Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileJoseph M. Replogle, Reuben A. Saunders, Angela N. Pogson, Jeffrey A. Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J. Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L. Bonnar, Marco Jost, Thomas M. Norman, Jonathan S. Weissman
doi: https://doi.org/10.1101/2021.12.16.473013
Joseph M. Replogle
1Medical Scientist Training Program, University of California, San Francisco; San Francisco, CA 94158, USA
2Tetrad Graduate Program, University of California, San Francisco; San Francisco, CA 94158, USA
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joseph M. Replogle
Reuben A. Saunders
2Tetrad Graduate Program, University of California, San Francisco; San Francisco, CA 94158, USA
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Angela N. Pogson
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey A. Hussmann
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexander Lenail
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alina Guna
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lauren Mascibroda
6Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston; Galveston, TX 77555, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eric J. Wagner
6Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston; Galveston, TX 77555, USA
7Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry; Rochester, NY 14642, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Karen Adelman
8Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School; Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gila Lithwick-Yanai
9Ultima Genomics; Newark, CA 94560, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nika Iremadze
9Ultima Genomics; Newark, CA 94560, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Florian Oberstrass
9Ultima Genomics; Newark, CA 94560, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Doron Lipson
9Ultima Genomics; Newark, CA 94560, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jessica L. Bonnar
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marco Jost
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
10Department of Microbiology, Harvard Medical School; Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thomas M. Norman
11Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: weissman@wi.mit.edu normantm@mskcc.org
Jonathan S. Weissman
3Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA 94158, USA
4Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
5Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
12David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
13Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: weissman@wi.mit.edu normantm@mskcc.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (pooled 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 and present a framework to power biological discovery with the resulting genotype-phenotype map. 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 the 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 function and cellular behavior.

Competing Interest Statement

JMR consults for Maze Therapeutics and is a consultant for and equity holder in Waypoint Bio. RAS consults for Maze Therapeutics. KA is a consultant for Syros Pharmaceuticals, is on the SAB of CAMP4 Therapeutics, and received research funding from Novartis not related to this work. GLY, NI, FO, and DL are employees and shareholders of Ultima Genomics. MJ consults for Maze Therapeutics and Gate Bioscience. TMN consults for Maze Therapeutics. JSW declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics and Third Rock Ventures. The Regents of the University of California with RAS, TMN, MJ, and JSW as inventors have filed patent applications related to CRISPRi/a screening and Perturb-seq.

Footnotes

  • ↵† Co-first authors

  • Revised to include Ultima Genomics sequencing data (Figure S13).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 28, 2022.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
Joseph M. Replogle, Reuben A. Saunders, Angela N. Pogson, Jeffrey A. Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J. Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L. Bonnar, Marco Jost, Thomas M. Norman, Jonathan S. Weissman
bioRxiv 2021.12.16.473013; doi: https://doi.org/10.1101/2021.12.16.473013
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
Joseph M. Replogle, Reuben A. Saunders, Angela N. Pogson, Jeffrey A. Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J. Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L. Bonnar, Marco Jost, Thomas M. Norman, Jonathan S. Weissman
bioRxiv 2021.12.16.473013; doi: https://doi.org/10.1101/2021.12.16.473013

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3686)
  • Biochemistry (7767)
  • Bioengineering (5666)
  • Bioinformatics (21237)
  • Biophysics (10553)
  • Cancer Biology (8159)
  • Cell Biology (11904)
  • Clinical Trials (138)
  • Developmental Biology (6737)
  • Ecology (10388)
  • Epidemiology (2065)
  • Evolutionary Biology (13838)
  • Genetics (9694)
  • Genomics (13054)
  • Immunology (8121)
  • Microbiology (19936)
  • Molecular Biology (7825)
  • Neuroscience (42959)
  • Paleontology (318)
  • Pathology (1276)
  • Pharmacology and Toxicology (2256)
  • Physiology (3350)
  • Plant Biology (7207)
  • Scientific Communication and Education (1309)
  • Synthetic Biology (1998)
  • Systems Biology (5528)
  • Zoology (1126)