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The persistence of human immunodeficiency virus (HIV) within viral reservoirs poses significant challenges to eradication efforts. Epigenetic alterations, including DNA methylation, are potential factors influencing HIV latency and persistence. This study details the development and application of techniques to assess CpG methylation in the promoter regions of the CCR5 and CXCR4 genes, key HIV-1 coreceptors. Using both Sanger sequencing and pyrosequencing methods, we examined 51 biological samples from 17 HIV-1-infected individuals at three time points: baseline (Week 0) and post-antiretroviral therapy (ART) at Weeks 24 and 48. Our results revealed that CXCR4 promoter CpG sites were largely unmethylated, while CCR5 promoter CpGs exhibited significant variability in methylation levels. Specifically, CCR5 CpG 1 showed a significant decrease in methylation from Week 0 to Week 48, while CXCR4 CpG 3 displayed a significant decrease between Week 0 and Week 24. These differences were statistically significant when compared with non-HIV-infected controls. These findings demonstrate distinct methylation patterns between CCR5 and CXCR4 promoters in HIV-1 positive individuals over time, suggesting that epigenetic modifications may play a role in regulating HIV-1 persistence. Our techniques provide a reliable framework for assessing gene promoter methylation and could be applied to further research in HIV epigenetics.