RT Journal Article
SR Electronic
T1 Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 196147
DO 10.1101/196147
A1 Jörg Morf
A1 Steven W. Wingett
A1 Irene Farabella
A1 Jonathan Cairns
A1 Mayra Furlan-Magaril
A1 Xin Liu
A1 Frank F. Craig
A1 Simon Andrews
A1 Marc A. Marti-Renom
A1 Peter Fraser
YR 2017
UL http://biorxiv.org/content/early/2017/09/29/196147.abstract
AB 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.