Chronic infection with human immunodeficiency virus (HIV)-1 is characterized by accumulation of proviral sequences in the genome of target cells. Integration of viral DNA in patients on long-term antiretroviral therapy selectively persists at preferential loci, suggesting site-specific crosstalk of viral sequences and human genes. This crosstalk likely contributes to chronic HIV disease through modulation of host immune pathways and emergence of clonal infected cell populations. To systematically interrogate such effects, we undertook genome engineering to generate Jurkat cell models that replicate integration of HIV-1 long terminal repeat (LTR) sequences at the BTB and CNC Homolog 2 (BACH2) integration locus. This locus is a prominent HIV-1 integration gene in chronic infection, found in 30 % of long-term treated patients with mapped proviral integrations. Using five clonal models carrying an LTR-driven reporter at different BACH2 intergenic regions, we here show that LTR transcriptional activity is repressed in BACH2 regions associated with proviral-DNA integrations in vivo but not in a control region. Our data indicates that this repression is in part epigenetically regulated, particularly through DNA methylation. Importantly, we demonstrate that transcriptional activity of the LTR is independent of BACH2 gene transcription and vice versa in our models. This suggests no transcriptional interference of endogenous and HIV-1 promoters. Taken together, our study provides first insights into how activity of HIV-1 LTR sequences is regulated at the BACH2 locus as prominent example for a recurrently-detected integration gene in chronic infection. Given the importance of integration-site dependent virus/host crosstalk for chronic HIV disease, our findings for the BACH2 locus have potential implications for future therapeutic strategies.

人类免疫缺陷病毒 (HIV)-1 慢性感染的特征是靶细胞基因组中前病毒序列的积累。长期抗逆转录病毒治疗患者中病毒 DNA 的整合选择性地持续存在于优先位点，表明病毒序列和人类基因的位点特异性串扰。这种串扰可能通过调节宿主免疫途径和克隆感染细胞群的出现导致慢性 HIV 疾病。为了系统地研究这种影响，我们进行了基因组工程以生成 Jurkat 细胞模型，该模型复制了 HIV-1 长末端重复 (LTR) 序列在B TB和C NC H处的整合。omolog 2 (BACH2) 整合基因座。这个基因座是慢性感染中一个突出的 HIV-1 整合基因，在 30% 的长期治疗患者中发现了前病毒整合。使用在不同 BACH2 基因间区域携带 LTR 驱动报告基因的五个克隆模型，我们在此显示 LTR 转录活性在与体内前病毒 DNA 整合相关的 BACH2 区域中受到抑制，但在控制区域中没有。我们的数据表明，这种抑制部分受到表观遗传调控，特别是通过 DNA 甲基化。重要的是，我们证明 LTR 的转录活性独立于 BACH2 基因转录，反之亦然在我们的模型中。这表明内源性和 HIV-1 启动子没有转录干扰。总之，我们的研究提供了关于 HIV-1 LTR 序列的活性如何在 BACH2 基因座上被调节的第一个见解，作为在慢性感染中反复检测到的整合基因的突出例子。鉴于整合位点依赖性病毒/宿主串扰对慢性 HIV 疾病的重要性，我们对 BACH2 基因座的发现对未来的治疗策略具有潜在意义。