Nucleosomes cluster together when chromatin folds in the cell to form heterogeneous groups termed “clutches”. These structural units add another level of chromatin regulation, for example during cell differentiation. Yet, the mechanisms that regulate their size and compaction remain obscure. Here, using our chromatin mesoscale model, we dissect clutch patterns in fibers with different combinations of nucleosome positions, linker histone density, and acetylation levels to investigate their role in clutch regulation. First, we isolate the effect of each chromatin parameter by studying systems with regular nucleosome spacing; second, we design systems with naturally-occurring linker lengths that fold onto specific clutch patterns; third, we model gene-encoding fibers to understand how these combined factors contribute to gene structure. Our results show how these chromatin parameters act together to produce different-sized nucleosome clutches. The length of nucleosome free regions (NFRs) profoundly affects clutch size, while the length of linker DNA has a moderate effect. In general, higher linker histone densities produce larger clutches by a chromatin compaction mechanism, while higher acetylation levels produce smaller clutches by a chromatin unfolding mechanism. We also show that it is possible to design fibers with naturally-occurring DNA linkers and NFRs that fold onto specific clutch patterns. Finally, in gene–encoding systems, a complex combination of variables dictates a gene-specific clutch pattern. Together, these results shed light onto the mechanisms that regulate nucleosome clutches and suggest a new epigenetic mechanism by which chromatin parameters regulate transcriptional activity via the three–dimensional folded state of the genome at a nucleosome level.

当染色质在细胞中折叠形成称为“离合器”的异质组时，核小体聚集在一起。这些结构单元增加了另一个层次的染色质调节，例如在细胞分化过程中。然而，调节它们的大小和压实度的机制仍然模糊不清。在这里，使用我们的染色质中尺度模型，我们剖析了具有不同核小体位置、接头组蛋白密度和乙酰化水平组合的纤维中的离合器模式，以研究它们在离合器调节中的作用。首先，我们通过研究具有规则核小体间距的系统来分离每个染色质参数的影响；其次，我们设计的系统具有自然发生的连接器长度，可以折叠到特定的离合器模式上；第三，我们对基因编码纤维进行建模，以了解这些组合因素如何影响基因结构。我们的结果显示了这些染色质参数如何共同作用以产生不同大小的核小体离合器。核小体自由区 (NFR) 的长度对离合器大小有很大影响，而接头 DNA 的长度则影响适中。通常，较高的接头组蛋白密度通过染色质压缩机制产生较大的离合器，而较高的乙酰化水平通过染色质展开机制产生较小的离合器。我们还表明，可以设计具有天然存在的 DNA 接头和 NFR 的纤维，这些纤维可以折叠到特定的离合器模式上。最后，在基因编码系统中，变量的复杂组合决定了基因特异性的离合器模式。一起，