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

Entry of HIV into latency is determined by a combination of factors, including fluctuations in the viral Tat protein, as well as the transcriptomic phenotype of the host cell. Determining the impact of the proviral integration site on viral expression has been challenging due to difficulty in measuring 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 scRNAseq/scATACseq dataset from 117,610 HIV infected primary CD4 T cells. We used the scATACseq data to recover HIV integration site information from 1530 cells, and correlated this information with viral RNA reads in the scRNAseq 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 versus reverse orientation. Furthermore, we found that there was no significant difference in HIV expression across 15 distinct chromatin compartments. Additionally, analysis of expression for host genes that were the target of proviral integration revealed strong upregulation of expression of the targeted host gene in ∼5% of the infected cells. 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. These findings suggest that HIV expression is relatively robust to the genomic context of the HIV integration site, and that HIV can strongly upregulate expression of integration site genes during infection.