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CRISPR-Cas base editing technology enables targeted nucleotide modifications and is rapidly deployed for research and potential therapeutic applications1.2. The most widely used base editors induce deamination of cytosine (C) DNA with the rat APOBEC1 enzyme (rAPOBEC1), which is targeted by a guide protein-RNA protein complex (TRNA)3.4. Previous studies on the specificity of the basic cytosine editor (CBE) have allowed for the identification of non-targeted DNA modifications in human cells.5.6. We show here that a CBE associated with rAPOBEC1 can cause extensive deletion of RNA cytosine at the transcriptome level in human cells, inducing tens of thousands of C-to-uracil (U) modifications with frequencies ranging from from 0.07% to 100% in 38% to 58%. of expressed genes. CBE-induced RNA changes occur in both the protein coding and non-coding sequences and generate missense mutations, nonsense, splice site, 5 'UTR and 3' UTR. We have developed two CBE variants carrying rAPOBEC1 mutations that significantly reduce the number of RNA modifications (> 390 fold and> 3,800 fold reductions) in human cells. These variants also showed a more accurate target DNA editing and, with the majority of the gRNAs tested, an editing efficiency comparable to that observed with a wild-type CBE. Finally, we show that the recently described adenine base (ABE) editors can also induce RNA modifications at the transcriptome scale. These results have important implications for research and therapeutic uses of basic editors, illustrate the feasibility of engineering improved variants with reduced RNA editing activities, and suggest the need to define and to further characterize the effects of non-targeted RNAs of deaminase enzymes in the basic editor. platforms.
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