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

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

2018 December | Holly A. Rees and David R. Liu
Base editing is a genome editing technique that allows for precise, single-base changes in DNA or RNA without creating double-stranded DNA breaks (DSBs). It utilizes components from CRISPR systems, such as a catalytically inactive nuclease fused to a deaminase enzyme, to directly modify bases. DNA base editors (BEs) convert cytosine (C) to thymine (T) or adenine (A) to guanine (G), while RNA base editors (ABEs) target RNA for similar conversions. These editors offer advantages over traditional CRISPR-based methods by minimizing off-target effects and enabling efficient editing in non-dividing cells. Cytosine base editors (CBEs) use APOBEC1 deaminase to deaminate cytosine to uracil, which is then converted to thymine. However, uracil DNA glycosylase (UNG) can remove uracil, leading to reversion of the edit. To prevent this, UGI (uracil DNA glycosylase inhibitor) is added to the editor. Third-generation CBEs (BE3) include a nickase domain to direct repair to the edited strand, improving efficiency. Similarly, adenine base editors (ABEs) use deoxyadenosine deaminase to convert adenine to inosine, which is recognized as guanine in mRNA. ABEs are more efficient and have higher specificity than CBEs. RNA base editing can be achieved using antisense oligonucleotides or Cas13-guided systems. Antisense-oligonucleotide-directed A-to-I editing uses ADAR enzymes to deaminate adenosine to inosine. Cas13-guided RNA editing uses dPspCas13b to localize ADAR to target RNA, enabling precise A-to-I editing. These methods have been optimized for efficiency and specificity, with REPAIR being a notable system that allows for broad sequence context compatibility. Base editing has limitations, including off-target effects, bystander editing, and sequence context dependencies. Improvements include the development of high-fidelity base editors, such as HF-BE3 and Sniper-BE3, which reduce off-target effects. Additionally, optimizing codon usage and nuclear localization sequences enhances intracellular expression and efficiency. Viral delivery methods, such as AAV, offer promising avenues for in vivo applications, though challenges remain in packaging large editing complexes. Overall, base editing represents a powerful tool for precise genome and transcriptome modification, with ongoing research aimed at improving efficiency, specificity, and applicability in both research and therapeutic settings.Base editing is a genome editing technique that allows for precise, single-base changes in DNA or RNA without creating double-stranded DNA breaks (DSBs). It utilizes components from CRISPR systems, such as a catalytically inactive nuclease fused to a deaminase enzyme, to directly modify bases. DNA base editors (BEs) convert cytosine (C) to thymine (T) or adenine (A) to guanine (G), while RNA base editors (ABEs) target RNA for similar conversions. These editors offer advantages over traditional CRISPR-based methods by minimizing off-target effects and enabling efficient editing in non-dividing cells. Cytosine base editors (CBEs) use APOBEC1 deaminase to deaminate cytosine to uracil, which is then converted to thymine. However, uracil DNA glycosylase (UNG) can remove uracil, leading to reversion of the edit. To prevent this, UGI (uracil DNA glycosylase inhibitor) is added to the editor. Third-generation CBEs (BE3) include a nickase domain to direct repair to the edited strand, improving efficiency. Similarly, adenine base editors (ABEs) use deoxyadenosine deaminase to convert adenine to inosine, which is recognized as guanine in mRNA. ABEs are more efficient and have higher specificity than CBEs. RNA base editing can be achieved using antisense oligonucleotides or Cas13-guided systems. Antisense-oligonucleotide-directed A-to-I editing uses ADAR enzymes to deaminate adenosine to inosine. Cas13-guided RNA editing uses dPspCas13b to localize ADAR to target RNA, enabling precise A-to-I editing. These methods have been optimized for efficiency and specificity, with REPAIR being a notable system that allows for broad sequence context compatibility. Base editing has limitations, including off-target effects, bystander editing, and sequence context dependencies. Improvements include the development of high-fidelity base editors, such as HF-BE3 and Sniper-BE3, which reduce off-target effects. Additionally, optimizing codon usage and nuclear localization sequences enhances intracellular expression and efficiency. Viral delivery methods, such as AAV, offer promising avenues for in vivo applications, though challenges remain in packaging large editing complexes. Overall, base editing represents a powerful tool for precise genome and transcriptome modification, with ongoing research aimed at improving efficiency, specificity, and applicability in both research and therapeutic settings.
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[slides and audio] Base editing%3A precision chemistry on the genome and transcriptome of living cells