Format

Send to

Choose Destination
Cell. 2019 Jul 11;178(2):473-490.e26. doi: 10.1016/j.cell.2019.05.027. Epub 2019 Jun 20.

Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

Author information

1
Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
2
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
3
Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
4
Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: howchang@stanford.edu.
5
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: ayting@stanford.edu.

Abstract

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.

KEYWORDS:

LADs; OXPHOS; UTRs; cycloheximide; motifs; nocodazole; retrotransposons; spatial transcriptomics; translation

PMID:
31230715
DOI:
10.1016/j.cell.2019.05.027

Supplemental Content

Loading ...
Support Center