Differential expression profiling of spleen microRNAs in response to two distinct type II interferons in Tetraodon nigroviridis.

Shibai Yi,Wan Peng,Danqi Lu,Haoran Lin,Ting Wang,Yong Zhang,Uwe Fischer

doi:10.1371/journal.pone.0096336

Abstract

MicroRNAs are endogenous, small non-coding RNAs approximately 18–26 nucleotides in length that regulate target gene expression at the post-transcription level. Interferon-γ (IFN-γ) is a Th1 cytokine that is involved in both the innate and adaptive immune responses. We previously identified two IFN-γ genes in green-spotted puffer fish (Tetraodon nigroviridis). To determine whether miRNAs participate in IFN-γ-related immune responses, T. nigroviridis spleen cells were treated with recombinant IFN-γ isoforms, and a Solexa high-throughput sequencing method was used to identify miRNAs. In total, 1,556, 1,538 and 1,573 miRNAs were found in the three samples, and differentially expressed miRNAs were determined. In total, 398 miRNAs were differentially expressed after rIFN-γ1 treatment, and 438 miRNAs were differentially expressed after rIFN-γ2 treatment; additionally, 403 miRNAs were differentially expressed between the treatment groups. Ten differentially expressed miRNAs were chosen for validation using qRT-PCR. Target genes for the differentially expressed miRNAs were predicted, and GO and KEGG analyses were performed. This study provides basic knowledge regarding fish IFN-γ-induced miRNAs and offers clues for further studies into the mechanisms underlying fish IFN-γ-mediated immune responses.

Highlights

MicroRNAs are small non-coding RNAs that regulate target messenger RNA expression by binding to mRNA 3’ untranslated regions (3’ UTR), resulting in mRNA cleavage or translational repression through the RNA-induced silencing complex (RISC) [1]
Two IFN-c genes were found in the channel catfish (I. punctatus) [35], common carp (Cyprinus carpio L.) [36], goldfish (Carassius aurutus L.) [37], and ginbuna crucian carp (Carassius auratus langsdorfii) [38]
Recombinant IFN-c1 and IFN-c2 from T. nigroviridis was produced as previously described [49]; rIFN-c1 and rIFN-c2 proteins at a final concentration of 10 ng/mL were added to the culture medium, and the control group (Sp-con) was treated with tissue culture medium (TCM)

Summary

Introduction

MicroRNAs (miRNAs) are small non-coding RNAs that regulate target messenger RNA (mRNA) expression by binding to mRNA 3’ untranslated regions (3’ UTR), resulting in mRNA cleavage or translational repression through the RNA-induced silencing complex (RISC) [1]. Two IFN-c genes were found in the channel catfish (I. punctatus) [35], common carp (Cyprinus carpio L.) [36], goldfish (Carassius aurutus L.) [37], and ginbuna crucian carp (Carassius auratus langsdorfii) [38]. Both isoforms are members of the type II interferon family and contain IFN-c signature motifs [30,33], but the fish-specific IFN-c1 does not contain the Cterminal nuclear translocation signal (NLS) motif required for IFN-c activity [35,39].

Methods

Results

Conclusion