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Updated: May 14, 2026
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
Protospacer recognition motifs: mixed identities and functional diversity
Shiraz A Shah1, Susanne Erdmann, Francisco J M Mojica
1Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
RNA Biology
|February 14, 2013
Summary
Protospacer adjacent motifs (PAMs) play dual roles in CRISPR-Cas systems, aiding both spacer acquisition and DNA interference. New terms, spacer acquisition motif (SAM) and target interference motif (TIM), are proposed for these distinct functions.
Area of Science:
- Molecular Biology
- Genetics
- Microbiology
Background:
- Protospacer adjacent motifs (PAMs) are short DNA sequences crucial for CRISPR-Cas systems.
- Initially linked to spacer acquisition, PAMs were later implicated in DNA interference by certain CRISPR-Cas types.
Purpose of the Study:
- To review the dual functional roles of PAM sequences in CRISPR-Cas systems.
- To propose distinct terminology for PAM recognition sites involved in different processes.
Main Methods:
- Literature review and bioinformatic analysis of existing experimental data.
- Examination of evidence from virus- and plasmid-targeting assays.
Main Results:
- PAM sequences are involved in both the excision/insertion of protospacers (acquisition) and DNA interference.
- While overlapping, the recognition sites for acquisition and interference are likely not identical.
- Evidence suggests distinct molecular mechanisms for these two processes.
Conclusions:
- PAM sequences exhibit dual roles in CRISPR-Cas adaptive immunity.
- The terms 'spacer acquisition motif' (SAM) and 'target interference motif' (TIM) are proposed to differentiate recognition sites.
- This distinction clarifies the functional specificity within CRISPR-Cas mechanisms.
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