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

The genome is highly organized, yet whether DNA structures, such as A/B compartments, represent locations that are permissive/impermissive for transcription or whether these structures are simply correlated with locations of active/inactive genes remains unknown. This is because current methods cannot simultaneously measure DNA organization and transcription. Recently, we developed RNA&DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of DNA and RNA. Here, we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and their spatial contacts within the nucleus. We find that transcription occurs within B compartments – with multiple, simultaneously active genes colocalizing within them – and at genes localized proximal to nucleoli. Together, 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. Overall design: RD-SPRITE was used to simultaneously map genomic structure (DNA-DNA interactions) and nascent transcription (RNA-RNA interactions and RNA-DNA interactions).