CRISPR repeats conserve RNA-like structure

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CRISPR repeats across microbes form clusters with conserved sequence and predicted RNA secondary structure.

Source

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Kunin V, Sorek R, Hugenholtz P · Genome biology · 2007

doi.org/10.1186/gb-2007-8-4-r61 Read the full paper ↗324 citationscc by

Study at a glance

Design: Computational / modelling — Genome-wide CRISPR array detection and repeat secondary-structure scoring
N: N=439 · 439 bacterial/archaeal genomes; 561 arrays in 195 genomes
Population: Bacterial and archaeal sequenced genomes
Outcome: Conserved CRISPR repeat sequence/structure features across clusters

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CRISPR repeats conserve RNA-like structure

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CRISPR repeats and spacers.

CRISPRs) are repetitive structures in Bacteria and Archaea composed of exact repeat sequences 24 to 48 bases long (herein called repeats) separated by unique spacers of similar length (herein called spacers) [,].

439 bacterial/archaeal genomes.

CRISPR composition [,]. Up to 45 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are hypothesized to be responsible for CRISPR propagation and functioning [,,].

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What they did

Scanned 439 genomes for CRISPR arrays and folded repeats to compare structure scores across clusters.

What they found

561 arrays in 195 genomes; some repeat clusters show consistently high folding potential supporting RNA intermediates.

The limits

What it doesn't show

Structure is computational prediction, not direct RNA structure proof for every array.

Key terms

CRISPR repeat: Short repeated sequence flanking spacers.
Spacer: Unique insert often from invaders.
CAS genes: CRISPR-associated protein families.
RNA fold: Predicted secondary structure.
PILER-CR: CRISPR array finder.
Horizontal transfer: Movement of CRISPR systems between lineages.

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Common questions

Genomes scanned?

439.

Arrays?

561.

Genomes with CRISPR?

44%.

Focus?

Repeat structure.