Multiplex base editing to convert TAG into TAA codons in the human genome

Yuting Chen; Eriona Hysolli; Anlu Chen; Stephen Casper; Songlei Liu; Kevin Yang; Chenli Liu; George Church

doi:10.1038/s41467-022-31927-8

Multiplex base editing to convert TAG into TAA codons in the human genome

Nat Commun. 2022 Aug 2;13(1):4482. doi: 10.1038/s41467-022-31927-8.

Authors

Yuting Chen^#^{1

2

3}, Eriona Hysolli^#^{4

5}, Anlu Chen^#⁶, Stephen Casper^#¹, Songlei Liu^{1

2}, Kevin Yang¹, Chenli Liu⁷, George Church^{8

9}

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
² Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115, USA.
³ CAS Key Laboratory of Quantitative Engineering Biology, Center for Genome Engineering and Therapy, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
⁴ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. eriona.hysolli@gmail.com.
⁵ Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115, USA. eriona.hysolli@gmail.com.
⁶ Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
⁷ CAS Key Laboratory of Quantitative Engineering Biology, Center for Genome Engineering and Therapy, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China. cl.liu@siat.ac.cn.
⁸ Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. gchurch@genetics.med.harvard.edu.
⁹ Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115, USA. gchurch@genetics.med.harvard.edu.

^# Contributed equally.

Abstract

Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
CRISPR-Cas Systems / genetics
Codon, Terminator
Exons
Gene Editing*
Genes, Essential
Genome, Human* / genetics
Humans
Mammals / genetics

Substances

Codon, Terminator