Evidence map›Paper›PMID 38781968›Full record

ArticleCell2024

Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9.

Amy R Eggers, Kai Chen, Katarzyna M Soczek, Owen T Tuck, Erin E Doherty, Bryant Xu, Marena I Trinidad, Brittney W Thornton, Peter H Yoon, Jennifer A Doudna

Abstract read
In one paragraph

Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.

0numbers the graph read from it
0cells of the map it votes in
41citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

41 citing papers in PubMed.

  1. Article
  2. Article
  3. Compact 9dBEs Enable Efficient and Precise Genome Editing in Mammalian Cells and In Vivo.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Biophysical characterization ofSensors & diagnostics · 2026
    Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Structural visualization of the molecular evolution of CRISPR-Cas9.Nature structural & molecular biology · 2026
    Article
  15. Article
  16. Article
  17. Stepwise DNA unwinding gates TnpB genome-editing activity.bioRxiv : the preprint server for biology · 2026
    Article
  18. Review
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Amy R EggersDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Kai ChenDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Katarzyna M SoczekDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
Owen T TuckInnovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
Erin E DohertyInnovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
Bryant XuDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Marena I TrinidadInnovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Brittney W ThorntonDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Peter H YoonDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Jennifer A DoudnaDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: doudna@berkeley.edu.

Funding

Project 3U54AI170792 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI John D Gross · 2022 to 2026
$35.7M
Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human DiseaseRM1HG009490 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Brittany S. Adamson, Martin Joseph Ankrah Aryee · 2017 to 2026
$22.7M
RESEARCH PROJECT 2U19AI135990 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Dexter Pratt · 2018 to 2026
$21.4M
Resource Core II: In Vivo CoreU19NS132303 · NINDS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ross C Wilson · 2023 to 2026
$19.7M
Cas9 RNP delivery to immune cells in vivo via molecular targetingUG3AI150552 · NIAID · UNIVERSITY OF CALIFORNIA BERKELEY · PI DOUDNA, JENNIFER A, WILSON, ROSS C · 2019 to 2021
$2.4M
Expanding CRISPR-Cas editing technology through exploration of novel Cas proteins and DNA repair systemsU01AI142817 · NIAID · UNIVERSITY OF CALIFORNIA BERKELEY · PI BANFIELD, JILLIAN, DOUDNA, JENNIFER A · 2018 to 2022
$2.0M
Cas9 RNP delivery to immune cells in vivo via molecular targetingUH3AI150552 · NIAID · UNIVERSITY OF CALIFORNIA BERKELEY · PI DOUDNA, JENNIFER A, WILSON, ROSS C · 2022 to 2022
$1.3M
Targeted Delivery of Cas9 to Lung Epithelial Cells using Enveloped Delivery VehiclesR21HL173710 · NHLBI · J. DAVID GLADSTONE INSTITUTES · PI DOUDNA, JENNIFER A · 2024 to 2025
$520k
Precision Deaminases to Expand the Scope of Diseases Amenable to CRISPR-mediated CorrectionF32GM153031 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Erin Doherty Blackett · 2024 to 2026
$229k
NHGRI NIH HHS RM1 HG009490NHLBI NIH HHS R21 HL173710NIAID NIH HHS U01 AI142817NIAID NIH HHS U19 AI135990NIAID NIH HHS U54 AI170792NIAID NIH HHS UG3 AI150552NIAID NIH HHS UH3 AI150552NIGMS NIH HHS F32 GM153031NINDS NIH HHS U19 NS132303
6 · The paper itself

Abstract

Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.

Indexed as

CRISPR-Associated Protein 9CRISPR-Cas SystemsCryoelectron MicroscopyDNAGene EditingBacterial ProteinsBiocatalysisGenome, HumanGeobacillus stearothermophilusHEK293 CellsHumansMagnesiumModels, MolecularNucleic Acid ConformationProtein DomainsProtein Structure, TertiaryBacterial ProteinsCRISPR-Associated Protein 9DNAMagnesiumCas9 engineeringCRISPR-Cascryo-EMDNA unwindinggenome editingGeoCas9iGeoCas9magnesiumR-loop formationWED domain

Identifiers

PMID38781968
PMCPMC11658890

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.