Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.

CRISPR-Cas Systems / genetics Chromosome Mapping Genomics Genotype Phenotype Single-Cell Analysis / methods
CRISPR Integrator complex Perturb-seq cell biology chromosomal instability genetic screens genotype-phenotype map mitochondrial genome stress response single-cell RNA sequencing

Journal

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

Informations de publication

Date de publication:
07 07 2022
Historique:
received: 10 01 2022
revised: 07 03 2022
accepted: 16 05 2022
pubmed: 11 6 2022
medline: 14 7 2022
entrez: 10 6 2022
Statut: ppublish

Résumé

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes to predict the function of poorly characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena-from RNA processing to differentiation. We leverage this ability to systematically identify genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene and cellular function.

Identifiants

DOI: 10.1016/j.cell.2022.05.013 PMID: 35688146 PMC: PMC9380471
pubmed: 35688146
pii: S0092-8674(22)00597-9
doi: 10.1016/j.cell.2022.05.013
pmc: PMC9380471
mid: NIHMS1812939
pii:
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

2559-2575.e28

Subventions

Organisme : NHGRI NIH HHS
ID : R44 HG010558
Pays : United States
Organisme : NIGMS NIH HHS
ID : R00 GM130964
Pays : United States
Organisme : NHGRI NIH HHS
ID : R44 HG011060
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG009490
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM087237
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA129105
Pays : United States
Organisme : NINDS NIH HHS
ID : F31 NS115380
Pays : United States
Organisme : NIGMS NIH HHS
ID : DP2 GM140925
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM134539
Pays : United States

Commentaires et corrections

Type : CommentIn

Informations de copyright

Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests J.M.R. consults for Maze Therapeutics and is a consultant for and equity holder in Waypoint Bio. R.A.S. consults for Maze Therapeutics. K.A. is a consultant for Syros Pharmaceuticals, is on the SAB of CAMP4 Therapeutics, and received research funding from Novartis not related to this work. G.L.-Y., N.I., F.O., and D.L. are employees and shareholders of Ultima Genomics. M.J. consults for Maze Therapeutics and Gate Bioscience. T.M.N. consults for Maze Therapeutics. J.S.W. declares outside interest in 5AM Ventures, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics, and Third Rock Ventures. The Regents of the University of California with R.A.S., T.M.N., M.J., and J.S.W. as inventors have filed patent applications related to CRISPRi/a screening and Perturb-seq.

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Auteurs

Joseph M Replogle (JM)

Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Reuben A Saunders (RA)

Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Angela N Pogson (AN)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Jeffrey A Hussmann (JA)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Alexander Lenail (A)

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Alina Guna (A)

Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Lauren Mascibroda (L)

Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.

Eric J Wagner (EJ)

Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.

Karen Adelman (K)

Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.

Gila Lithwick-Yanai (G)

Ultima Genomics, Newark, CA 94560, USA.

Nika Iremadze (N)

Ultima Genomics, Newark, CA 94560, USA.

Florian Oberstrass (F)

Ultima Genomics, Newark, CA 94560, USA.

Doron Lipson (D)

Ultima Genomics, Newark, CA 94560, USA.

Jessica L Bonnar (JL)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

Marco Jost (M)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.

Thomas M Norman (TM)

Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: normantm@mskcc.org.

Jonathan S Weissman (JS)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: weissman@wi.mit.edu.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Mapping information-rich genotype-phenotype...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Cartographie chromosomique › Mapping information-rich genotype-phenotype...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Mapping information-rich genotype-phenotype...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Mapping information-rich genotype-phenotype...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › Mapping information-rich genotype-phenotype...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse sur cellule unique › Mapping information-rich genotype-phenotype...