Efficiency of SpCas9 and AsCpf1 (Cas12a) programmable nucleases at genomic safe harbor loci in HEK293 cells

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Abstract

Rationale: The development of eukaryote genome engineering tools based on CRISPR-Cas programmable bacterial nucleases systems opens wide horizons for gene therapies, human disease cell modeling, as well as investigation into manifestation of disease phenotypes and visualization of cellular processes. The safety and approximation of experiments both at the cellular and organismal levels depend on the accuracy of introducing double-stranded breaks into the target DNA regions. The search for new variants of more accurate CRISPR-Cas nucleases and evaluation of their ability to hydrolyze nucleosome DNA in vivo is considered a critical task for the development of the genome engineering technologies.

Aim: To analyze the activity of the programmable nuclease AsCpf1 (Cas12a), with low level of off-target activity, in the human genome loci that are safe for the introduction of transgenic constructs (“safe harbor”) and to compare its efficiency with that of the widely used SpCas9 nuclease in HEK293 cells.

Materials and methods: We performed the bioinformatics analysis of the association between target regions with nucleosomes and other proteins in the safe harbor loci AAVS1 and GSH-Ch1 and the transcriptionally inactive gene MYBPC3 (cardiac myosin binding protein 3) based on ATAC-seq data for the HEK293FT cells obtained from the NCBI SRA database. Plasmids encoding SpCas9 and AsCpf1 nucleases and guide RNA to the target regions were constructed and transfected into the HEK293FT cells. Events in the target regions of the HEK293FT cell genome were studied in the sequenograms with the TIDE algorithm.

Results: The results of the ATAC-seq experiments for HEK293FT cells have shown that the AAVS1 locus can be referred as open chromatin with a low nucleosome density, while the GSH-Ch1 locus can be attributed to closed chromatin. In HEK293FT cells, the cardiac MYBPC3 gene has intermediate chromatin density. Assessment of the efficiency of introducing breaks into the studied HEK293FT cell chromatin loci by nucleases has shown that SpCas9 is able to cope with chromatin of any nucleosome density, while AsCpf1 can effectively introduce DNA breaks only at loci with open chromatin, such as AAVS1 and MYBPC3. Editing events occur at a very low rate at the GSH-Ch1 locus with a high nucleosome density.

Conclusion: We have found low efficiency of the AsCpf1 nuclease in the genomic safe harbor locus GSH-Ch1, which is characterized by a high nucleosome density. When planning an experiment on AsCpf1 nuclease genome editing, the epigenetic chromatin landscape and the nucleosome density should be considered, as well as chromatin opening substances should be used.

About the authors

S. V. Pavlova

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences

Author for correspondence.
Email: sonpavlova@gmail.com
ORCID iD: 0000-0003-1095-3692

Sophia V. Pavlova – PhD (in Biol.), Research Fellow, Laboratory of Developmental Epigenetics

1–16 Mal'tseva ul., Novosibirsk, 630090

 

Russian Federation

E. A. Elisaphenko

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences

Email: antares@bionet.nsc.ru
ORCID iD: 0000-0002-3204-8178

Evgeny A. Elisaphenko – PhD (in Biol.), Senior Research Fellow, Laboratory of Developmental Epigenetics

10 Akademika Lavrent'yeva prospekt, Novosibirsk, 630090

Russian Federation

L. Sh. Shayakhmetova

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences;
Novosibirsk State University

Email: fake@neicon.ru

Lilia Sh. Shayakhmetova – Laboratory Assistant Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences; Bachelor Novosibirsk State University

10 Akademika Lavrent'yeva prospekt, Novosibirsk, 630090;

1 Pirogova ul., Novosibirsk, 630090

Russian Federation

S. P. Medvedev

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences

Email: fake@neicon.ru
ORCID iD: 0000-0002-1520-5549

Sergey P. Medvedev – PhD (in Biol.), Leading Research Fellow, Laboratory of Developmental Epigenetics

10 Akademika Lavrent'yeva prospekt, Novosibirsk, 630090

Russian Federation

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Copyright (c) 2021 Pavlova S.V., Elisaphenko E.A., Shayakhmetova L.S., Medvedev S.P.

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