Discovery and Characterization of a Hidden Retroviral Enhancer by Viral DNA-capture-seq Approach

Abstract Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that causes a cancer of infected cells called adult T-cell leukemia (ATL). There is both sense and antisense transcription from the integrated provirus. Sense transcription tends to be suppressed, but antisense transcription is constitutively active in vivo even in proviruses lacking the 5’ long terminal repeat (LTR), a known viral enhancer and promoter. Various efforts have been made to elucidate the regulatory mechanism of HTLV-1 provirus for several decades; however, it remains unknown how HTLV-1 antisense transcription is maintained. Here, using proviral DNA-capture followed by high-throughput sequencing, we found a previously unidentified viral enhancer not in the LTR but in the middle of the HTLV-1 provirus. The host transcription factors, SRF and ELK-1, bind to this enhancer region both in cell lines and in freshly isolated ATL cells. HTLV-1 containing mutations in the SRF- and ELK-1-binding sites markedly decreased chromatin openness at the viral enhancer, viral gene transcription, and enhancing effects on host gene transcription near the viral integration site. Aberrant host genome transcription was observed at nearby integration sites in defective proviruses containing the enhancer in ATL cells. This finding reveals how the exogenous retrovirus achieves persistent infection in the host via the internal viral enhancer and resolves certain long-standing questions concerning HTLV-1 infection. We anticipate that the DNA-capture-seq approach can be applied to analyze regulatory mechanisms of other oncogenic viruses integrated into the host cellular genome.