RNA 邻近测序揭示了细胞核中转录组的空间组织。
RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
机构信息
Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.
Bioinformatics, Babraham Institute, Cambridge, UK.
出版信息
Nat Biotechnol. 2019 Jul;37(7):793-802. doi: 10.1038/s41587-019-0166-3. Epub 2019 Jul 1.
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.
使用现有的方法很难确定 RNA 分子在细胞核中的整体三维结构。在这里，我们介绍了 Proximity RNA-seq，它可以识别新生和完全转录的 RNA 对或 RNA 组在核内的共定位偏好。Proximity RNA-seq 基于在油包水乳液滴中的亚核颗粒进行大规模高通量 RNA 条形码标记，然后进行 cDNA 测序。我们的结果表明，不同组织特异性表达、RNA 聚合酶延伸速度和选择性剪接程度的 RNA 位于距核仁不同的距离处。同时检测彼此靠近的多个 RNA 可以将 RNA 密集区与稀疏区分开。Proximity RNA-seq 的应用将有助于研究核内转录本的空间组织，包括非编码 RNA，及其功能相关性。
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