A nanopore-based HIV-1 reference epitranscriptome

Post-transcriptional modifications to RNA, which comprise the epitranscriptome, play important roles in RNA metabolism, gene regulation, and disease pathogenesis. However, mapping modifications and characterizing their function is often challenged by a lack of consensus on their presence and significance. The availability of reference epitranscriptomes to benchmark data would significantly advance epitranscriptomic studies. Toward this goal, we established a reference epitranscriptome for human immunodeficiency virus 1 (HIV-1), an important human pathogen. We sequenced a model HIV-1 genome from infected T cells using the latest nanopore technology. A sense and novel preliminary antisense HIV-1 epitranscriptome were generated, where N6-methyladenosine, 5-methylcytidine, pseudouridine, inosine, and 2'-O-methyl modifications were mapped by multiplexed base calling at nucleotide resolution. Modification miscalling due to sequence and modification context was corrected with synthetic RNA fragments, and m6A was validated with an inhibitor. Modifications were consistent under combination antiretroviral therapy treatment, in primary CD4+ T cells, and in HIV-1 virions. In contrast, spliced transcript-dependent modification levels were observed. Sequencing samples from people living with HIV revealed substantial conservation of m6A in circulating strains. Our approach offers a benchmark reference to advance HIV-1 epitranscriptomics and provides a roadmap for the creation of reference epitranscriptomes for other viruses or pathogens.