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Nat Biotechnol. 2019 Jul;37(7):793-802. doi: 10.1038/s41587-019-0166-3. Epub 2019 Jul 1.

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.

Author information

1
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. jorg.morf@gmail.com.
2
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.
3
Bioinformatics, Babraham Institute, Cambridge, UK.
4
CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
5
CRG, Centre for Genomic Regulation, Barcelona, Spain.
6
Quantitative Biology department, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK.
7
Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
8
Department of Cell Biology, Faculty of Sciences, National Autonomous University of Mexico, Mexico City, Mexico.
9
Sphere Fluidics Limited, Babraham Research Campus, Cambridge, UK.
10
Imaging Facility, Babraham Institute, Cambridge, UK.
11
Universitat Pompeu Fabra, Barcelona, Spain.
12
Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
13
Department of Biological Science, Florida State University, Tallahassee, FL, USA.

Abstract

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.

PMID:
31267103
DOI:
10.1038/s41587-019-0166-3

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