Research

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Victor Kunin^*†, Rotem Sorek^† and Philip Hugenholtz

• * Corresponding author: Victor Kunin vkunin@lbl.gov

• † Equal contributors

Author Affiliations

DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

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Genome Biology 2007, 8:R61 doi:10.1186/gb-2007-8-4-r61

Published: 18 April 2007

Abstract

Background

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes.

Results

Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. Some of the clusters present stable, highly conserved RNA secondary structures, while others lack detectable structures. Stable secondary structures exhibit multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation.

Conclusion

We show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification, including specific relationships between CRISPR and CAS subtypes.