Regulatory T (Treg) cell identity is defined by the lineage-specifying transcription factor (TF) Foxp3. Here we examined mechanisms of Foxp3 function by leveraging naturally occurring genetic variation in wild-derived inbred mice, which enables the identification of DNA sequence motifs driving epigenetic features. Chromatin accessibility, TF binding, and gene expression patterns in resting and activated subsets of Treg cells, conventional CD4 T cells, and cells expressing a Foxp3 reporter null allele revealed that the majority of Foxp3-dependent changes occurred at sites not bound by Foxp3. Chromatin accessibility of these indirect Foxp3 targets depended on the presence of DNA binding motifs for other TFs, including TCF1. Foxp3 expression correlated with decreased TCF1 and reduced accessibility of TCF1-bound chromatin regions. Deleting one copy of the Tcf7 gene recapitulated Foxp3-dependent negative regulation of chromatin accessibility. Thus, Foxp3 defines Treg cell identity in a largely indirect manner by fine-tuning the activity of other major chromatin remodeling TFs such as TCF1.

调节性 T (Treg) 细胞身份由谱系特异性转录因子 (TF) Foxp3 定义。在这里，我们通过利用野生近交小鼠中自然发生的遗传变异来检查 Foxp3 功能的机制，这能够识别驱动表观遗传特征的 DNA 序列基序。Treg 细胞、传统 CD4 T 细胞和表达Foxp3 的细胞的静息和活化亚群中的染色质可及性、TF 结合和基因表达模式记者无效等位基因显示，大多数 Foxp3 依赖性变化发生在不受 Foxp3 约束的位点。这些间接 Foxp3 目标的染色质可及性取决于其他 TF（包括 TCF1）的 DNA 结合基序的存在。Foxp3 表达与降低的 TCF1 和降低的 TCF1 结合染色质区域的可及性相关。删除Tcf7基因的一个副本，重现了Foxp3 依赖性染色质可及性的负调控。因此，Foxp3 通过微调其他主要染色质重塑 TF（如 TCF1）的活性，以很大程度上间接的方式定义了 Treg 细胞身份。