Quantitative analysis of Tat-dependent and host-driven HIV transcription by ChIP-seq and RNA-seq

In this study, we performed integrated chromatin and transcriptional profiling to quantitatively compare Tat-dependent and host-driven regulation of HIV and cellular gene expression. Jurkat T cells were infected with isogenic HIV constructs expressing functional Tat (TatWT) or lacking Tat expression (TatNull) and analyzed under non-stimulated and stimulated conditions.

Genome-wide chromatin occupancy of Tat and transcriptional machinery was measured by ChIP-seq, and corresponding transcriptional output from both the HIV provirus and host genome was quantified by RNA sequencing. These datasets define the baseline host-driven transcriptional state of HIV in the absence of Tat and enable direct comparison with Tat-amplified transcriptional responses. Together, this integrated ChIP-seq and RNA-seq resource provides a quantitative framework for dissecting Tat-dependent and Tat-independent mechanisms of HIV transcriptional regulation in chromatin.