Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Kunin, Victor, Sorek, Rotem and Hugenholtz, Philip (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 4 Article # R61: R61-1-R61-3. doi:10.1186/gb-2007-8-4-r61


Author Kunin, Victor
Sorek, Rotem
Hugenholtz, Philip
Title Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-7596
Publication date 2007-01-01
Sub-type Article (original research)
DOI 10.1186/gb-2007-8-4-r61
Open Access Status DOI
Volume 8
Issue 4 Article # R61
Start page R61-1
End page R61-3
Total pages 4
Place of publication London, England, U.K.
Publisher BioMed Central
Language eng
Formatted 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.
Keyword DNA repeats
Identification
Prokaryotes
Archaea
Bacteria
Genomes
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: ERA 2012 Admin Only
School of Chemistry and Molecular Biosciences
 
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Created: Mon, 28 Nov 2011, 19:43:40 EST by Hong Lee on behalf of School of Chemistry & Molecular Biosciences