Quantitative limits of host-driven HIV transcription and host gene control by the viral transactivator Tat

HIV transcription is amplified by the viral transactivator Tat, yet two quantitative issues remain unresolved in chromatin: the extent to which host machinery sustains transcription in the absence of Tat, and why Tat's widespread chromatin association yields limited host-gene output. We engineered an isogenic Tat-deficient derivative of the HIVGKO dual-reporter virus that preserves native proviral architecture, enabling longitudinal measurements across diverse integration sites in primary CD4⁺ T cells and Jurkat cells. Across thousands of proviruses, host factors alone supported a restricted baseline, with Tat-null proviruses producing ∼4%-15% of wild-type protein output and remaining constrained under strong stimulation. Chromatin immunoprecipitation-seq profiling revealed that Tat is dispensable for promoter-proximal RNAPII engagement and pausing but required for efficient CDK9 recruitment, Ser2 phosphorylation, and productive elongation, defining a ceiling for Tat-independent transcription. Tat deficiency reduced overall RNAPII occupancy without increased promoter-proximal accumulation. Genome-wide mapping using Tat-null controls revealed broad Tat association with active host loci and modest increases in elongation-factor occupancy; however, host-gene RNA gains were small (∼1.05-1.49×) and poorly correlated with Tat binding. Instead, elongation-associated chromatin features better predicted responsiveness. Together, these findings define a framework separating host-driven transcription from Tat-dependent scaling and explain Tat's disproportionate potency at the provirus.