RNA-Seq of CD8+ T cells expressing different levels of Runx3 in during LCMV infection (in vivo). RNA-Seq of CD8+ T cells expressing different levels of Runx3 in during LCMV infection (in vivo)

T cell receptor (TCR) stimulation of naïve CD8+ T cells initiates reprogramming of cis-regulatory landscapes that specify effector and memory cytotoxic T lymphocyte (CTL) differentiation. We mapped regions of hyper-accessible chromatin in naïve cells during TCR stimulation and discovered that the transcription factor (TF) Runx3 controls de novo access to memory CTL-specific cistromes prior to the first cell division, and is essential for memory CTL differentiation. Runx3 specifically promotes accessibility of cis-acting regions highly enriched with IRF, bZIP and Prdm1-like family TF motifs, upregulates IRF4 and establishes feed-forward transcriptional circuits that induce fundamental CTL attributes in memory precursor cells. Runx3 drives uncoupling from the naïve cell state, but subsequently restrains terminal differentiation of nascent CTL by preventing high expression of the TF T-bet and slowing effector cell proliferation. Enforced Runx3 expression enhances memory CTL differentiation and increases their numbers during iterative infections. Thus, Runx3 functions in a pioneering role to initialize and then ensure memory CTL differentiate. Overall design: 20 samples, 2 replicates each

初始CD8+ T细胞的T细胞受体（T cell receptor, TCR）刺激可启动顺式调控景观的重编程，该景观决定了效应性与记忆性细胞毒性T淋巴细胞（cytotoxic T lymphocyte, CTL）的分化方向。我们绘制了T细胞刺激过程中初始细胞内染色质高开放区域的图谱，发现转录因子（transcription factor, TF）Runx3可在首次细胞分裂前，介导记忆性CTL特异性顺式调控组的从头开放，且对于记忆性CTL的分化至关重要。Runx3可特异性促进富含IRF、bZIP及Prdm1样家族转录因子基序的顺式作用区域的开放，上调IRF4的表达，并构建前馈转录环路，在记忆前体细胞中诱导CTL的核心功能特征。Runx3可推动细胞脱离初始细胞状态，但随后通过抑制转录因子T-bet的高表达、减缓效应细胞增殖，来抑制新生CTL的终末分化。强制过表达Runx3可增强记忆性CTL的分化能力，并在反复感染过程中增加其细胞数量。综上，Runx3发挥先驱功能，先启动并后续保障记忆性CTL的分化。实验总体设计：共20个样本，每组设置2个生物学重复。