DNA methylation of CiRIG-I gene notably relates to the resistance against GCRV and negatively-regulates mRNA expression in grass carp, Ctenopharyngodon idella

Retinoic acid-inducible gene I (RIG-I), a crucial member of cytoplasmic pattern recognition receptors (PRRs), is initially characterized as a dsRNA-binding protein triggering interferon (IFN) induction in response to virus invasion. While the antiviral regulatory mechanism of RIG-I remains largely unclear. In this study, the mechanism of CiRIG-I (Ctenopharyngodon idella RIG-I) against grass carp reovirus (GCRV) would be revealed from the perspective of epigenetics. By prediction, three CpG islands (CGIs) were located in 5′-flanking region and the first exon. The first CGI and the second one, both located in the 5′-flanking region, were 109 base pairs (bp) and 134 bp in length, involving five CpG sites and four loci, respectively. The third CGI was of 386 bp spanning the 5′-flanking region and the first exon, densely possessing 24 CpG sites. DNA methylation statuses of CpG sites were identified by virtue of the bisulfite sequencing PCR (BSP) in spleen of all susceptible and resistant individuals post the challenge experiment. The resistance association analysis was performed with Chi-square test. And the relationship between DNA methylation and gene expression in CiRIG-I was investigated by quantitative real-time RT-PCR (qRT-PCR). Results indicated only the methylation of -534 CpG site in the second CGI possessing tight association with the resistance against GCRV, which was significantly higher in the susceptible individuals than that in the resistant individuals. In addition, the average expression of CiRIG-I was down-regulated in the susceptible group compared with the resistant one demonstrating gene transcription may be negatively-regulated by DNA methylation in CiRIG-I. Collectively, the methylation statuses of CiRIG-I were extremely related to the resistance against GCRV and maybe serve as a negative modulator on antiviral transcription of CiRIG-I. This study revealed the underlying antiviral regulatory mechanism of CiRIG-I and laid a theoretical foundation for the nosogenesis of hemorragic diseases in C. idella.