Le CRISPR, an acronyme for Clustered Regularly Interspaced Short Palindromic Repeats, was first observed in the E. coli genome in 1987. These genetic loci consist of short, repeated DNA sequences separated by unique ‘spacer’ sequences derived from foreign genetic elements. Initially termed SRSR, their biological function was unknown, but their unique structure suggested an important, albeit mysterious, role within prokaryotic genomes.
The initial discovery of what would later be named CRISPR was an incidental finding during the sequencing of the IAP gene in Escherichia coli. Researchers dirigé by Yoshizumi Ishino at Osaka University noticed an unusual series of 29-nucleotide repeats, partially palindromic, arranged in a cluster. These repeats were separated by non-repetitive, unique sequences of 32 nucleotides, which were later termed ‘spacers’. This peculiar structure was unlike anything previously described in bacterial genomes. At the time, DNA sequencing was a laborious process, and the function of these repeats was a complete mystery. The authors noted the structure in their publication but could not assign a biological role to it.
Similar structures were subsequently identified in a wide range of other bacteria and archaea, indicating that this was a widespread feature of prokaryotic genomes. The consistent structure—alternating repeats and spacers—and the conservation of the repeat sequences within a given species suggested a functional importance. The palindromic nature of the repeats hinted at the potential for forming secondary structures like hairpins in RNA transcripts, a common feature in regulatory elements. However, it was the unique nature of the spacer sequences that held the key to CRISPR’s function, a puzzle that would not be solved for over a decade. This foundational, observational discovery laid the essential groundwork for all subsequent research into the CRISPR-Cas system’s role in adaptive immunity and its eventual application in biotechnology.
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