RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus
Por:
Morf, Jorg, Wingett, Steven W., Farabella, Irene, Cairns, Jonathan, Furlan-Magaril, Mayra, Jimenez-Garcia, Luis F., Liu, Xin, Craig, Frank F., Walker, Simon, Segonds-Pichon, Anne, Andrews, Simon, Marti-Renom, Marc A., Fraser, Peter
Publicada:
1 ene 2019
Resumen:
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.
Filiaciones:
Morf, Jorg:
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, United Kingdom
Babraham Inst, Lab Nucl Dynam, Cambridge, England
Wingett, Steven W.:
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, United Kingdom
Bioinformatics, Babraham Institute, Cambridge, United Kingdom
Babraham Inst, Lab Nucl Dynam, Cambridge, England
Babraham Inst, Bioinformat, Cambridge, England
Farabella, Irene:
CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
CRG, Centre for Genomic Regulation, Barcelona, Spain
Barcelona Inst Sci & Technol, Ctr Genom Regulat, CNAG CRG, Barcelona, Spain
Ctr Genom Regulat, Barcelona, Spain
Cairns, Jonathan:
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, United Kingdom
Quantitative Biology Department, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
Babraham Inst, Lab Nucl Dynam, Cambridge, England
AstraZeneca, IMED Biotech Unit, Discovery Sci, Quantitat Biol Dept, Cambridge, England
Furlan-Magaril, Mayra:
Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
Univ Nacl Autonoma Mexico, Inst Fisiol Celular, Dept Genet Mol, Mexico City, DF, Mexico
Jimenez-Garcia, Luis F.:
Department of Cell Biology, Faculty of Sciences, National Autonomous University of México, Mexico City, Mexico
Univ Nacl Autonoma Mexico, Fac Sci, Dept Cell Biol, Mexico City, DF, Mexico
Liu, Xin:
Sphere Fluidics Limited, Babraham Research Campus, Cambridge, United Kingdom
Sphere Fluid Ltd, Babraham Res Campus, Cambridge, England
Craig, Frank F.:
Sphere Fluidics Limited, Babraham Research Campus, Cambridge, United Kingdom
Sphere Fluid Ltd, Babraham Res Campus, Cambridge, England
Walker, Simon:
Imaging Facility, Babraham Institute, Cambridge, United Kingdom
Babraham Inst, Imaging Facil, Cambridge, England
Segonds-Pichon, Anne:
Bioinformatics, Babraham Institute, Cambridge, United Kingdom
Babraham Inst, Bioinformat, Cambridge, England
Andrews, Simon:
Bioinformatics, Babraham Institute, Cambridge, United Kingdom
Babraham Inst, Bioinformat, Cambridge, England
Marti-Renom, Marc A.:
CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
CRG, Centre for Genomic Regulation, Barcelona, Spain
Universitat Pompeu Fabra, Barcelona, Spain
Catalan Institution for Research and Advanced Studies, Barcelona, Spain
Barcelona Inst Sci & Technol, Ctr Genom Regulat, CNAG CRG, Barcelona, Spain
Ctr Genom Regulat, Barcelona, Spain
Univ Pompeu Fabra, Barcelona, Spain
Catalan Inst Res & Adv Studies, Barcelona, Spain
Fraser, Peter:
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, United Kingdom
Department of Biological Science, Florida State University, Tallahassee, FL, United States
Babraham Inst, Lab Nucl Dynam, Cambridge, England
Florida State Univ, Dept Biol Sci, B-157, Tallahassee, FL 32306 USA
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