by Subhankar Chakraborty

Created on: December 12, 2006   Last Updated: May 02, 2007

Simple sequence repeats (SSR)
SSRs comprise two groups of repeat elements, micro and macro/minisatellites. SSRs are defined as tandemly repeated short motifs. Microsatellite repeats typically have between 1 upto 6 bases in each repeat, while macrosatellites have a minimum of 5-6 and upwards ranging upto several dozen per repeating element. These repeat elements are present in both coding as well as non-coding regions of the genome, but predominantly reside in the non-coding portion. There are two types of repeats, pure and impure. Pure or perfect repeats are those in which all the repeating elements are identical, while impure repeats have substitutions in one or more of their repeating elements. Previously, SSRs had been regarded as "junk DNA". But recent evidence suggests that they regulate gene expression as a function of the number of times they are repeated (and in turn their length) and thus are a mechanism for genetic change in response to the environmental factors.

Some examples that illustrate the role of SSRs in regulating gene expression are:
In Drosophila, the gene regulating the circadian clock (period or per gene) has two variants of a hexanucleotide SSRs which encodes for Thr-Gly dimer. The longer variant encodes for (Thr-Gly) 20 and its role is to reduce variations in the circadian rhythm with temperature changes. The shorter variant of this SSR encodes (Thr-Gly) 17 and its function is to maintain the length of the circadian rhythm at 24 hours in warm temperatures. It is noted that in temperate climates of Europe, the longer allele is expressed more often. Similarly in the Mount Caramel area of Israel there is a canyon where on one side there is always sunshine while the other side remains in darkness and hence is cooler. Fruit flies on the cooler side of the canyon predominantly express the longer allele in order to maintain their circadian clocks inspite of the lower temperature.
Wheat growing in the same canyon referred to above showed variation in their SSRs when the plants growing on the cooler slope were compared with those on the sunny slopes. This indicates that SSRs are a tool used by organisms to adapt themselves to their immediate environment.
The difference in social behavior of prairie versus meadow voles represents another example of the effect of SSR length on gene expression. In this case, higher expression of the vasopressin receptor in the ventral forebrain of prairie voles is associated with social and caring behavior for their

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