Self-targeting by CRISPR: gene regulation or autoimmunity?

Abstract

CRISPR/Cas is a recently discovered prokaryotic immune system, which is based on small RNAs ("spacers") that restrict phage and plasmid infection. It has been hypothesized that CRISPRs can also regulate self gene expression by utilizing spacers that target self genes. By analyzing CRISPRs from 330 organisms we found that one in every 250 spacers is self targeting, and that such self-targeting occurs in 18% of all CRISPR-bearing organisms. However, complete lack of conservation across species, combined with abundance of degraded repeats near self-targeting spacers, suggests that self-targeting is a consequence of autoimmunity rather than gene regulation. We propose that accidental incorporation of self nucleic-acids by CRISPR can incur an autoimmune fitness cost, which may explain the abundance of degraded CRISPR systems across prokaryotes. CRISPR/Cas, an acquired anti-viral system in prokaryotesClustered regularly interspaced short palindromic repeats (CRISPR) loci are found in nearly all of archaeal and about 40% of sequenced bacterial genomes. CRISPR loci, together with their associated cas genes, have recently been shown to constitute a defense system that restricts propagation of incoming viruses and plasmids [1,2]. CRISPR arrays are composed of short repeat sequences separated by similarly sized hyper-variable "spacer" sequences, flanked on one side by an AT-rich sequence called the leader. The discovery that CRISPR spacers often match DNA from foreign elements led to the realization that they represent a "memory of past genetic aggressions" [3][4][5].Step by step, the mechanism underlying CRISPR defense has begun to unravel, yet our understanding of this system is far from complete. It has been revealed that the CRISPR locus is transcribed into a single RNA transcript, which is then further cleaved by the Cas proteins to generate smaller CRISPR RNA (crRNA) units, each including one targeting spacer [6]. These units then interfere with the incoming foreign genetic material by complementary base-pairing with the foreign nucleic acids [7][8][9][10]. CRISPR systems have been divided into different clusters based on their repeat sequences [11], which correlate with different subtypes of cas genes [12]. cas subtypes mtube, ecoli and nmeni were shown to likely target DNA [2,5,6,13], whereas the cas module ramp was shown to target RNA [14].© 2010 Elsevier Ltd. All rights reserved. * Corresponding author: rotem.sorek@weizmann.ac.il. † These authors contributed equally Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Although CRISPR/Cas was initially prophesized to be ...

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