Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase

Abstract DNA base editors could enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here, by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants, we developed a deaminase-free glycosylase-based thymine base editor (gTBE) with the ability of direct T editing. By several rounds of UNG mutagenesis via rational screening, we demonstrated that gTBE with engineered UNG variants could achieve T editing efficiency by up to 81.5%. Furthermore, the gTBE exhibited high T-to-S (i.e., T-to-C or T-to-G) conversion ratio with up to 0.97 in cultured human cells. Using similar strategy, we developed a deaminase-free cytosine base editor (gCBE) facilitating specifically direct C editing by engineered UNG with mutations different from gTBE. Thus, we provide two novel base editors, gTBE and gCBE, with corresponding engineered UNG variants, broadening the targeting scope of base editors. Competing Interest Statement H.T., H.W., N.L., D.W., Y.L., G.L., H.L., Y.Z., and Y.Y. are employees of HuidaGene Therapeutics Co., Ltd. H.Y., L.S. and X.Y. are cofounders of HuidaGene Therapeutics Co., Ltd. The remaining authors declare no competing interests.