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CRISPR Evolution, Mechanisms and Infection

RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns

Judith Zoephel, Lennart Randau
Biochemical Society Transactions Nov 20, 2013, 41 (6) 1459-1463; DOI: 10.1042/BST20130129
Judith Zoephel
Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany
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Lennart Randau
Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany
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  • For correspondence: lennart.randau@mpi-marburg.mpg.de
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Abstract

In bacteria and archaea, RNA-Seq deep sequencing methodology allows for the detection of abundance and processing sites of the small RNAs that comprise a CRISPR (clustered regularly interspaced short palindromic repeats) RNome. Comparative analyses of these CRISPR RNome sets highlight conserved patterns that include the gradual decline of CRISPR RNA abundance from the leader-proximal to the leader-distal end. In the present review, we discuss exceptions to these patterns that indicate the extensive impact of individual spacer sequences on CRISPR array transcription and RNA maturation. Spacer sequences can contain promoter and terminator elements and can promote the formation of CRISPR RNA–anti-CRISPR RNA duplexes. In addition, potential RNA duplex formation with host tRNA was observed. These factors can influence the functionality of CRISPR–Cas (CRISPR-associated) systems and need to be considered in the design of synthetic CRISPR arrays.

  • antisense RNA
  • clustered regularly interspaced short palindromic repeats (CRISPR)
  • RNA processing
  • RNA-Seq

Footnotes

  • CRISPR Evolution, Mechanisms and Infection: A Biochemical Society Focused Meeting held at the University of St Andrews, U.K., 17–19 June 2013. Organized and Edited by Emmanuelle Charpentier (Laboratory for Molecular Infection Medicine Sweden, Sweden), John van der Oost (Wageningen University, The Netherlands) and Malcolm White (University of St Andrews, U.K.).

Abbreviations: Cas, CRISPR-associated; CRISPR, clustered regularly interspaced short palindromic repeats; crRNA, CRISPR RNA; pre-crRNA, precursor CRISPR RNA

  • © The Authors Journal compilation © 2013 Biochemical Society
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December 2013

Volume: 41 Issue: 6

Biochemical Society Transactions: 41 (6)
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RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns
Judith Zoephel, Lennart Randau
Biochemical Society Transactions Dec 2013, 41 (6) 1459-1463; DOI: 10.1042/BST20130129
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RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns
Judith Zoephel, Lennart Randau
Biochemical Society Transactions Dec 2013, 41 (6) 1459-1463; DOI: 10.1042/BST20130129

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  • Article
    • Abstract
    • Introduction
    • Common features of CRISPR RNomes
    • Spacer sequences that promote and terminate transcription
    • Spacer sequences can form RNA duplexes with a host tRNA
    • Influence of spacer elements on crRNA maturation
    • Discussion
    • Funding
    • Acknowledgments
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    • References
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Keywords

antisense RNA
clustered regularly interspaced short palindromic repeats (CRISPR)
RNA processing
RNA-Seq

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