Detection of spacer precursors formed in vivo during primed CRISPR adaptation

Anna A. Shiriaeva, Ekaterina Savitskaya, Kirill A. Datsenko, Irina O. Vvedenskaya, Iana Fedorova, Natalia Morozova, Anastasia Metlitskaya, Anton Sabantsev, Bryce E. Nickels, Konstantin Severinov, Ekaterina Semenova

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Type I CRISPR-Cas loci provide prokaryotes with a nucleic-acid-based adaptive immunity against foreign DNA. Immunity involves adaptation, the integration of ~30-bp DNA fragments, termed prespacers, into the CRISPR array as spacers, and interference, the targeted degradation of DNA containing a protospacer. Interference-driven DNA degradation can be coupled with primed adaptation, in which spacers are acquired from DNA surrounding the targeted protospacer. Here we develop a method for strand-specific, high-throughput sequencing of DNA fragments, FragSeq, and apply this method to identify DNA fragments accumulated in Escherichia coli cells undergoing robust primed adaptation by a type I-E or type I-F CRISPR-Cas system. The detected fragments have sequences matching spacers acquired during primed adaptation and function as spacer precursors when introduced exogenously into cells by transformation. The identified prespacers contain a characteristic asymmetrical structure that we propose is a key determinant of integration into the CRISPR array in an orientation that confers immunity.

Original languageEnglish (US)
Article number4603
JournalNature communications
Issue number1
StatePublished - Dec 1 2019


All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Shiriaeva, A. A., Savitskaya, E., Datsenko, K. A., Vvedenskaya, I. O., Fedorova, I., Morozova, N., Metlitskaya, A., Sabantsev, A., Nickels, B. E., Severinov, K., & Semenova, E. (2019). Detection of spacer precursors formed in vivo during primed CRISPR adaptation. Nature communications, 10(1), [4603].