We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

中文翻译：

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APEX-Seq 揭示的亚细胞 RNA 定位图谱。

我们介绍 APEX-seq，这是一种基于使用过氧化物酶 APEX2 直接邻近标记 RNA 的 RNA 测序方法。APEX-seq 在九个不同的亚细胞区域中生成了人类转录组作为资源的纳米分辨率空间图，揭示了不同 RNA 类别和转录亚型的广泛定位模式。我们发现了核转录组的放射状组织，该组织在核孔的内表面被门控，用于加工转录物的细胞质输出。我们确定了信使 RNA 定位到线粒体的两条不同途径，每条途径都与特定的转录本相关，用于在细胞器内构建互补的大分子机器。APEX-seq 应广泛适用于许多系统，从而能够对空间转录组进行全面研究。