Genome-wide CRISPR knockout screen identifies Activating Transcription Factor (ATF1) as an activator of HIV gene expression that restricts entry into latency

Introduction of antiretroviral therapy has limited the spread of HIV and improved clinical outcomes. Yet, a complete cure for infection remains out of reach, as in the face of therapy, a transcriptionally silent but replication-competent provirus persists in a long-lived cell reservoir. Towards identifying new host proteins that regulate HIV gene transcription and latency, we performed a genome-wide CRISPR knockout screen in human CD4+ T cells. We identified the Activating Transcription Factor as a regulator of HIV gene transcription. ATF1 is recruited to the HIV promoter and activates viral gene expression. Gain and loss of function experiments demonstrate that depletion of ATF1 expression decreases HIV gene expression and promotes latency in primary CD4+ infected T cells. Interestingly, ATF1 regulates CCR5 expression and indirectly affects R5-tropic HIV infection. Mechanistically, ATF1 depletion impairs occupancy of RNA Polymerase II on the HIV promoter, and this is accompanied with elevated levels of H3K9me3 repression histone mark around the viral promoter. Genome wide analysis of ATF1 shows that it occupies cellular gene promoters including HIV, thereby controls gene targets that indirectly affect HIV infection. We conclude that ATF1 is an activator of gene transcription that dictates HIV gene expression via both direct and indirect mechanisms. Overall design: Jurkat T cells that stabley express HA-ATF1 were subjected to CUT and RUN analysis according to the Epocipher protocol. Samples were subjected to NGS sequencing (pair end). Experiment was performed with several antibodies including: HA (abcam) and H3K4me3 (Ephchipher) and IgG as control. Replicates were performed for each antibody experiment. Libraries were generated according to the Epicipher kit