How non-coding RNAs shape nuclear structure to regulate gene expression

Abstract

The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring this role has remained a challenge because no existing methods can simultaneously measure RNA and DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the spatial organization of all RNAs relative to DNA. Using this approach, we identify hundreds of ncRNAs that form high-concentration territories in spatial proximity to their transcriptional loci and show that dozens of ncRNAs guide diffusible regulatory proteins into these 3D structures. We show that many of these ncRNA-mediated compartments act to regulate RNA processing, heterochromatin assembly, and gene expression. Our results demonstrate a unique mechanism by which ncRNAs act to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions. Moreover, we discuss how ncRNAs can drive amplification of regulatory proteins in 3D space to enable robust control of gene expression.