Evidence map›Paper›PMID 39026836›Full record

ArticlebioRxiv : the preprint server for biology2024

Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing.

Long T Nguyen, Noah R Rakestraw, Brianna L M Pizzano, Cullen B Young, Yujia Huang, Kate T Beerensson, Anne Fang, Sydney G Antal, Katerina V Anamisis, Coleen M D Peggs and 7 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Long T NguyenDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-0061-9941
Noah R RakestrawDepartment of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA.ORCID 0009-0001-2403-3101
Brianna L M PizzanoDepartment of Chemical Engineering, University of Florida, Gainesville, FL, USA.ORCID 0000-0003-2401-5648
Cullen B YoungDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.
Yujia HuangDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.
Kate T BeerenssonDepartment of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
Anne FangDepartment of Chemical Biology, University of Florida, Gainesville, FL, USA.
Sydney G AntalDepartment of Chemical Engineering, University of Florida, Gainesville, FL, USA.
Katerina V AnamisisDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
Coleen M D PeggsHealth Services Research, Management and Policy, University of Florida, Gainesville, FL, USA.
Jun YanDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.
Yangwode JingDepartment of Chemistry, Princeton University, Princeton, NJ, USA.
Rebecca D BurdineDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0001-6620-5015
Britt AdamsonDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-9451-5819
Jared E ToettcherDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-1546-4030
Cameron MyhrvoldDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-8971-184X
Piyush K JainDepartment of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA.ORCID 0000-0001-7153-442X

Funding

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
Methods and Logic in Molecular Biology Training ProgramT32GM148739 · NIGMS · PRINCETON UNIVERSITY · PI Ileana M. Cristea · 2023 to 2026
$3.6M
Control of the 4D chromatin landscape underlying gene activity during developmentU01DK127429 · NIDDK · PRINCETON UNIVERSITY · PI GREGOR, THOMAS, LEVINE, MICHAEL STEVEN · 2020 to 2024
$3.2M
Discovery and engineering of CRISPR/Cas systemsR35GM147788 · NIGMS · UNIVERSITY OF FLORIDA · PI Piyush K Jain · 2022 to 2026
$1.8M
NHGRI NIH HHS RM1 HG009490NIDDK NIH HHS U01 DK127429NIGMS NIH HHS R35 GM147788NIGMS NIH HHS T32 GM148739
6 · The paper itself

Abstract

Prime editing has emerged as a precise and powerful genome editing tool, offering a favorable gene editing profile compared to other Cas9-based approaches. Here we report new nCas9-DNA polymerase fusion proteins to create chimeric oligonucleotide-directed editing (CODE) systems for search-and-replace genome editing. Through successive rounds of engineering, we developed CODEMax and CODEMax(exo+) editors that achieve efficient genome modifications in human cells with low unintended edits. CODEMax and CODEMax(exo+) contain an engineered Bst DNA polymerase derivative known for its robust strand displacement ability. Additionally, CODEMax(exo+) features a 5' to 3' exonuclease activity that promotes effective strand invasion and repair outcomes favoring the incorporation of the desired edit. We demonstrate CODEs can perform small insertions, deletions, and substitutions with improved efficiency compared to PEMax at many loci. Overall, CODEs complement existing prime editors to expand the toolbox for genome manipulations without double-stranded breaks.

Identifiers

PMID39026836
PMCPMC11257564

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.