longstanding dogmas that defined gene regulation [1]. These studies revealed that miRNAs were a class of small noncoding RNAs that function as guide molecules in RNA silencing machinery, often termed the RNA-induced silencing complex (RISC). RISC regulates gene expression at the messenger RNA level either by degrading mRNAs targeted by the miRNAs or preventing their translation [1–3]. Functional studies indicate that miRNAs have diverse expression patterns and regulate almost every cellular process, including developmental, physiological, and pathophysiological processes [3,5,6].

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