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

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

Cytosine base editors (CBEs) enable efficient, programmable reversion of T•A to C•G point mutations in the human genome. Recently, cytosine base editors with rAPOBEC1 were reported to induce unguided cytosine deamination in genomic DNA and cellular RNA. Here we report eight next-generation CBEs (BE4...

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Bibliographic Details
Published in:Nature communications Vol. 11; no. 1; pp. 2052 - 10
Main Authors: Yu, Yi, Leete, Thomas C., Born, David A., Young, Lauren, Barrera, Luis A., Lee, Seung-Joo, Rees, Holly A., Ciaramella, Giuseppe, Gaudelli, Nicole M.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 28-04-2020
Nature Publishing Group
Nature Portfolio
Subjects:
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APOBEC-1 Deaminase - metabolism
Cytosine
Cytosine - metabolism
Cytosine Deaminase - metabolism
Deamination
Deoxyribonucleic acid
DNA
DNA - genetics
DNA Replication - genetics
Editing
Gene Editing
Gene expression
Genome
Genomes
HEK293 Cells
Humanities and Social Sciences
Humans
Mammalian cells
multidisciplinary
Mutagenesis - genetics
Mutation
Reduction
Reversion
Ribonucleic acid
RNA
RNA - genetics
Science
Science (multidisciplinary)
Transcription, Genetic
Transcriptome - genetics
Transfection
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Description
Summary:Cytosine base editors (CBEs) enable efficient, programmable reversion of T•A to C•G point mutations in the human genome. Recently, cytosine base editors with rAPOBEC1 were reported to induce unguided cytosine deamination in genomic DNA and cellular RNA. Here we report eight next-generation CBEs (BE4 with either RrA3F [wt, F130L], AmAPOBEC1, SsAPOBEC3B [wt, R54Q], or PpAPOBEC1 [wt, H122A, R33A]) that display comparable DNA on-target editing frequencies, whilst eliciting a 12- to 69-fold reduction in C-to-U edits in the transcriptome, and up to a 45-fold overall reduction in unguided off-target DNA deamination relative to BE4 containing rAPOBEC1. Further, no enrichment of genome-wide C•G to T•A edits are observed in mammalian cells following transfection of mRNA encoding five of these next-generation editors. Taken together, these next-generation CBEs represent a collection of base editing tools for applications in which minimized off-target and high on-target activity are required. Cytosine base editors have been reported to induce off-target mutations in DNA and RNA. Here the authors identify next-generation CBEs with reduced guide-independent off-target editing profiles and retain high on-target editing activity.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-020-15887-5