Identification of DNA methylation and transcriptional regulatory regions in the promoter of duck retinoic acid inducible gene I (RIG-I)

DNA methylation and single-nucleotide polymorphisms in DDX58 are associated with hand, foot and mouth disease caused by enterovirus 71

BACKGROUND

This research aimed to explore the association between the RIG-I-like receptor (RIG-I and MDA5 encoded by DDX58 and IFIH1, respectively) pathways and the risk or severity of hand, foot, and mouth disease caused by enterovirus 71 (EV71-HFMD). In this context, we explored the influence of gene methylation and polymorphism on EV71-HFMD.

METHODOLOGY/PRINCIPAL FINDINGS

60 healthy controls and 120 EV71-HFMD patients, including 60 mild EV71-HFMD and 60 severe EV71-HFMD patients, were enrolled. First, MiSeq was performed to explore the methylation of CpG islands in the DDX58 and IFIH1 promoter regions. Then, DDX58 and IFIH1 expression were detected in PBMCs using RT-qPCR. Finally, imLDR was used to detect DDX58 and IFIH1 single-nucleotide polymorphism (SNP) genotypes. Severe EV71-HFMD patients exhibited higher DDX58 promoter methylation levels than healthy controls and mild EV71-HFMD patients. DDX58 promoter methylation was significantly associated with severe HFMD, sex, vomiting, high fever, neutrophil abundance, and lymphocyte abundance. DDX58 expression levels were significantly lower in mild patients than in healthy controls and lower in severe patients than in mild patients. Binary logistic regression analysis revealed statistically significant differences in the genotype frequencies of DDX58 rs3739674 between the mild and severe groups. GeneMANIA revealed that 19 proteins displayed correlations with DDX58, including DHX58, HERC5, MAVS, RAI14, WRNIP1 and ISG15, and 19 proteins displayed correlations with IFIH1, including TKFC, IDE, MAVS, DHX58, NLRC5, TSPAN6, USP3 and DDX58.

CONCLUSIONS/SIGNIFICANCE

DDX58 expression and promoter methylation were associated with EV71 infection progression, especially in severe EV71-HFMD patients. The effect of DDX58 in EV71-HFMD is worth further attention.

Epigenetic regulation of RNA sensors: Sentinels of immune response

Living host system possess mechanisms like innate immune system to combat against inflammation, stress singling, and cancer. These mechanisms are initiated by PAMP and DAMP mediated recognition by PRR. PRR is consist of variety of nucleic acid sensors like-RNA sensors. They play crucial role in identifying exogenous and endogenous RNA molecules, which subsequently mediate pro/inflammatory cytokine, IFN and ISGs response in traumatized or tumorigenic conditions. The sensors can sensitize wide range of nucleic acid particle in term of size and structure, while each category sensors belongs subclasses with differentially expressed in cell and distinguished functioning mechanisms. They are also able to make comparison between self and non-self-nucleic acid molecules through specific mechanisms. Besides exhibiting anti-inflammatory and anti-tumorigenic responses, RNA sensors cover the broad spectrum of response mechanisms. Transcriptionally RNA sensors undergo with tight epigenetic regulations. In this review study, we will be going to discuss about the details of RNA sensors, their functional mechanisms and epi-transactional regulations.

The core promoter controls basal and inducible expression of duck retinoic acid inducible gene-I (RIG-I)

Retinoic acid inducible gene-I (RIG-I) is a cytoplasmic RNA sensor for detecting a variety of RNA viruses including influenza A viruses. Detection ultimately produces Type I interferon (IFN), which stimulates expression of interferon stimulated genes (ISGs), including RIG-I itself in a positive feedback loop. The structure and function of RIG-I is conserved across phylogeny, despite significant protein sequence divergence, however, the promoter sequences do not show the expected phylogenetic relationships and it is not known whether they are similarly regulated. We previously cloned duck RIG-I and showed it is highly induced during influenza A infection consistent with induction by the interferon produced. Here, we identified the Pekin duck RIG-I promoter and constructed promoter reporter vectors, which we transfected into duck embryonic fibroblasts or chicken DF-1 cells and tested in dual luciferase assays. We showed that activation of the Mitochondrial Antiviral Signalling (MAVS) pathway using the constitutively active N-terminal region of RIG-I or polyinosinic-polycytidylic acid (poly I:C) led to stimulation of duck RIG-I promoter activity. Using deletion constructs we showed the core promoter lies in the proximal 250 basepairs, and we identified essential cis-regulatory elements, a GC-box and an interferon-sensitive response element (ISRE), responsible for basal and inducible expression, respectively. Using mCherry-tagged interferon regulatory factors (IRFs) cloned from chickens and ducks, we show overexpression of chIRF7 induced the duck RIG-I promoter, and this required the ISRE site. Finally, we also demonstrated that overexpressed chIRF7 translocated to the nucleus, which was augmented by MAVS activation using RIG-I 2CARD. Our findings demonstrate that RIG-I expression is induced by chIRF7, in a positive regulatory loop. These studies show that the duck RIG-I promoter is appropriately regulated in chicken cells, necessary for the potential generation of transgenic chickens expressing RIG-I.