Developing high-efficiency base editors by combining optimized synergistic core components with new types of nuclear localization signal peptide

Abstract

The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein (Cas) system has been widely used for genome editing. In this system, the cytosine base editor (CBE) and adenine base editor (ABE) allow generating precise and irreversible base mutations in a programmable manner and have been used in many different types of cells and organisms. However, their applications are limited by low editing efficiency at certain genomic target sites or at specific target cytosine (C) or adenine (A) residues. Using a strategy of combining optimized synergistic core components, we developed a new multiplex super-assembled ABE (sABE) in rice that showed higher base-editing efficiency than previously developed ABEs. We also designed a new type of nuclear localization signal (NLS) comprising a FLAG epitope tag with four copies of a codon-optimized NLS (F4NLSr2) to generate another ABE named F4NLS-sABE. This new NLS increased editing efficiency or edited additional A at several target sites. A new multiplex super-assembled CBE (sCBE) and F4NLSr2 involved F4NLS-sCBE were also created using the same strategy. F4NLS-sCBE was proven to be much more efficient than sCBE in rice. These optimized base editors will serve as powerful genome-editing tools for basic research or molecular breeding in rice and will provide a reference for the development of superior editing tools for other plants or animals.