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bioRxiv · 10.64898/2026.07.09.737519

CRISPR-Cas interference decays rapidly with distance from the leader sequence in a long array

Ceelen, M. H.·Albertini, M.·Velicer, G. J.·Wielgoss, S.
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Abstract

Spacer efficacy generally declines with distance from the leader sequence, but the scarcity of fine-scale studies hampers comparisons across taxa. Here, we investigated positional effects across an exceptionally long 121-spacer CRISPR array associated with the type I-C cas operon of a Myxococcus xanthus natural isolate. In plasmid-interference assays, we found that interference rapidly declined with distance from the leader sequence, with only the proximal [~]4% of spacers conferring measurable interference. This contrasts strikingly with a study in Vibrio cholerae, in which it was shown that [~]95% of spacers in a shorter (39-spacer) array were effective. Our results suggest that there is great variation in the effective proportion of spacers across species, highlighting the need for fine-scale studies of CRISPR-array activity across diverse bacterial lineages.

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Ceelen, M. H., Albertini, M., Velicer, G. J., Wielgoss, S.. 2026-07-09. CRISPR-Cas interference decays rapidly with distance from the leader sequence in a long array. https://doi.org/10.64898/2026.07.09.737519

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