Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA869722 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21065600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21065600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21065599_1.fastq.gz | Fastqsanger.gz | |||
| SRR21065599_2.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description: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.
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