Transcriptomic and Epitranscriptomic Landscape of Integrated HTLV-1 in MT2 Cells

Human T-lymphotropic virus type 1 (HTLV-1), the first human retrovirus identified, is linked to adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. However, its post-transcriptional regulation remains poorly understood. Here, we used Oxford Nanopore direct RNA sequencing to profile the HTLV-1 transcriptome and epitranscriptome in MT2 cells. We identified 23 transcript isoforms, encompassing canonical and novel splice variants. Polyadenylation analysis revealed a predominant poly(A) tail length of around 50-100 nucleotides with transcript-specific variations. Distinct RNA modifications, including pseudouridine, N⁶-methyladenosine, and 5-methylcytidine, were enriched near the 3' end and varied among transcript classes, with generally lower modification ratios in viral transcripts. These findings provide a more comprehensive map of HTLV-1 RNA splicing, polyadenylation, and modifications in MT2 cells, offering new insights into viral gene regulation and pathogenic mechanisms.