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Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates

Jörg Morf, Steven W. Wingett, Irene Farabella, Jonathan Cairns, Mayra Furlan-Magaril, Xin Liu, Frank F. Craig, Simon Andrews, Marc A. Marti-Renom, Peter Fraser
doi: https://doi.org/10.1101/196147
Jörg Morf
1Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge, UK
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Steven W. Wingett
1Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge, UK
2Bioinformatics, Babraham Institute, Cambridge, UK
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Irene Farabella
3CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
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Jonathan Cairns
1Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge, UK
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Mayra Furlan-Magaril
5Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México
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Xin Liu
6Sphere Fluidics Limited, Babraham Research Campus, Cambridge, UK
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Frank F. Craig
6Sphere Fluidics Limited, Babraham Research Campus, Cambridge, UK
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Simon Andrews
2Bioinformatics, Babraham Institute, Cambridge, UK
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Marc A. Marti-Renom
3CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
4Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Peter Fraser
1Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge, UK
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Abstract

Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which enriches for nascent transcripts, and identifies contact preferences for individual RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA-barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing. We show a bipartite organization of the nuclear transcriptome in which compartments of different RNA density correlate with transcript families, tissue specificity and extent of alternative splicing. Integration of proximity measurements at the DNA and NA level identify transcriptionally active genomic regions with increased nucleic acid density and faster RNA polymerase II elongation located close to compact chromatin.

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Posted September 29, 2017.
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Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates
Jörg Morf, Steven W. Wingett, Irene Farabella, Jonathan Cairns, Mayra Furlan-Magaril, Xin Liu, Frank F. Craig, Simon Andrews, Marc A. Marti-Renom, Peter Fraser
bioRxiv 196147; doi: https://doi.org/10.1101/196147
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Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates
Jörg Morf, Steven W. Wingett, Irene Farabella, Jonathan Cairns, Mayra Furlan-Magaril, Xin Liu, Frank F. Craig, Simon Andrews, Marc A. Marti-Renom, Peter Fraser
bioRxiv 196147; doi: https://doi.org/10.1101/196147

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