cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers

The canonical BAF complex (cBAF) is essential for chromatin opening at enhancers. However, the nature of the open chromatin remains unclear. Here we show that in addition to producing histone-free DNA, cBAF generates stable hemisome-like subnucleosomal particles containing the four core histones associated with 50-80 base pairs of DNA. Our genome-wide analysis indicates that cBAF makes these particles by targeting and splitting fragile nucleosomes. In mouse embryonic stem cells, these subnucleosomes become an in vivo binding substrate for the master transcription factor OCT4 independently of the presence of OCT4 DNA motifs. At enhancers, the OCT4-subnucleosome interaction increases OCT4 occupancy and amplifies the genomic interval bound by OCT4 by up to one order of magnitude, compared to the region occupied on histone-free DNA. We propose that cBAF-dependent subnucleosomes orchestrate a molecular mechanism that projects OCT4 function in chromatin opening beyond its DNA motifs.经典BAF复合物（canonical BAF complex，cBAF）对增强子区域的染色质开放至关重要。然而，开放染色质的本质仍未阐明。本研究表明，除了生成不含组蛋白的DNA之外，cBAF还可产生稳定的类半核小体亚核小体颗粒，这类颗粒包含与50~80个碱基对DNA结合的四种核心组蛋白。我们的全基因组分析（genome-wide analysis）显示，cBAF通过靶向并裂解脆弱核小体来生成这类颗粒。在小鼠胚胎干细胞中，这类亚核小体可成为核心转录因子OCT4的体内结合底物，且其结合不依赖于OCT4 DNA基序的存在。在增强子区域，相较于结合于不含组蛋白DNA的区域，OCT4与亚核小体的相互作用可提升OCT4的结合占有率，并将OCT4结合的基因组区间扩大至多一个数量级。我们提出，依赖于cBAF的亚核小体可调控一种分子机制，使OCT4在染色质开放中的功能得以超越其DNA基序的限制。