Intra-pol proviral open region of HTLV-1 controls the transcription from both long terminal repeats

Background Human T-cell leukemia virus type 1 (HTLV-1) infects mainly CD4 ⁺ T lymphocytes and causes two types of disease: the aggressive malignancy known as Adult T-cell leukemia/lymphoma (ATL) and a number of chronic inflammatory syndromes. HTLV-1 infection is established by integration of proviral DNA (~9000bp) into the host genome. In HTLV-1, two viral genes, tax and HBZ, play critical roles in viral transcription and promotion of T-cell proliferation, respectively. The present study was undertaken to test the hypothesis that the higher-order structure of proviral chromatin regulates its transcription on both the plus strand and the minus strand. Results ATAC-seq analysis identified an open chromatin region in the pol gene of proviral DNA, which we name IPOR, in many ATL cases. Using reporter assays, it was found that the sequence of IPOR suppresses the transcription of the plus strand and activates that of the minus strand. Binding motifs of Eomes and TEAD proteins were predicted in this region, and we confirmed recruitment of the transcription factors to their respective motifs by ChIP-qPCR. A mutant of IPOR which cannot bind the transcription factors weakened the transcriptional activating effects compared with the wild type, suggesting that the IPOR and those transcription factors suppress the 5' long terminal repeat (LTR) but activate the 3'LTR. In addition, a mutant HTLV-1 molecular clone, which possesses the IPOR mutant, produced a higher titer of virus than the wild type. RNA-seq analysis of HTLV-1-infected cell lines, in which Tax expression can be traced after induction, revealed that EOMES expression decreases during the tax transcriptional burst and resumes following termination of the burst. These findings suggested that the expression dynamics of Eomes affect the transient expression of Tax. Conclusions The IPOR sequence appears to regulate the transcription from both LTRs, suppressing the 5'LTR but activating the 3'LTR. We hypothesize that IPOR and the recruited transcription factors control not only viral replication but also proliferation of infected cells, which involve Tax and HBZ respectively. This strategy fine-tunes the modes of viral propagation, facilitating viral persistence in vivo .