Evidence map›Paper›PMID 40121079›Full record

ArticleMethods in enzymology2025

Genome editing with programmable base editors in human cells.

Nicola R B Osgood, Natalie M Zawalick, Courtney B Sawyer, Quinn T Cowan, Sifeng Gu, S J Mawson, Brodie L Ranzau, Lehan Li, Melissa Gymrek, Alon Goren and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in enzymology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Collapsing retroviruses for efficient delivery of viro-toxic cargoes.bioRxiv : the preprint server for biology · 2026
    Article
  2. Review
  3. Article
  4. Article
  5. HAMMER: Hairpin-based APOBEC3A-mediated mRNA editing reporter.bioRxiv : the preprint server for biology · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Nicola R B OsgoodDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Natalie M ZawalickDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Courtney B SawyerDepartment of Medicine, University of California San Diego, La Jolla, CA, United States.
Quinn T CowanDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Sifeng GuDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
S J MawsonDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Brodie L RanzauDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Lehan LiDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States.
Melissa GymrekDepartment of Medicine, University of California San Diego, La Jolla, CA, United States; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, United States.
Alon GorenDepartment of Medicine, University of California San Diego, La Jolla, CA, United States.
Alexis C KomorDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, United States; Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, United States. Electronic address: akomor@ucsd.edu.

Funding

Contemporary Approaches to Cancer Cell Signaling and CommunicationT32CA009523 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DONOGHUE, DANIEL J, YANG, JING · 1985 to 2025
$12.1M
MOLECULAR BIOPHYSICS TRAINING PROGRAMT32GM008326 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KOMIVES, ELIZABETH A. · 1989 to 2020
$7.5M
Supplement to R35 "Development and Application of New Genome Editing Tools for the Functional Investigation of Genetic Variants of Uncertain Significance"R35GM138317 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Alexis C. Komor · 2020 to 2026
$2.8M
A framework for interpreting global effects of genetic variants contributing to disease riskR56HG013535 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GOREN, ALON, GYMREK, MELISSA · 2024 to 2024
$757k
Chemical Biology Interfaces at UC San DiegoT32GM112584 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BURKART, MICHAEL D. · 2015 to 2019
$729k
NCI NIH HHS T32 CA009523NHGRI NIH HHS R56 HG013535NIGMS NIH HHS R35 GM138317NIGMS NIH HHS T32 GM008326NIGMS NIH HHS T32 GM112584
6 · The paper itself

Abstract

Genome editing has garnered significant attention over the last decade, resulting in a massive expansion of the genome engineering toolbox. Base editors encompass a class of tools that enable installing single-nucleotide changes in genomic DNA without the use of double-strand breaks. With the ever-increasing development of new and/or improved base editor systems, it is easy to be overwhelmed by the abundance of options. Here, we provide clear guidance to facilitate the selection of a base editor and to design guide RNAs (gRNAs) to suit various needs. Additionally, we describe in detail how to generate gRNA plasmids, transfect various mammalian cell types, and evaluate editing efficiencies. Finally, we give alternative methods and troubleshooting tips for some common pitfalls encountered during base editing.

Indexed as

CRISPR-Cas SystemsGene EditingRNA, Guide, CRISPR-Cas SystemsGenome, HumanHEK293 CellsHumansPlasmidsTransfectionRNA, Guide, CRISPR-Cas SystemsAdenine Base Editor (ABE)Base editingCytosine Base Editor (CBE)ElectroporationFluorescence-activated cell sorting (FACS)gRNA synthesisGuide RNA (gRNA) designHigh throughput sequencing (HTS)IPSC base editingIsogenic cell line generationNext generation sequencing (NGS)Single-cell sortingTransfection

Identifiers

PMID40121079
PMCPMC11948366

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.