Using CAPTURE to detect spacer acquisition in native CRISPR arrays

Abstract

CRISPR–Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection; however, this often occurs at low frequency within a population, which can make it difficult to detect. Here we describe CAPTURE (CRISPR adaptation PCR technique using reamplification and electrophoresis), a versatile and adaptable protocol to detect spacer-acquisition events by electrophoresis imaging with high-enough sensitivity to identify spacer acquisition in 1 in 105 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, thus allowing the removal of unexpanded arrays from the sample pool and enabling 1,000-times more sensitive detection of new spacers than alternative PCR protocols. CAPTURE is a straightforward method that requires only 1 d to enable the detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unraveling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.

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Fig. 1: Overview of the CAPTURE protocol.
Fig. 2: CAPTURE decision chart.
Fig. 3: Primer design for amplifying the CRISPR arrays within a population.
Fig. 4: Gel electrophoresis images of CRISPR arrays before (Step 5) and after (Step 15) size selection.
Fig. 5: Primer design options for reamplification of expanded CRISPR arrays.
Fig. 6: Anticipated detection results after reamplification.

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Acknowledgements

S.J.J.B. is supported by European Research Council (ERC) StG grant 639707, NWO Vidi grant 864.11.005 and a TU Delft startup grant. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience (NanoFront) program. The authors thank members of the Brouns lab for discussions on the manuscript and feedback.

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Contributions

R.E.M., C.A., J.N.A.V. and S.J.J.B. conceived and designed the experiments; R.E.M., C.A. and J.N.A.V. performed the experiments; R.E.M., C.A., J.N.A.V. and S.J.J.B. analyzed the data; R.E.M. and S.J.J.B. wrote the paper with input from all other authors.

Corresponding author

Correspondence to Stan J. J. Brouns.

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The authors declare no competing interests.

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Key reference using this protocol

Kieper, S. N. et al. Cell Rep. 22, 3377–3384 (2018): https://doi.org/10.1016/j.celrep.2018.02.103

Integrated supplementary information

Supplementary Figure 1 Sequence view of primer sets designed for CAPTURE.

The double-stranded DNA sequence of the array is shown here, including the leader sequence (black), repeat sequences (gray) and the sequence of spacer 1 (blue). Primer sets designed for the type I-E CRISPR system of E. coli K12 are indicated with black boxes and directional arrows.

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Supplementary Figure 1 and Supplementary Table 1

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McKenzie, R.E., Almendros, C., Vink, J.N.A. et al. Using CAPTURE to detect spacer acquisition in native CRISPR arrays. Nat Protoc 14, 976–990 (2019). https://doi.org/10.1038/s41596-018-0123-5

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