Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1
Qian Peng,
Jialu Qiao,
Weiling Li,
Qiang You,
Song Hu,
Yuchen Liu,
Wei Liu,
Kanghong Hu,
Binlian Sun
Affiliations
Qian Peng
Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China; Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Jialu Qiao
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China; Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
Weiling Li
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Qiang You
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Song Hu
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Yuchen Liu
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Wei Liu
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
Kanghong Hu
Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China; Corresponding author.
Binlian Sun
Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China; Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China; Corresponding author.Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China.
N6-methyladenosine (m6A) methylation of human immunodeficiency virus type 1 (HIV-1) RNA regulates viral replication, and the m6A of host RNA is affected by HIV-1 infection, but its global pattern and function are still unclear. In this study, we report that the number and position of m6A peaks in huge genes of human microglial HMC3 cells were modulated by a single cycle HIV-1 pseudotyped with VSV-G envelope glycoprotein infection using methylated RNA immunoprecipitation sequencing (MeRIP-seq). A conjoint analysis of MeRIP-seq and high-throughput sequencing for mRNA (RNA-seq) explored four groups of clearly classified genes, including 45 hyper-up (m6A-mRNA), 45 hyper-down, 120 hypo-up, and 54 hypo-down genes, in HIV-1 infected cells compared to uninfected ones. KEGG pathway analysis showed that these genes were mainly enriched in the Wnt and TNF signaling pathway, and cytokine–cytokine receptor interaction, which might be related to the immune response in HMC3 cells. And some of these genes might be associated with the pathway of axon guidance and neuroactive ligan-receptor interaction, which affect the neuronal state. However, the cognitive disorders caused by HIV-1 is associated with inflammatory changes that have not yet been well clarified. Furthermore, we confirmed the expression and m6A levels of four genes using RT-PCR and MeRIP-qPCR. Similar to the sequencing results, the expressions of these genes were significantly upregulated by HIV-1 infection. And the m6A level of IL-6 was downregulated, and those of HLA-B, CFB, and OLR1 were upregulated. These results suggest that HIV-1-induced changes in gene expression may be achieved through the regulation of methylation. Our study revealed the global m6A methylation and gene expression patterns under HIV-1 infection in human microglia, which might provide clues for understanding the interaction between HIV-1 and host cells and the cognitive disorders caused by HIV-1.
