During the CRISPR–Cas adaptation process, the Cas1–Cas2 complex inserts new spacers between the leader sequence and the first repeat of the CRISPR array. Now, Nivala et al. report that non-canonical off-target integrations can occur in vivo at CRISPR repeat-like sequences within the genome of Escherichia coli. Most of the off-target spacer integrations occured downstream of endogenous promoters within protein-coding regions of non-essential genes and off-target integration products were shown to be expressed. The authors propose that, although probably mostly deleterious, off-target integration could potentially lead to the expression of functional CRISPR RNAs and increase spacer diversity. They also uncovered putative off-target spacer integration events in previously sequenced genomes of Yersinia pestis and Sulfolobus islandicus, and termed the phenomenon of non-canonical spacer integration 'neo-CRISPR genesis'.
Nivala, J., Shipman, S. L. & Church, G. M. Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat. Microbiol. https://doi.org/10.1038/s41564-017-0097-z (2018)