Simple Repeats


The eukaryotic genome deviates in many aspects from a random base composition. One interesting deviation is that some parts of the genome are less complex than expected, leading to an overrepresentation of short sequence motifs. Owing to their low complexity, these genomic regions are called simple sequences. The most extreme case is the tandem repetition of a single motif. Once the motif is repeated multiple times (at least ≈ 10x), this sequence is called a microsatellite. Like the rest of the genome, simple sequences acquire base substitutions, but on top of this they have a proprietary mutation process – deoxyribonucleic acid replication slippage. With increasing simplicity, this mutation process becomes increasingly important, resulting in the gain and loss of repeat units. Their high mutation rate provides the basis for the successful use of microsatellites as genetic markers.

Key Concepts

  • Some parts of the genome have low complexity
  • These simple sequences have a proprietary mutation process called DNA replication slippage.
  • DNA replication slippage adds/removes repeat units.
  • Microsatellites are an informative genetic marker.
  • Simple sequences are distributed throughout the entire genome, making them an excellent tool for gene mapping.

Keywords: microsatellite; DNA replication slippage; simple sequences; cryptic simplicity; genetic marker

Figure 1. Dot plot of a cryptic simple sequence. (a) Dot plot using the partial human coagulation factor IX gene. Only identities of at least 75% in an 8‐base‐pair window are shown. (b) Alignment of a region off the diagonal that shows sequence similarity.
Figure 2. Microsatellite nomenclature. The uninterrupted microsatellite consists of a perfect repetition of CT dinucleotides, the imperfect microsatellite has a C substituted by an A, the interrupted microsatellite has an insertion of three As, which interrupt the CT repeat, and the composite repeat consists of two different juxtaposed repeats.
Figure 3. Model of DNA replication slippage adding (a) or removing (b) one repeat unit. (1) First round of DNA replication. (2) DNA slippage, causing one repeat unit to loop out; the dashed arrow indicates the direction of DNA slippage. (3) DNA synthesis continues without repair of the loop. (4) Second round of DNA replication leads to the addition or deletion of one repeat unit in one of the strands.


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Further Reading

Buschiazzo E and Gemmell NJ (2006) The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays 28: 1040–1050. DOI: 10.1002/bies.20470.

Goldstein DB and Schlötterer C (1999) Microsatellites: Evolution and Applications. Oxford: Oxford University Press.

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How to Cite close
Schlötterer, Christian(Sep 2016) Simple Repeats. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005066.pub2]