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

## TL;DR

This study maps the RNA structure and modifications of HTLV-1 in MT2 cells, revealing new details about viral gene regulation.

## Contribution

The study provides the first detailed transcriptomic and epitranscriptomic profile of HTLV-1 in MT2 cells using direct RNA sequencing.

## Key findings

- 23 HTLV-1 transcript isoforms were identified, including novel splice variants.
- Poly(A) tail lengths varied between 50–100 nucleotides with transcript-specific differences.
- RNA modifications like pseudouridine and m6A were enriched near the 3′ end and differed among transcript classes.

## Abstract

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.