Single-cell analysis of HIV expression and integration sites reveals robust viral expression across diverse chromatin environments

Entry of HIV into latency is likely determined by a combination of factors, including stochastic fluctuations in the viral Tat protein during infection, as well as the transcriptomic phenotype of the host cell. Determining the impact of the proviral integration site on viral expression and latency has been challenging, in part due to difficulty in measuring the integration site and viral expression from the same cell. To investigate the influence of the HIV integration site on HIV expression, we analyzed a combined scRNA-seq/scATAC-seq data set from 117,610 HIV-infected primary CD4 T cells. We used the scATAC-seq data to recover HIV integration site information from 1,530 cells and correlated this information with viral RNA reads in the scRNA-seq data. We observed that, overall, HIV expression did not differ, depending on the genomic features of viral integration, such as genic vs non-genic, intron vs exon, and forward vs reverse orientation. Furthermore, we found that there was no significant difference in HIV expression across 15 distinct chromatin compartments. Additionally, single-cell expression analysis of HIV integration target genes revealed frequent (~5% of infections) insertional activation of host cell gene expression by HIV. This insertional activation occurred almost exclusively when HIV was integrated in the same orientation as the host cell gene and occurred as a result of integration within diverse positions across a gene body. These findings suggest that, overall, HIV expression is relatively robust to the genomic context of the HIV integration site and that HIV frequently upregulates expression of integration site genes during infection. IMPORTANCE: HIV integrates into the host genome during viral replication. In this study, we examine the impact of the integration site on HIV expression. We find that HIV expression is largely robust to variation in the genomic location of integration. We also find that HIV integration can often dramatically upregulate expression of host genes that HIV integrates into. Insertional activation of host cell genes could have important implications for HIV persistence during therapy and for pathogenesis. These findings provide new insight into how the virus HIV and the host cell interact and affect each other during viral replication.