Brief Communication
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Open Access
Featured
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Article
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Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes
Lineage tracing using both transcriptomics and chromatin accessibility provides mechanistic insights into cell fate.
- Kunal Jindal
- , Mohd Tayyab Adil
- & Samantha A. Morris
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Article |
Adenine transversion editors enable precise, efficient A•T-to-C•G base editing in mammalian cells and embryos
A base editor for precise adenine transversions is demonstrated in mouse embryos.
- Liang Chen
- , Mengjia Hong
- & Dali Li
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Article |
Deep learning models to predict the editing efficiencies and outcomes of diverse base editors
The best base editor for specific applications is predicted with a deep learning model.
- Nahye Kim
- , Sungchul Choi
- & Hyongbum Henry Kim
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Brief Communication |
High-throughput retrieval of target sequences from complex clone libraries using CRISPRi
A CRISPRi method retrieves sequences of interest from large metagenomic libraries.
- Ján Burian
- , Vincent K. Libis
- & Sean F. Brady
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Article |
Modular, programmable RNA sensing using ADAR editing in living cells
Specific RNAs are detected in live cells by harnessing endogenous ADAR enzymes.
- K. Eerik Kaseniit
- , Noa Katz
- & Xiaojing J. Gao
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Article |
A red light–responsive photoswitch for deep tissue optogenetics
A photoswitch based on a bacterial phytochrome enables optogenetic manipulations using red light.
- Yuto Kuwasaki
- , Kazushi Suzuki
- & Moritoshi Sato
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Matters Arising |
Assessing the efficiency of Verily’s automated process for production and release of male Wolbachia-infected mosquitoes
- Jérémy Bouyer
- , Hamidou Maiga
- & Marc J. B. Vreysen
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News & Views |
Pathogenic or benign?
CRISPR base- and prime-editing pooled screens reveal the function of genetic variants at unprecedented resolution.
- Peter P. Du
- , Katherine Liu
- & Gaelen T. Hess
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Article |
High-throughput functional evaluation of human cancer-associated mutations using base editors
Cancer-associated variants of unknown significance are identified using base editing.
- Younggwang Kim
- , Seungho Lee
- & Hyongbum Henry Kim
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Article
| Open Access
CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA
Continuously evolved double-stranded DNA deaminases increase the efficiency and targeting scope of all-protein base editors.
- Beverly Y. Mok
- , Anna V. Kotrys
- & David R. Liu
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Article |
Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo
Circular ADAR-recruiting RNAs improve RNA editing in vitro and in a mouse disease model.
- Zongyi Yi
- , Liang Qu
- & Wensheng Wei
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Article |
Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs
Circular guide RNAs boost the efficiency of RNA editing with endogenous ADARs.
- Dhruva Katrekar
- , James Yen
- & Prashant Mali
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News & Views |
Improving CRISPR tools by elucidating DNA repair
Genome-editing tools are optimized by identifying genes that affect DNA repair.
- Jung Min Lim
- & Hyongbum Henry Kim
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Article
| Open Access
Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus
A miniature CRISPR system may enable genome editing using single AAV vectors.
- Do Yon Kim
- , Jeong Mi Lee
- & Yong-Sam Kim
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Article |
Adenine base editor engineering reduces editing of bystander cytosines
Engineered variants of adenine base editors have reduced cytosine base editing or a specific C-to-G base editing activity.
- You Kyeong Jeong
- , SeokHoon Lee
- & Sangsu Bae
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News & Views |
CRISPR base editing lowers cholesterol in monkeys
Targeting a gene linked to cardiovascular disease shows therapeutic promise.
- Sebastiaan Johannes van Kampen
- & Eva van Rooij
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Letter |
Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands
Mutations present at a low frequency in a sample are detected with high sensitivity and a low error rate.
- Joshua D. Cohen
- , Christopher Douville
- & Bert Vogelstein
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Article |
Predicting the efficiency of prime editing guide RNAs in human cells
Prime editing is optimized by a method to choose the most efficient guide RNA.
- Hui Kwon Kim
- , Goosang Yu
- & Hyongbum Henry Kim
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Letter |
Targeted, efficient sequence insertion and replacement in rice
Rice genes are replaced using chemically modified donor DNA and CRISPR targeting.
- Yuming Lu
- , Yifu Tian
- & Jian-Kang Zhu
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Letter |
Sequence-specific prediction of the efficiencies of adenine and cytosine base editors
The activity of adenine or cytosine base editors at specific target nucleotides is predicted computationally.
- Myungjae Song
- , Hui Kwon Kim
- & Hyongbum Henry Kim
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Article |
Prediction of the sequence-specific cleavage activity of Cas9 variants
Deep-learning models predict the Cas9 variant with optimal activity and specificity for any target sequence.
- Nahye Kim
- , Hui Kwon Kim
- & Hyongbum Henry Kim
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Brief Communication |
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing
A base editor that concurrently modifies both adenine and cytosine broadens the potential applications of base editing.
- Julian Grünewald
- , Ronghao Zhou
- & J. Keith Joung
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Article |
Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity
A continuously evolved adenine base editor is compatible with various Cas proteins and mediates efficient A•T-to-G•C base conversions at a wide variety of PAM sites.
- Michelle F. Richter
- , Kevin T. Zhao
- & David R. Liu
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Article |
Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform
Combining Cas9 and Cas12a outperforms previous approaches for combinatorial screening in mammalian cells.
- Thomas Gonatopoulos-Pournatzis
- , Michael Aregger
- & Jason Moffat
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Article |
Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors
Methods to efficiently detect Cas9-independent cytosine base editor off-target activity enable the identification and development of variants with minimal off-target editing and robust on-target editing.
- Jordan L. Doman
- , Aditya Raguram
- & David R. Liu
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Article |
Continuous evolution of SpCas9 variants compatible with non-G PAMs
PAM sequences without G bases can be edited with SpCas9 variants that were continuously evolved in the laboratory.
- Shannon M. Miller
- , Tina Wang
- & David R. Liu
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Letter |
Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency
Precise genome editing is made more efficient by stabilizing Cas9 and enhancing shuttling to the nucleus.
- David N. Nguyen
- , Theodore L. Roth
- & Alexander Marson
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Letter |
Harnessing type I CRISPR–Cas systems for genome engineering in human cells
A type I CRISPR–Cas system, rather than the conventional type II CRISPR systems, is adapted for gene editing by fusing Cascade to the FokI nuclease domain.
- Peter Cameron
- , Mary M. Coons
- & Samuel H. Sternberg
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Letter |
Adenine base editors catalyze cytosine conversions in human cells
In addition to causing A-to-G base transitions, adenine base editors also cause C base substitutions
- Heon Seok Kim
- , You Kyeong Jeong
- & Sangsu Bae
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Article |
Enhancing gene editing specificity by attenuating DNA cleavage kinetics
Engineered zinc finger nucleases achieve 98% knockout of a target gene in human T cells without detectable off-target activity.
- Jeffrey C. Miller
- , Deepak P. Patil
- & Edward J. Rebar
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Brief Communication |
Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells
A machine learning model based on data from primary human T cells accurately predicts repair outcomes after CRISPR–Cas9 editing.
- Ryan T. Leenay
- , Amirali Aghazadeh
- & James Zou
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Article |
Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs
Cellular RNAs are edited with high specificity using engineered ADAR-recruiting RNAs.
- Liang Qu
- , Zongyi Yi
- & Wensheng Wei
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Letter |
Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors
Wider editing windows and different PAM requirements enable a broad set of genomic positions to be targeted with A and C base editors.
- Tony P. Huang
- , Kevin T. Zhao
- & David R. Liu
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News & Views |
To BE or not to BE, that is the question
In vivo studies indicate that cytosine but not adenine base editors induce elevated levels of genome-wide off-target substitutions.
- Jia Chen
- , Bei Yang
- & Li Yang
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Article |
Increasing the specificity of CRISPR systems with engineered RNA secondary structures
Changes to the secondary structure of the guide RNA enable substantial increases in specificity of Cas9 and Cas12 variants
- D. Dewran Kocak
- , Eric A. Josephs
- & Charles A. Gersbach
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Letter |
Genome-wide target specificity of CRISPR RNA-guided adenine base editors
Unbiased detection of off-target editing by adenine base editors in vitro uncovers differences in the specificity patterns of adenine and cytosine base editors, and of unmodified Cas9.
- Daesik Kim
- , Da-eun Kim
- & Jin-Soo Kim
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Correspondence |
CRISPResso2 provides accurate and rapid genome editing sequence analysis
- Kendell Clement
- , Holly Rees
- & Luca Pinello
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Correspondence |
EU court casts new plant breeding techniques into regulatory limbo
- Kai P Purnhagen
- , Esther Kok
- & Justus Wesseler
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Correspondence |
A call for science-based review of the European court's decision on gene-edited crops
- Fyodor D Urnov
- , Pamela C Ronald
- & Dana Carroll
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Brief Communication |
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Optimization of cytidine and adenine base editors increases editing efficiency.
- Luke W Koblan
- , Jordan L Doman
- & David R Liu
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Article
| Open Access
A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes
Complete population collapse of malaria vector Anopheles gambiae in cages is achieved using a gene drive that targets doublesex.
- Kyros Kyrou
- , Andrew M Hammond
- & Andrea Crisanti
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Brief Communication |
Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion
Increased efficiency of base editing in methylated DNA using human APOBEC3A as a deaminase.
- Xiao Wang
- , Jianan Li
- & Li Yang
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News & Views |
Unexpected CRISPR on-target effects
Cas9 can induce extensive on-target damage, including large deletions, inversions, and insertions.
- Hyunji Lee
- & Jin-Soo Kim
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Letter |
Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements
Cas9-induced double stranded breaks can cause large deletions near the target site and more complex genomic rearrangements in mouse and human stem cells.
- Michael Kosicki
- , Kärt Tomberg
- & Allan Bradley
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News & Views |
A new route to synthetic DNA
An enzymatic approach to oligonucleotide synthesis promises to extend the length and fidelity of synthetic DNA
- Adam Clore
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Letter |
Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos
Knock-in mice with precise insertions are efficiently generated through delivery of CRISPR–Cas9 to two-cell embryos.
- Bin Gu
- , Eszter Posfai
- & Janet Rossant
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Letter |
High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast
An optimized method to introduce precise modifications into the yeast genome enables high-throughput characterization of the phenotypic effect of mutations.
- Xiaoge Guo
- , Alejandro Chavez
- & George M Church
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Article |
Multiplexed precision genome editing with trackable genomic barcodes in yeast
A method to introduce defined mutations into the yeast genome enables saturation mutagenesis of a gene and genome-scale introduction of genetic variants.
- Kevin R Roy
- , Justin D Smith
- & Lars M Steinmetz
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Letter |
Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy
Adenine base editing is used to treat a mouse model of Duchenne muscular dystrophy and to create defined mutations in mouse embryos.
- Seuk-Min Ryu
- , Taeyoung Koo
- & Jin-Soo Kim
Efficient prime editing in two-cell mouse embryos using PEmbryo