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

ABSTRACT: 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 pr

SUBMITTER: Goronzy IN 

PROVIDER: S-EPMC9793828 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature