Assessing the Impact of Histone-Modifying Compounds on HIV Integration Using a Novel Long-Read Sequencing Assay

HIV integration into the host genome is a critical step in the viral life cycle that influences replication, latency, and persistence. Chromatin structure and histone modifications play key roles in integration site selection, with implications for both viral pathogenesis and therapeutic strategies. Although existing assays can map HIV integration sites, they lack the resolution and scalability needed to detect changes in integration profiles. To address this gap, we developed a novel Nanopore-compatible long-read sequencing assay that enables high-resolution integration site analysis. Using this assay, we investigated how histone-modifying compounds, including A-485 and SAHA, alter integration across chromatin regions in Jurkat cells. This approach reliably captured integration events and revealed that compound-induced changes in chromatin accessibility influence HIV integration patterns. Together, these findings highlight the utility of long-read sequencing for studying chromatin-dependent viral integration and provide insight into epigenetic regulation of HIV targeting.