Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation

• Among 501 possible mono- to hexameric SSRs, only 73 are enriched in vertebrates.
• Many SSRs show non-random distribution, being associated with TSS and CpG islands.
• A number of SSR associated genes are involved in genome organization and regulation.
• Preferential accumulation of SSRs reflects positive selection pressure.

Simple sequence repeats (SSRs) or microsatellites are tandemly repeated short DNA sequence motifs found to be abundant in higher eukaryotes. Enrichment of SSRs with increasing genome complexity points to a positive selection and their functional relevance. We analyzed genomes of 24 organisms to find features that may help understand the functional relevance of SSRs. Of the 501 possible SSRs, only 73 show length specific enrichment. We also noticed that ~ 45 bp is the optimum length for a majority of them particularly in the human genome. Finally, we observed non-random distribution of ACG and CCG, enriched around transcriptional start sites (TSSs) in several species. Taken together, these results suggest that SSRs are functionally relevant with potential regulatory role. We propose that such repeats are evolving under positive selection pressure like any other functional element in the genome.