Position of Deltaproteobacteria Cas12e nuclease cleavage sites depends on spacer length of guide RNA

Polina Selkova, Aleksandra Vasileva, Georgii Pobegalov, Olga Musharova, Anatolii Arseniev, Maksim Kazalov, Tatyana Zyubko, Nataliia Shcheglova, Tatyana Artamonova, Mikhail Khodorkovskii, Konstantin Severinov, Iana Fedorova

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


Cas12e proteins (formerly CasX) form a distinct subtype of Class II type V CRISPR-Cas effectors. Recently, it was shown that DpbCas12e from Deltaproteobacteria and PlmCas12e from Planctomycetes can introduce programmable double-stranded breaks in mammalian genomes. Thus, along with Cas9 and Cas12a Class II effectors, Cas12e could be harnessed for genome editing and engineering. The location of cleavage points in DNA targets is important for application of Cas nucleases in biotechnology. DpbCas12e was reported to produce extensive 5ʹ-overhangs at cleaved targets, which can make it superior for some applications. Here, we used high throughput sequencing to precisely map the DNA cut site positions of DpbCas12e on several DNA targets. In contrast to previous observations, our results demonstrate that DNA cleavage pattern of Cas12e is very similar to that of Cas12a: DpbCas12e predominantly cleaves DNA after nucleotide position 17–19 downstream of PAM in the non-target DNA strand, and after the 22nd position of target strand, producing 3–5 nucleotide-long 5ʹ-overhangs. We also show that reduction of spacer sgRNA sequence from 20nt to 16nt shifts Cas12e cleavage positions on the non-target DNA strand closer to the PAM, producing longer 6–8nt 5ʹ-overhangs. Overall, these findings advance the understanding of Cas12e endonucleases and may be useful for developing of DpbCas12e-based biotechnology instruments.

Original languageEnglish
Pages (from-to)1472-1479
Number of pages8
JournalRNA Biology
Issue number10
Publication statusPublished - 2 Oct 2020
Externally publishedYes


  • AsCas12a
  • AsCpf1
  • CasX
  • CRISPR-Cas
  • cut site mapping
  • DpbCas12e
  • sgRNA
  • SpCas9


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