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 () and Ekaterina Semenova ()
Additional contact information
Anna A. Shiriaeva: Center of Life Sciences, Skolkovo Institute of Science and Technology
Ekaterina Savitskaya: Center of Life Sciences, Skolkovo Institute of Science and Technology
Kirill A. Datsenko: Rutgers University
Irina O. Vvedenskaya: Rutgers University
Iana Fedorova: Center of Life Sciences, Skolkovo Institute of Science and Technology
Natalia Morozova: Center of Life Sciences, Skolkovo Institute of Science and Technology
Anastasia Metlitskaya: Institute of Molecular Genetics, Russian Academy of Sciences
Anton Sabantsev: Peter the Great St. Petersburg Polytechnic University
Bryce E. Nickels: Rutgers University
Konstantin Severinov: Center of Life Sciences, Skolkovo Institute of Science and Technology
Ekaterina Semenova: Rutgers University

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: Abstract 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.

Date: 2019
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-019-12417-w Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12417-w

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-019-12417-w

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().