Thrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relationship between cis-regulatory activity and chromatin architecture. We show that TPO profoundly alters the transcriptome of HSPCs, with key hematopoietic regulators being transcriptionally repressed within 30 min of TPO. By examining cis-regulatory dynamics and chromatin architectures, we demonstrate that these changes are accompanied by rapid and extensive epigenome remodeling of cis-regulatory landscapes that is spatially coordinated within topologically associating domains (TADs). Moreover, TPO-responsive enhancers are spatially clustered and engage in preferential homotypic intra- and inter-TAD interactions that are largely refractory to TPO signaling. By further examining the link between cis-regulatory dynamics and chromatin looping, we show that rapid modulation of cis-regulatory activity is largely independent of chromatin looping dynamics. Finally, we show that, although activated and repressed cis-regulatory elements share remarkably similar DNA sequence compositions, transcription factor binding patterns accurately predict rapid cis-regulatory responses to TPO.

血小板生成素（TPO）是调节造血干细胞维持和分化为巨核细胞谱系的关键细胞因子。然而，人们对 TPO 信号传导引发的转录和染色质动力学知之甚少。在这里，我们研究了造血干/祖细胞 (HSPC) 中对 TPO 的即时早期转录和顺式调节反应，并使用这种细胞因子信号传导到染色质的范例来剖析顺式调节活性和染色质结构之间的关系。我们发现，TPO 深刻地改变了 HSPC 的转录组，关键的造血调节因子在 TPO 的 30 分钟内被转录抑制。通过检查顺式调节动力学和染色质结构，我们证明这些变化伴随着顺式调节景观的快速和广泛的表观基因组重塑，该景观在拓扑关联域（TAD）内空间协调。此外，TPO 响应增强子在空间上聚集，并优先参与 TAD 内和 TAD 间的同型相互作用，而这些相互作用在很大程度上对 TPO 信号传导是无效的。通过进一步检查顺式调节动力学和染色质环化之间的联系，我们发现顺式调节活性的快速调节在很大程度上独立于染色质环化动力学。最后，我们表明，尽管激活和抑制的顺式调节元件具有非常相似的 DNA 序列组成，但转录因子结合模式准确预测对 TPO 的快速顺式调节反应。