Cellular identity requires the concerted action of multiple transcription factors (TFs) bound together to enhancers of cell-type-specific genes. Despite TFs recognizing specific DNA motifs within accessible chromatin, this information is insufficient to explain how TFs select enhancers¹. Here we compared four different TF combinations that induce different cell states, analysing TF genome occupancy, chromatin accessibility, nucleosome positioning and 3D genome organization at the nucleosome resolution. We show that motif recognition on mononucleosomes can decipher only the individual binding of TFs. When bound together, TFs act cooperatively or competitively to target nucleosome arrays with defined 3D organization, displaying motifs in particular patterns. In one combination, motif directionality funnels TF combinatorial binding along chromatin loops, before infiltrating laterally to adjacent enhancers. In other combinations, TFs assemble on motif-dense and highly interconnected loop junctions, and subsequently translocate to nearby lineage-specific sites. We propose a guided-search model in which motif grammar on nucleosome fibres acts as signpost elements, directing TF combinatorial binding to enhancers.

细胞身份需要多种转录因子 （TF） 的协同作用，这些转录因子 （TF） 与细胞类型特异性基因的增强子结合在一起。尽管 TF 识别可接近染色质中的特定 DNA 基序，但此信息不足以解释 TF 如何选择增强子 ¹ 。在这里，我们比较了诱导不同细胞状态的四种不同的 TF 组合，分析了 TF 基因组占有率、染色质可及性、核小体定位和核小体分辨率下的 3D 基因组组织。我们表明单核小体上的基序识别只能破译 TFs 的单个结合。当结合在一起时，TF 以合作或竞争方式发挥作用，以靶向具有明确 3D 组织的核小体阵列，以特定模式显示基序。在一种组合中，基序方向性沿染色质环汇集 TF 组合结合，然后横向渗透到相邻的增强子。在其他组合中，TF 组装在基序密集且高度互连的环连接上，随后转移到附近的谱系特异性位点。我们提出了一种引导搜索模型，其中核小体纤维上的基序语法充当路标元素，将 TF 组合结合引导到增强子。