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

• Published in: Nucleic acids research 2018-08, Vol.46 (14), p.e84-e84
• Main Authors: St. Martin, Amber, Salamango, Daniel, Serebrenik, Artur, Shaban, Nadine, Brown, William L, Donati, Francesco, Munagala, Uday, Conticello, Silvestro G, Harris, Reuben S
• Format: Article
• Language: English
• Subjects: Animals; Chlorocebus aethiops; CHO Cells; COS Cells; Cricetulus; CRISPR-Associated Protein 9; Cytidine Deaminase; DNA Cleavage; Fluorescent Dyes; Gene Editing; Genes, Reporter; Green Fluorescent Proteins; HEK293 Cells; HeLa Cells; Humans; Luminescent Proteins; Methods Online; Minor Histocompatibility Antigens; Proteins; Red Fluorescent Protein
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky332

Abstract Base editing is an exciting new genome engineering technology. C-to-T mutations in genomic DNA have been achieved using ribonucleoprotein complexes comprised of rat APOBEC1 single-stranded DNA deaminase, Cas9 nickase (Cas9n), uracil DNA glycosylase inhibitor (UGI), and guide (g)RNA. Here, we report the first real-time reporter system for quantification of APOBEC-mediated base editing activity in living mammalian cells. The reporter expresses eGFP constitutively as a marker for transfection or transduction, and editing restores functionality of an upstream mCherry cassette through the simultaneous processing of two gRNA binding regions that each contain an APOBEC-preferred 5′TCA target site. Using this system as both an episomal and a chromosomal editing reporter, we show that human APOBEC3A-Cas9n-UGI and APOBEC3B-Cas9n-UGI base editing complexes are more efficient than the original rat APOBEC1-Cas9n-UGI construct. We also demonstrate coincident enrichment of editing events at a heterologous chromosomal locus in reporter-edited, mCherry-positive cells. The mCherry reporter also quantifies the double-stranded DNA cleavage activity of Cas9, and may therefore be adaptable for use with many different CRISPR systems. The combination of a rapid, fluorescence-based editing reporter system and more efficient, structurally defined DNA editing enzymes broadens the versatility of the rapidly expanding toolbox of genome editing and engineering technologies.