Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Nucleic Acids Res. 2020 Jul 9;48(12):6699-6714. doi: 10.1093/nar/gkaa457.
Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.
非编码 RNA（ncRNAs）参与各种生物过程，包括调节转录和维持基因组的 3D 组织。在这里，我们提出了一种称为 Red-C 的方法，该方法利用邻近连接来鉴定细胞核中所有 RNA 分子与基因组的接触。使用 Red-C，我们揭示了人类 K562 细胞的 RNA-DNA 相互作用组，并鉴定了数百种富含活跃或抑制染色质的 ncRNAs，包括以前未描述的 RNA。对 RNA-DNA 相互作用组的分析还使我们能够追踪信使 RNA 产生的动力学。我们的数据支持共转录内含子剪接的模型，但不支持活跃转录基因环化的假说。
