SIVagm coevolution leads to altered epigenetic control of CD4 expression [Bisulfite-seq]

African green monkeys (AGMs) are natural hosts of Simian immunodeficiency virus (SIV) that post-thymically down-regulate CD4 to maintain a large population of CD4-CD8aa+ virus-resistant cells with T-helper functionality. AGMs can become aviremic and seemingly cured of SIV by down-regulating CD4 in all CD4+ T cells in vivo. To understand the mechanisms of this process we performed genome-wide transcriptional analysis on T cells induced to down-regulate CD4 in vitro from AGMs and closely-related Patas monkeys, and T cells that maintain CD4 expression from rhesus macaques. In cells that down-regulated CD4, pathway analysis of genes common to AGM and Patas natural hosts yet unique from divided rhesus CD4+ T cells revealed an atypical regulation of the DNA methylation machinery, which de-repressed CD4 expression when pharmacologically targeted with 5-aza-2 deoxycytidine. This signature was driven largely by the dioxygenase TET3 that became down-regulated with loss of CD4 expression. CpG motifs within the AGM CD4 promoter region became methylated during CD4 downregulation in vitro and were stably imprinted in AGM CD4-CD8aa+ T cells sorted directly ex vivo. These results suggest AGMs employ epigenetic mechanisms to durably silence the CD4 gene. Manipulation of these mechanisms could provide avenues for modulating SIV and human immunodeficiency virus (HIV)-1 entry receptor expression in hosts that become progressively SIV-infected, which could lead to novel therapeutic interventions aimed to reduce HIV viremia in vivo. Overall design: Examination of CpG methylation frequency of CD4 gene regulatory regions in sorted CD4+, CD4-CD8aa+, and CD4-CD8ab+ AGM T cells. Cryopreserved splenocytes were flow-sorted directly ex vivo for canonical CD4+ T cells, CD4-CD8aa+ T cells, and classical CD4-CD8ab+ T cells. The IDs in the "title" column specify African green for "AG" followed by the animal ID and corresponding T cell population sorted.