Atlas of Subcellular RNA Localization Revealed by APEX-Seq

• Published in: Cell Vol. 178; no. 2; pp. 473 - 490.e26
• Main Authors: Fazal, Furqan M., Han, Shuo, Parker, Kevin R., Kaewsapsak, Pornchai, Xu, Jin, Boettiger, Alistair N., Chang, Howard Y., Ting, Alice Y.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11.07.2019
• Subjects: cycloheximide; DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism; Endonucleases - metabolism; Fluorescent Dyes - chemistry; HEK293 Cells; Humans; LADs; messenger RNA; Microscopy, Fluorescence; mitochondria; Mitochondria - genetics; motifs; Multifunctional Enzymes - metabolism; nocodazole; nuclear pore; OXPHOS; peroxidase; retrotransposons; RNA - chemistry; RNA - metabolism; RNA, Messenger - chemistry; RNA, Messenger - metabolism; sequence analysis; Sequence Analysis, RNA - methods; spatial transcriptomics; Transcriptome; translation; UTRs; cycloheximide; spatial transcriptomics; motifs; UTRs; LADs; translation; OXPHOS; retrotransposons; nocodazole
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2019.05.027

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. [Display omitted] •A transcriptome-wide subcellular RNA atlas was generated by proximity labeling•Isoform-level subcellular localization patterns for over 3,200 genes identified•RNA-transcript location correlates with genome architecture and protein localization•Two modes of mRNA localization to the outer mitochondrial membrane uncovered A newly developed technique reveals the subcellular transcriptomes at many landmarks in the nucleus and cytosol and connects mRNA localization to genome architecture, protein location, and local-translation mechanisms.