RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
IF: 68.164
Cited by: 27


The global, three-dimensional organization of RNA molecules in the nucleus is difficult to determine using existing methods. Here we introduce Proximity RNA-seq, which identifies colocalization preferences for pairs or groups of nascent and fully transcribed RNAs in the nucleus. Proximity RNA-seq is based on massive-throughput RNA barcoding of subnuclear particles in water-in-oil emulsion droplets, followed by cDNA sequencing. Our results show RNAs of varying tissue-specificity of expression, speed of RNA polymerase elongation and extent of alternative splicing positioned at varying distances from nucleoli. The simultaneous detection of multiple RNAs in proximity to each other distinguishes RNA-dense from sparse compartments. Application of Proximity RNA-seq will facilitate study of the spatial organization of transcripts in the nucleus, including non-coding RNAs, and its functional relevance.


Spatial Transcriptomics
Gene Expression
Intron seqFISH

MeSH terms

Cell Line, Tumor
Cell Nucleus
DNA Barcoding, Taxonomic
High-Throughput Nucleotide Sequencing


Morf, Jörg
Wingett, Steven W
Farabella, Irene
Cairns, Jonathan
Furlan-Magaril, Mayra
Jiménez-García, Luis F
Liu, Xin
Craig, Frank F
Walker, Simon
Segonds-Pichon, Anne
Andrews, Simon
Marti-Renom, Marc A
Fraser, Peter

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