The Design and Application of DNA-Editing Enzymes as Base Editors

CRISPR-based genome editing through the lens of DNA repair

(2022) Tarun S. Nambiar et al.   MOLECULAR CELL

Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases

(2022) Kayeong Lim et al.   Nature Communications

Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA editing activity and specificity

(2022) Dhruva Katrekar et al.   eLife

Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases

(2022) Sung-Ik Cho et al.   CELL

CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA

(2022) Beverly Y. Mok et al.   NATURE BIOTECHNOLOGY

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination

(2022) Riccardo Pecori et al.   NATURE REVIEWS GENETICS

Mitochondrial genome engineering coming-of-age

(2022) Jose Domingo Barrera-Paez et al.   TRENDS IN GENETICS

Combined Theoretical, Bioinformatic, and Biochemical Analyses of RNA Editing by Adenine Base Editors

(2022) Kartik L. Rallapalli et al.   CRISPR Journal

Engineering a precise adenine base editor with minimal bystander editing

(2022) Liang Chen et al.   Nature Chemical Biology

Precision genome editing using cytosine and adenine base editors in mammalian cells

(2021) Tony P. Huang et al.   Nature Protocols

An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations

(2021) Marcos H de Moraes et al.   eLife

Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering

(2021) Aaron Cravens et al.   Nature Communications

Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins

(2021) Liwei Chen et al.   Nature Communications

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

Interactions of APOBEC3s with DNA and RNA

(2021) Atanu Maiti et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s

(2021) Shurong Hou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

(2021) Luke W. Koblan et al.   NATURE BIOTECHNOLOGY

Mitochondrial disease: Replace or edit?

(2021) Eli Y. Adashi et al.   SCIENCE

A split cytosine deaminase architecture enables robust inducible base editing

(2021) Jie Long et al.   FASEB JOURNAL

Controllable genome editing with split-engineered base editors

(2021) Kiara N. Berríos et al.   Nature Chemical Biology

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects

(2020) Daniel Hofacker et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

(2020) Chao Li et al.   NATURE BIOTECHNOLOGY

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

(2020) Jordan L. Doman et al.   NATURE BIOTECHNOLOGY

Continuous evolution of SpCas9 variants compatible with non-G PAMs

(2020) Shannon M. Miller et al.   NATURE BIOTECHNOLOGY

Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases

(2020) Eszter Tóth et al.   NUCLEIC ACIDS RESEARCH

Expanding the genome-targeting scope and the site selectivity of high-precision base editors

(2020) Junjie Tan et al.   Nature Communications

Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors

(2020) Kartik L. Rallapalli et al.   Science Advances

Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses

(2020) Jonathan M. Levy et al.   Nature Biomedical Engineering

Directed evolution of adenine base editors with increased activity and therapeutic application

(2020) Nicole M. Gaudelli et al.   NATURE BIOTECHNOLOGY

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

(2020) Michelle F. Richter et al.   NATURE BIOTECHNOLOGY

Dual base editor catalyzes both cytosine and adenine base conversions in human cells

(2020) Xiaohui Zhang et al.   NATURE BIOTECHNOLOGY

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

(2020) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Base editors for simultaneous introduction of C-to-T and A-to-G mutations

(2020) Rina C. Sakata et al.   NATURE BIOTECHNOLOGY

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

(2020) Erwei Zuo et al.   NATURE METHODS

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity

(2020) Yi Yu et al.   Nature Communications

Targeted DNA demethylation of the Fgf21 promoter by CRISPR/dCas9-mediated epigenome editing

(2020) Nozomi Hanzawa et al.   Scientific Reports

A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing

(2020) Beverly Y. Mok et al.   NATURE

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells

(2020) Ibrahim C. Kurt et al.   NATURE BIOTECHNOLOGY

Glycosylase base editors enable C-to-A and C-to-G base changes

(2020) Dongdong Zhao et al.   NATURE BIOTECHNOLOGY

DNA capture by a CRISPR-Cas9–guided adenine base editor

(2020) Audrone Lapinaite et al.   SCIENCE

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

(2020) Linfeng Gao et al.   Nature Communications

Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects

(2020) Sangsin Lee et al.   Science Advances

Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

(2020) Zhiquan Liu et al.   BMC BIOLOGY

ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems

(2020) Jingke Xie et al.   BMC BIOLOGY

Base editing: advances and therapeutic opportunities

(2020) Elizabeth M. Porto et al.   NATURE REVIEWS DRUG DISCOVERY

A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes

(2019) A. St. Martin et al.   Scientific Reports

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

(2019) Benjamin P. Kleinstiver et al.   NATURE BIOTECHNOLOGY

Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG

(2019) Zhaohui Zhong et al.   Molecular Plant

Cas9-NG greatly expands the targeting scope of genome-editing toolkit by recognizing NG and other atypical PAMs in rice

(2019) Bin Ren et al.   Molecular Plant

Improved base editor for efficient editing in GC contexts in rabbits with an optimized AID-Cas9 fusion

(2019) Zhiquan Liu et al.   FASEB JOURNAL

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors

(2019) Tony P. Huang et al.   NATURE BIOTECHNOLOGY

Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision

(2019) Woo-Chan Ahn et al.   Nature Chemical Biology

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

(2019) Henriette O’Geen et al.   Epigenetics & Chromatin

DNAmod: the DNA modification database

(2019) Ankur Jai Sood et al.   Journal of Cheminformatics

Increasing Cytosine Base Editing Scope and Efficiency With Engineered Cas9-PmCDA1 Fusions and the Modified sgRNA in Rice

(2019) Ying Wu et al.   Frontiers in Genetics

Analysis and minimization of cellular RNA editing by DNA adenine base editors

(2019) Holly A. Rees et al.   Science Advances

Reprogrammable CRISPR/dCas9-based recruitment of DNMT1 for site-specific DNA demethylation and gene regulation

(2019) Anrui Lu et al.   Cell Discovery

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

Targeted removal of epigenetic barriers during transcriptional reprogramming

(2019) Valentin Baumann et al.   Nature Communications

Off-Target Editing by CRISPR-Guided DNA Base Editors

(2019) SeHee Park et al.   BIOCHEMISTRY

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

(2019) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Adenine base editors catalyze cytosine conversions in human cells

(2019) Heon Seok Kim et al.   NATURE BIOTECHNOLOGY

Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system

(2019) Goran Josipović et al.   NUCLEIC ACIDS RESEARCH

Multiplex nucleotide editing by high-fidelity Cas9 variants with improved efficiency in rice

(2019) Wen Xu et al.   BMC PLANT BIOLOGY

Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways

(2019) Aziz Taghbalout et al.   Nature Communications

Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system

(2019) Jeong Gu Kang et al.   Scientific Reports

Editing the Epigenome: Reshaping the Genomic Landscape

(2018) Liad Holtzman et al.   Annual Review of Genomics and Human Genetics

CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells

(2018) Nicolas Marx et al.   Biotechnology Journal

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

(2018) X. Shawn Liu et al.   CELL

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

(2018) Christian Pflueger et al.   GENOME RESEARCH

Structural basis for DNMT3A-mediated de novo DNA methylation

(2018) Zhi-Min Zhang et al.   NATURE

Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy

(2018) Seuk-Min Ryu et al.   NATURE BIOTECHNOLOGY

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC–Cas9 or cleavage by Cas9 in living cells

(2018) Amber St. Martin et al.   NUCLEIC ACIDS RESEARCH

Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells

(2018) Tafadzwa Mlambo et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Genome Engineering: The Revolution May Not Be CRISPR-Ized

(2018) Payam A. Gammage et al.   TRENDS IN GENETICS

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells

(2018) Nicolas Marx et al.   Biotechnology Journal

Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases

(2018) Lin Lin et al.   GigaScience

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion

(2018) Xiao Wang et al.   NATURE BIOTECHNOLOGY

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Directed evolution of CRISPR-Cas9 to increase its specificity

(2018) Jungjoon K. Lee et al.   Nature Communications

High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis

(2018) Xingbo Xu et al.   Nature Communications

Genome, Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells

(2018) Brodie L. Ranzau et al.   BIOCHEMISTRY

BE-FLARE: a fluorescent reporter of base editing activity reveals editing characteristics of APOBEC3A and APOBEC3B

(2018) Matthew A. Coelho et al.   BMC BIOLOGY

Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase

(2018) Juanjuan Yuan et al.   MOLECULAR CELL

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Proteins

(2017) Fumiaki Ito et al.   JOURNAL OF MOLECULAR BIOLOGY

AID Recognizes Structured DNA for Class Switch Recombination

(2017) Qi Qiao et al.   MOLECULAR CELL

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Stabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells

(2017) Masahiro Okada et al.   Epigenetics & Chromatin

Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

(2017) Yong Lei et al.   Nature Communications

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

(2017) Takahide Kouno et al.   Nature Communications

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

(2017) Holly A. Rees et al.   Nature Communications

Effective gene editing by high-fidelity base editor 2 in mouse zygotes

(2017) Puping Liang et al.   Protein & Cell

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

Targeted DNA methylation in human cells using engineered dCas9-methyltransferases

(2017) Tina Xiong et al.   Scientific Reports

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro approach to protein engineering

(2016) Y. Gumulya et al.   BIOCHEMICAL JOURNAL

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

(2016) K. Nishida et al.   SCIENCE

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Epigenome Editing: State of the Art, Concepts, and Perspectives

(2016) Goran Kungulovski et al.   TRENDS IN GENETICS

Engineering and optimising deaminase fusions for genome editing

(2016) Luhan Yang et al.   Nature Communications

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter

(2016) Samrat Roy Choudhury et al.   Oncotarget

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Structural insight into substrate preference for TET-mediated oxidation

(2015) Lulu Hu et al.   NATURE

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

(2014) Hao Wu et al.   CELL

Inosine in DNA and RNA

(2014) Ingrun Alseth et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

(2013) Hideharu Hashimoto et al.   NATURE

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter

(2013) Hui Chen et al.   NUCLEIC ACIDS RESEARCH

Base Excision Repair

(2013) H. E. Krokan et al.   Cold Spring Harbor Perspectives in Biology

Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases

(2012) WeiShen Aik et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Epigenetic reprogramming of cancer cells via targeted DNA methylation

(2012) Ashley G. Rivenbark et al.   Epigenetics

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

(2012) Liang Zhang et al.   Nature Chemical Biology

DNA Methylation and Its Basic Function

(2012) Lisa D Moore et al.   NEUROPSYCHOPHARMACOLOGY

Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes

(2012) M. L. de Groote et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

(2011) Brad R Rosenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

(2011) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

(2010) J. Song et al.   SCIENCE

AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity

(2009) Meng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G

(2008) Kuan-Ming Chen et al.   NATURE

The AID/APOBEC family of nucleic acid mutators

(2008) Silvestro G Conticello   GENOME BIOLOGY