Genome-wide CRISPR knockout screen identifies activating transcription factor (ATF1) as an activator of HIV gene expression

ABSTRACT Antiretroviral therapy against the human immunodeficiency virus (HIV) has significantly prolonged the life span of people living with HIV, transforming viral infection into a latent condition that is characterized with undetectable viral loads. Yet, a complete cure of infection is out of reach, as transcriptionally silent but replication-competent proviruses persist in a long-lived reservoir that is resistant to therapy. The current work follows a genome-wide CRISPR knockout screen in human CD4+ T cells and defines the activating transcription factor 1 (ATF1) as an activator of HIV gene transcription with elevated expression levels in cells that carry transcriptionally active provirus. Additional gain and loss-of-function experiments show that depletion of ATF1 promotes latency. ATF1 directly occupies the HIV promoter, where it regulates the recruitment of RNA Polymerase II and the levels of H3K9me3 histone repression mark. Genome-wide, ATF1 binds cellular gene promoters. Among its targets, ATF1 modulates the levels of CCR5 antisense lncRNA, thereby regulating the protein expression of the CCR5 HIV co-receptor. We conclude that ATF1 is an activator of gene transcription that dictates HIV gene expression via both direct and indirect mechanisms.IMPORTANCEHIV persists in resting CD4+ primary infected cells, forming a reservoir that is resistant to therapy, and thus a main barrier toward elimination of viral infection. An understanding of the mechanisms that control HIV gene expression and drive viral latency is therefore of high clinical importance. This study identifies activating transcription factor 1 (ATF1) as an activator of HIV gene expression. ATF1 binds the HIV promoter, where it modulates the occupancy of RNA Polymerase II and the levels of H3K9me3 histone repression mark. Genome-wide, ATF1 also occupies cellular promoters. One target of ATF1 is the antisense (AS) lncRNA. Through binding to CCR5-AS lncRNA, ATF1 induces CCR5 mRNA stability, thereby indirectly controlling HIV infection. Overall, we provide an additional understanding of the host transcription pathways that regulate HIV gene expression and potentially open new ways to manipulate its reservoir size.