Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of “chromatin hubs”—they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chromatin hubs throughout differentiation. A subset of elements bound by MYOD1 in myoblasts exhibit early opening in a PBX1- and MEIS1-dependent manner. Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale.

将调节性DNA元件与其靶基因（可能相距几百个碱基）相联系，仍然具有挑战性。在这里，我们介绍Cicero，一种使用单细胞染色质可访问性数据识别可共访问的DNA元素对的算法，然后将调控元素连接到其推定的靶基因。我们应用西塞罗来调查动态可访问元素如何协调分化成肌细胞的基因调控。与Cicero连接的调节元件组符合“染色质中心”的标准-它们在物理上接近而富集，与一组常见的转录因子相互作用，并经历了可预测基因表达变化的组蛋白标记的协同变化。伪时态分析表明，大多数DNA元素在整个分化过程中都保留在染色质集线器中。成肌细胞中MYOD1结合的元素的子集表现出以PBX1和MEIS1依赖的方式提前开放。我们的策略可用于剖析结构，序列决定因素和机制全基因组范围内的顺式调节。