Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases

Commun Biol. 2021 Jul 2;4(1):830. doi: 10.1038/s42003-021-02351-3.

Abstract

Genome-wide identification of DNA double-strand breaks (DSBs) induced by CRISPR-associated protein (Cas) systems is vital for profiling the off-target events of Cas nucleases. However, current methods for off-target discovery are tedious and costly, restricting their widespread applications. Here we present an easy alternative method for CRISPR off-target detection by tracing the integrated oligonucleotide Tag using next-generation-sequencing (CRISPR-Tag-seq, or Tag-seq). Tag-seq enables rapid and convenient profiling of nuclease-induced DSBs by incorporating the optimized double-stranded oligodeoxynucleotide sequence (termed Tag), adapters, and PCR primers. Moreover, we employ a one-step procedure for library preparation in Tag-seq, which can be applied in the routine workflow of a molecular biology laboratory. We further show that Tag-seq successfully determines the cleavage specificity of SpCas9 variants and Cas12a/Cpf1 in a large-scale manner, and discover the integration sites of exogenous genes introduced by the Sleeping Beauty transposon. Our results demonstrate that Tag-seq is an efficient and scalable approach to genome-wide identification of Cas-nuclease-induced off-targets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Associated Protein 9 / genetics
  • CRISPR-Associated Protein 9 / metabolism*
  • CRISPR-Cas Systems*
  • DNA / genetics
  • DNA Breaks, Double-Stranded*
  • Gene Editing / methods*
  • Genome, Human / genetics
  • Genome-Wide Association Study / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Oligodeoxyribonucleotides / genetics
  • Reproducibility of Results

Substances

  • Oligodeoxyribonucleotides
  • DNA
  • CRISPR-Associated Protein 9