The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain <i>Cd4</i> silencing in cytotoxic T cells

The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the <i>Cd4</i> gene is stably repressed in CD8⁺ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for <i>Cd4</i> repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in <i>Cd4</i> silencing. When CAF-1 was lacking, <i>Cd4</i> derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the <i>Cd4</i> locus. Instead, Dnmt3a deficiency sensitized CD8⁺ T cells to <i>Cd4</i> derepression mediated by compromised functions of histone-modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the <i>Cd4</i> gene in CD8⁺ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes.