Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Open accessAbstract
Base editors enable targeted single-nucleotide conversions in genomic DNA. Here we show that expression levels are a bottleneck in base-editing efficiency. We optimize cytidine (BE4) and adenine (ABE7.10) base editors by modification of nuclear localization signals (NLS) and codon usage, and ancestral reconstruction of the deaminase component. The resulting BE4max, AncBE4max, and ABEmax editors correct pathogenic SNPs with substantially increased efficiency in a variety of mammalian cell types.
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Base editors with restricted sequence context, such as AncBE4max, exhibit low editing efficiencies in a GC context.
“Base editors with restricted sequence context, such as AncBE4max, exhibit low editing efficiencies in a GC context.”
From Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools (2024) · cites this paper as [24]
The paper’s main text (indexed under Abstract; no page supplied) identifies AncBE4max and reports improved editing at tested loci, but does not report its efficiency in a GC sequence context. Searches for “GC context,” “sequence context,” and GC-specific editing found no passage establishing the claimed restriction or low efficiency. (LLM, conf=0.77)
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“9max; n = 669 for BE4max).”
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“…spanning positions 4 – 8 nt in the protospacer region, with the PAM located at positions 21 – 23 nt. Enhancements in editing ef fi ciency were achieved by optimizing the codon usage and incorporating an additional nuclear localization sequence (NLS) for use in mammalian cells (Koblan et al., 2018).”
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- Authors
- Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Liu, David R
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2018-05-29
- Volume
- 36
- Issue
- 9
- Pages
- 843-846
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC6126947
- OpenAlex
- W2805505209
- Cited by
- 944
- References
- 8
- Citations by year
- 2026: 81 · 2025: 117 · 2024: 144 · 2023: 164 · 2022: 123 · 2021: 129 · 2020: 103 · 2019: 73 · 2018: 9
- FWCI
- 28.19
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (RM1HG009490)
- National Cancer Institute (P30CA014051)
- National Institute of General Medical Sciences (T32GM095450, R35GM118062)
- National Institute of Biomedical Imaging and Bioengineering (R01EB022376)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Keywords
- base editors, adenine base editors, expression optimization, nuclear localization signal, codon usage, ancestral state reconstruction, deaminase, genome editing efficiency
- MeSH terms
- Gene Editing, Adenine, Codon, Cytidine, DNA, Humans, HEK293 Cells, CRISPR-Cas Systems
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