Atlas of Subcellular RNA Localization Revealed by APEX-Seq

Furqan M Fazal; Shuo Han; Kevin R Parker; Pornchai Kaewsapsak; Jin Xu; Alistair N Boettiger; Howard Y Chang; Alice Y Ting

doi:10.1016/j.cell.2019.05.027

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

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

Authors

Furqan M Fazal¹, Shuo Han², Kevin R Parker¹, Pornchai Kaewsapsak², Jin Xu¹, Alistair N Boettiger³, Howard Y Chang⁴, Alice Y Ting⁵

Affiliations

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism*
Endonucleases / metabolism*
Fluorescent Dyes / chemistry
HEK293 Cells
Humans
Microscopy, Fluorescence
Mitochondria / genetics
Multifunctional Enzymes / metabolism*
RNA / chemistry
RNA / metabolism*
RNA, Messenger / chemistry
RNA, Messenger / metabolism
Sequence Analysis, RNA / methods*
Transcriptome

Substances

Fluorescent Dyes
Multifunctional Enzymes
RNA, Messenger
RNA
Endonucleases
APEX2 protein, human
DNA-(Apurinic or Apyrimidinic Site) Lyase

Abstract

Publication types

MeSH terms

Substances

Grants and funding