Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

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, Messenger / chemistry Sequence Analysis, RNA / methods Transcriptome
LADs OXPHOS UTRs cycloheximide motifs nocodazole retrotransposons spatial transcriptomics translation

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
11 07 2019
Historique:
received: 31 08 2018
revised: 31 12 2018
accepted: 14 05 2019
pubmed: 25 6 2019
medline: 9 4 2020
entrez: 25 6 2019
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.cell.2019.05.027 PMID: 31230715 PMC: PMC6786773
pubmed: 31230715
pii: S0092-8674(19)30555-0
doi: 10.1016/j.cell.2019.05.027
pmc: PMC6786773
mid: NIHMS1531987
pii:
doi:

Substances chimiques

Fluorescent Dyes 0
Multifunctional Enzymes 0
RNA, Messenger 0
RNA 63231-63-0
Endonucleases EC 3.1.-
APEX2 protein, human EC 4.2.99.18
DNA-(Apurinic or Apyrimidinic Site) Lyase EC 4.2.99.18

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

473-490.e26

Subventions

Organisme : NHGRI NIH HHS
ID : RM1 HG007735
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG004361
Pays : United States
Organisme : NHGRI NIH HHS
ID : P50 HG007735
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA186568
Pays : United States
Organisme : NIH HHS
ID : S10 OD018220
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States

Informations de copyright

Copyright © 2019 Elsevier Inc. All rights reserved.

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Auteurs

Furqan M Fazal (FM)

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.

Shuo Han (S)

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.

Kevin R Parker (KR)

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.

Pornchai Kaewsapsak (P)

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.

Jin Xu (J)

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.

Alistair N Boettiger (AN)

Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Howard Y Chang (HY)

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.

Alice Y Ting (AY)

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.

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Classifications MeSH

questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Lyases › Carbon-oxygen lyases › DNA-(apurinic or apyrimidinic site) lyase › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Hydrolases › Esterases › Endonucleases › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Actions chimiques et utilisations › Utilisations spécialisées de produits chimiques › Produits chimiques de laboratoire › Indicateurs et réactifs › Luminescents › Colorants fluorescents › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Cellules › Cellules épithéliales › Cellules HEK293 › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Techniques d'investigation › Microscopie de fluorescence › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Cellules › Structures cellulaires › Fractions subcellulaires › Mitochondries › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Enzymes multifonctionnelles › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Atlas of Subcellular RNA Localization Revealed...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Atlas of Subcellular RNA Localization Revealed...