A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance.

Bin Yin,Shaoping Weng,Peng Zhu,Chaozheng Li,Jianguo He,Haiyang Wang

doi:10.3389/fgene.2019.01257

Abstract

Simple sequence repeats (SSRs) of short nucleotide motifs occur very frequently in the 5′ untranslated coding region (5′-UTR) of genes and have been implicated in the regulation of gene expression. In this study, we identified an SSR with a variable number of CT repeats in the 5′-UTR of the Litopenaeus vannamei IRF (LvIRF) gene that has been shown to mediate antiviral responses by inducing the expression of Vago, a functional homolog of mammalian IFN. We then explored the effects of varying the number of (CT)n repeats on the expression of LvIRF using both dual-luciferase reporter assays and Western blots. Our results demonstrate that the length of the (CT)n-SSR in this gene can influence the expressional level of LvIRF, in that a shorter (CT)n repeat had a stronger ability to induce the expression of LvIRF. Moreover, we found that the (CT)n repeat in LvIRF was associated with viral resistance in shrimp. Individual shrimps with shorter (CT)n repeats in the 5′-UTR of LvIRF exhibited high tolerance to white spot syndrome virus (WSSV), and this trait was inherited in offspring. Taken together, these results indicated that this (CT)n-SSR could be used as a molecular marker for shrimp breeding for WSSV resistance.

Highlights

Simple sequence repeats (SSRs), known as microsatellites or short tandem repeats (STRs), are tandem repeats of short sequence motifs occurring ubiquitously in eukaryotic genomes
Litopenaeus vannamei interferon regulatory factor (IRF) (LvIRF) has been shown to bind the promoter of L. vannamei Vago4 (LvVago4) to regulate its transcription, which plays a role in the defense against white spot syndrome virus (WSSV) infection (Li et al, 2015)
Considering that the (CT)n repeat is composed of two parts, we explored whether the different numbers of the two (CT) n repeats were implicated in LvIRF expression

Summary

Introduction

Simple sequence repeats (SSRs), known as microsatellites or short tandem repeats (STRs), are tandem repeats of short sequence motifs occurring ubiquitously in eukaryotic genomes. They exhibit extensive polymorphism due to variations in the copy number of each specific repeat motif, and are considered useful as genetic markers for genetic diversity analysis, DNA fingerprinting, and linkage mapping. SSRs in UTRs have been found to be Polymorphic (CT)n-SSR Resistance to WSSV in Shrimp associated with gene expression by affecting transcription factor binding, methylation of CpG and/or DNA structure modification (Li et al, 2004). Three novel downstream elements, which show homology to GAGA factor binding sequences, can regulate promoter activity and preferentially affect transcription start site (TSS) selection at the 5′-UTR end of promoters (Lee et al, 2010)

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Conclusion