title: Length and sequence dependent accumulation of simple sequence repeats in vertebrates: potential role in genome organization and regulation.
abstract: 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.
authors.affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India; International Institute of Information Technology, Gachibowli, Hyderabad 500032, India.
authors.forename: Senthilkumar
authors.initials: S
authors.lastname: Ramamoorthy
authors.affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.
authors.forename: Hita Sony
authors.initials: HS
authors.lastname: Garapati
authors.affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India. Electronic address: mishra@ccmb.res.in.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Mishra
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D005095:Exoribonucleases; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D006801:Humans; D051379:Mice; D018895:Microsatellite Repeats / Q000235:genetics*; D002679:Pan troglodytes / Q000235:genetics; D051381:Rats; D013045:Species Specificity; D024363:Transcription Initiation Site; D018911:Trinucleotide Repeats / Q000235:genetics; D014714:Vertebrates / Q000145:classification / Q000235:genetics*
chemical_list: D005095:Exoribonucleases; C065486:oligonucleotidase
keywords: DNA; Genome; Microsatellites; Simple sequence repeats