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RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns.

Judith Zoephel1, Lennart Randau

  • 1*Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany.

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|November 22, 2013
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Summary
This summary is machine-generated.

CRISPR RNA abundance typically decreases along the array. However, individual spacer sequences significantly impact CRISPR RNA processing and transcription, affecting CRISPR-Cas system function.

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Area of Science:

  • Microbiology
  • Molecular Biology
  • RNA Biology

Background:

  • CRISPR (clustered regularly interspaced short palindromic repeats) RNome analysis in bacteria and archaea uses RNA-Seq to detect small RNAs.
  • Comparative analyses reveal conserved patterns in CRISPR RNome, such as decreasing RNA abundance from leader-proximal to distal ends.

Purpose of the Study:

  • To review exceptions to conserved CRISPR RNome patterns.
  • To highlight the impact of individual spacer sequences on CRISPR array transcription and RNA maturation.

Main Methods:

  • RNA-Seq deep sequencing methodology.
  • Comparative analyses of CRISPR RNome sets.
  • Review of existing literature on CRISPR array transcription and RNA processing.

Main Results:

  • Exceptions to typical CRISPR RNA abundance patterns exist.
  • Spacer sequences can contain regulatory elements (promoters, terminators).
  • Spacers can mediate RNA duplex formation (CRISPR RNA-anti-CRISPR RNA, CRISPR RNA-tRNA).

Conclusions:

  • Individual spacer sequences extensively influence CRISPR array transcription and RNA maturation.
  • These sequence-specific effects impact CRISPR-Cas system functionality.
  • Consideration of spacer sequence elements is crucial for designing synthetic CRISPR arrays.