Upstream Stimulatory Factors regulate HIV-1 latency and are required for robust T cell activation

Abstract

RBF-2, composed minimally of the factors USF1, USF2, and TFII-I, is the cognate binding complex of stringently conserved cis-elements on the HIV-1 LTR, designated RBE3 and RBE1. Mutations of these elements prevent induction of provirus in response to T cell signaling. However, the function of USF1 and USF2 for this effect are relatively uncharacterized. Here, we find that deletion of the USF2 but not USF1 gene in T cells abrogates HIV-1 expression. Loss of USF2 caused a reduction in expression of USF1 protein, an effect that was not associated with decreased USF1 mRNA abundance. USF1 and USF2 were previously shown to exist predominately as heterodimers on DNA in vivo and cooperatively regulate target genes. To examine this, we performed RNA-seq analysis of T cell lines bearing knockouts of genes encoding these factors. In untreated cells we found limited evidence of coordinated global gene regulation between USF1 and USF2. In contrast we observed a high degree of genome-wide cooperative regulation of RNA expression between these factors in cells stimulated with the combination of PMA and ionomycin. In particular, we found that USF1 deletion resulted in a restricted T cell activation response, and this phenotype was exaggerated in USF2 knockout cells. These observations indicate that USF2, but not USF1, is crucial for HIV-1 expression, but the combined function of these factors is required for full T cell response.