Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments—with multiple active genes simultaneously colocalizing within the same B compartment—and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription. ; This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). We thank Kyle Xiong and Jian Ma for sub-compartment annotations for mESCs, Mario Blanco for comments on the manuscript, Peter Chovanec for help with SPRITE experiments and analyses, Shawna Hiley for editing, and Inna-Marie Strazhnik for illustrations. This work was funded by NIH 4DN (U01 DA040612 and U01 HL130007); NIH Directors' Transformative Research Award (R01 DA053178); the Chan Zuckerberg Initiative; an HHMI Gilliam and Hanna H. Gray Fellowship (S.A.Q.); NIH UCLA-Caltech Medical Scientist Training Program (T32GM008042) (I.G.); American Cancer Society Fellowship (N.O.); Caltech BBE fellowship (J.W.J.); and NIH T32 GM 7616-40, NIH NRSA CA247447, Josephine De Karman Fellowship Trust, and the UCLA-Caltech Medical Scientist Training Program (P.B.). Imaging was ...