High-throughput base editing KO screening of cellular factors for enhanced GBE

Jie Yang; Dongdong Zhao; Xiagu Zhu; Yuanzhao Yang; Bo Li; Siwei Li; Chang-Hao Bi; Xue-Li Zhang

doi:10.1016/j.jgg.2023.05.007

Volume 50 Issue 8

Aug. 2023

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2023 > 50(8): 611-614

PDF( 514 KB)

High-throughput base editing KO screening of cellular factors for enhanced GBE

doi: 10.1016/j.jgg.2023.05.007

Jie Yang^a,b,c,d,
Dongdong Zhao^b,c,d,
Xiagu Zhu^a,b,c,d,
Yuanzhao Yang^a,b,c,d,
Bo Li^b,c,d,e,
Siwei Li^b,c,d,
Chang-Hao Bi^b,c,d,
Xue-Li Zhang^b,c,d

a College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China;
b Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
c Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
d National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China;
e University of Chinese Academy of Sciences, Beijing 100049, China

Funds:

This work was financially supported by the National Key Research and Development Program of China (2018YFA0901300), the National Natural Science Foundation of China (32171449, 81903776), a Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-KJGG-001), Tianjin Natural Science Foundation (20JCYBJC00310), and Youth Innovation Promotion Association CAS (2022177).

Received Date: 2023-01-26
Publish Date: 2023-05-25

Abstract

FullText(HTML)

References(15)

References

Arbab, M., Shen, M.W., Mok, B., Wilson, C., Matuszek, Z., Cassa, C.A., Liu, D.R., 2020. Determinants of base editing outcomes from target library analysis and machine learning. Cell 182, 463-480.

Gaudelli, N.M., Komor, A.C., Rees, H.A., Packer, M.S., Badran, A.H., Bryson, D.I., Liu, D.R., 2017. Programmable base editing of A T to G C in genomic DNA without DNA cleavage. Nature 551, 464-471.

Jiang, G., Wang, J., Zhao, D., Chen, X., Pu, S., Zhang, C., Li, J., Li, Y., Yang, J., Li, S., et al., 2021. Molecular mechanism of the cytosine CRISPR base editing process and the roles of translesion DNA polymerases. ACS Synth. Biol. 10, 3353-3358.

Kim, H.K., Min, S., Song, M., Jung, S., Choi, J.W., Kim, Y., Lee, S., Yoon, S., Kim, H.H., 2018. Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat. Biotechnol. 36, 239-241.

Koblan, L.W., Doman, J.L., Wilson, C., Levy, J.M., Tay, T., Newby, G.A., Maianti, J.P., Raguram, A., Liu, D.R., 2018. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol. 36, 843-846.

Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A., Liu, D.R., 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424.

Li, B., Li, Y.Q., Zhao, D., Yang, J., Ma, Y.H., Bi, C.H., Zhang, X.L., 2022a. Sequence motifs and prediction model of GBE editing outcomes based on target library analysis and machine learning. J. Genet. Genomics 49, 254-257.

Li, G., Li, X., Zhuang, S., Wang, L., Zhu, Y., Chen, Y., Sun, W., Wu, Z., Zhou, Z., Chen, J., et al., 2022b. Gene editing and its applications in biomedicine. Sci. China Life Sci. 65, 660-700.

Maalouf, M., 2011. Logistic regression in data analysis:an overview. Int. J. Data Anal. Tech. Strat. 3, 281-299.

Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., et al., 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729.

Sakamoto, A.N., Kaya, H., Endo, M., 2018. Deletion of TLS polymerases promotes homologous recombination in Arabidopsis. Plant Signal. Behav. 13, e1483673.

Song, M., Kim, H.K., Lee, S., Kim, Y., Seo, S.Y., Park, J., Choi, J.W., Jang, H., Shin, J.H., Min, S., et al., 2020. Sequence-specific prediction of the efficiencies of adenine and cytosine base. Nat. Biotechnol. 38, 1037-1043.

Uriarte-Arcia, A.V., Lopez-Yanez, I., Yanez-Marquez, C., 2014. One-hot vector hybrid associative classifier for medical data classification. PLoS ONE 9, e95715.

Xu, P., Liu, Z., Liu, Y., Ma, H., Xu, Y., Bao, Y., Zhu, S., Cao, Z., Wu, Z., Zhou, Z., et al., 2021. Genome-wide interrogation of gene functions through base editor screens empowered by barcoded sgRNAs. Nat. Biotechnol. 39, 1403-1413.

Zhao, D., Li, J., Li, S., Xin, X., Hu, M., Price, M.A., Rosser, S.J., Bi, C.H., Zhang, X., 2021. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat. Biotechnol. 39, 35-40.

Relative Articles

Supplements(0)

Cited By

Proportional views