Lineage-specific and non-specific cytokine-sensing genes respond differentially to the master regulator STAT5. Mus musculus

STAT5, a member of the family of Signal Transducers and Activators of Transcription senses cytokines and controls the biology of cell lineages, including mammary, liver and T cells. Here we show that STAT5 activates lineage-specific and widely expressed genes through different mechanisms. STAT5 preferentially binds to promoter sequences of cytokine-responsive genes expressed across cell types and to putative enhancers of lineage-specific genes. While chromatin accessibility of STAT5-based enhancers was dependent on cytokine exposure, STAT5-responsive promoters of widely expressed target genes were generally constitutively accessible. While the contribution of STAT5 to enhancers is well established, its role on promoters is poorly understood. To address this we focused on Socs2, a widely expressed cytokine-sensing gene. Upon deletion of the STAT5 response elements from the Socs2 promoter, cytokine induction was abrogated, while basal activity remained intact. Our data suggest that promoter-bound STAT5 modulates cytokine responses and enhancer-bound STAT5 is mandatory for gene activation. Overall design: ChIP-seq for STAT5, GR, H3K27ac and Dnase-seq in mammary tissues from wild-type (WT) and Socs2-Δs (Mut) at pregancy day 13 (p13), lactation day 1 (L1) and involution day 1 (I1). mRNA-seq in WT and Socs2-Δs mammary gland at mid-pregancy (p13).

STAT5作为信号转导与转录激活因子（Signal Transducers and Activators of Transcription, STAT）家族成员，可感知细胞因子并调控乳腺、肝脏及T细胞等多种细胞谱系的生物学过程。本研究揭示，STAT5可通过不同机制激活谱系特异性基因与广泛表达基因：STAT5优先结合跨细胞类型均表达的细胞因子应答基因的启动子序列，以及谱系特异性基因的潜在增强子区域。尽管STAT5依赖的增强子的染色质开放性依赖于细胞因子刺激，但广泛表达靶基因的STAT5应答启动子通常呈组成型开放状态。目前学界已明确STAT5对增强子的调控作用，但其在启动子层面的功能却鲜有研究。为解答这一科学问题，本研究聚焦于广泛表达的细胞因子感知基因Socs2。实验结果显示，敲除Socs2启动子区域的STAT5应答元件后，细胞因子诱导的基因表达被完全阻断，而基础转录活性则保持完好。本研究数据表明，结合于启动子的STAT5可调控细胞因子应答反应，而结合于增强子的STAT5则是基因激活所必需的。
实验整体设计：在妊娠第13天（p13）、泌乳第1天（L1）以及乳腺退化第1天（I1）的野生型（WT）与Socs2-Δs（Mut）小鼠乳腺组织中，开展STAT5、糖皮质激素受体（Glucocorticoid Receptor, GR）、组蛋白H3K27乙酰化（H3K27ac）的染色质免疫共沉淀测序（ChIP-seq）与DNase测序（Dnase-seq）；在妊娠中期（p13）的野生型与Socs2-Δs小鼠乳腺组织中开展mRNA测序（mRNA-seq）。