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Proximity RNA-seq is a new method that helps researchers identify how RNA molecules are organized and grouped together in the nucleus of cells.
The technique uses RNA barcoding and cDNA sequencing to analyze RNA positioning and interactions within subnuclear structures.
Findings from this method reveal that different types of RNAs show specific colocalization patterns and spatial relationships, enhancing our understanding of how RNA organization affects cell function.
Article 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.
