RNA, DNA, and protein molecules are highly organized within three-dimensional (3D) structures in the nucleus. Although RNA has been proposed to play a role in nuclear organization, exploring this has been challenging because existing methods cannot measure higher-order RNA and DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the spatial organization of RNA and DNA. These maps reveal higher-order RNA-chromatin structures associated with three major classes of nuclear function: RNA processing, heterochromatin assembly, and gene regulation. These data demonstrate that hundreds of ncRNAs form high-concentration territories throughout the nucleus, that specific RNAs are required to recruit various regulators into these territories, and that these RNAs can shape long-range DNA contacts, heterochromatin assembly, and gene expression. These results demonstrate a mechanism where RNAs form high-concentration territories, bind to diffusible regulators, and guide them into compartments to regulate essential nuclear functions.

RNA、DNA 和蛋白质分子在细胞核的三维 (3D) 结构中高度组织。尽管 RNA 已被提议在核组织中发挥作用，但探索这一点一直具有挑战性，因为现有方法无法测量 3D 结构内的高阶 RNA 和 DNA 接触。为了解决这个问题，我们开发了 RNA & DNA SPRITE (RD-SPRITE) 来全面绘制 RNA 和 DNA 的空间组织图。这些图揭示了与核功能的三大类相关的高阶 RNA 染色质结构：RNA 加工、异染色质组装和基因调控。这些数据表明，数百个 ncRNA 在整个细胞核中形成了高浓度区域，需要特定的 RNA 才能将各种监管机构招募到这些区域，并且这些 RNA 可以塑造远程 DNA 接触、异染色质组装和基因表达。这些结果证明了一种机制，其中 RNA 形成高浓度区域，与可扩散调节剂结合，并引导它们进入隔室以调节基本的核功能。