Simple Sequence Repeats in the Human Genome: Evolution

Donald E Riley, VA Puget Sound Health Care System, Seattle, Washington, USA
John N Krieger, VA Puget Sound Health Care System, Seattle, Washington, USA

Published online: May 2008

DOI: 10.1002/9780470015902.a0020839

Recent evolutionary findings suggest important functions for even-numbered, simple sequence repeats (SRs). During evolution, weak-folding SRs whose single-stranded forms were incapable of forming classically paired duplex stems, replaced other weak-folding repeats. Strong-folding repeats replaced other strong-folding repeats. Among untranslated regions, SRs were associated with genes encoding membrane-related functions and genes encoding transcription factors. Among all possible SR sequences, evolution selected primarily weak-folding repeats. The evolution of many of the differences comparing human SR usage with other mammals can now be mapped using publically available genome sequences. Human SR sites evolved by a variety of pathways.

Keywords: evolution; genome; single stranded; species differences; UTRs

Figure 1. Frequency distributions of dinucleotide SRs among M. musculus and H. sapiens UTRs. Total M. musculus UTRs in the nonredundant UTRdb=33 923. Total H. sapiens UTRs in the nonredundant UTRdb=59 366. Asterisks indicate SRs with statistically significant differences.
Figure 2. Frequency distributions of tetranucleotide SRs among M. musculus and H. sapiens UTRs. Only SRs that occurred in at least one of the two species are shown. Total M. musculus UTRs in the nonredundant UTRdb=33 923. Total H. sapiens UTRs in the nonredundant UTRdb=59 366. Asterisks indicate SRs with statistically significant differences.
Figure 3. SRs present in M. musculus whereas absent in H. sapiens. In these cases, mouse SR-flanking sequences were conserved among M. musculus, H. sapiens and other mammals. (a) Upper sequence, M. musculus carbonic anhydrase 10 (car10), cDNA (GenBank accession number, NM_028296). Lower sequence, H. sapiens CAR10, cDNA (BC020577). (b) Upper sequence, M. musculus fibrosin 1 (fbs1), mRNA (BC027193). Lower sequence, H. sapiens fibrosin 1 (FBS1), cDNA, (NM_022452). (c) Upper sequence, M. musculus adult male liver cDNA, with 74% similarity to rap2a (AK075712). Lower sequence, H. sapiens RAP2A, member of RAS oncogene family, cDNA (BC041333). (d) Upper sequence, M. musculus sepmaphorin 6D-like UTR (sema6D) (xm_141337). Lower sequence, H. sapiens SEMA6D isoform 1 (AF389430). For each pair, the similarity continues and improves in upstream and downstream sequences (not shown). Underscores mark identical bases.
Figure 4. Abbreviated results of a comparison of the human fibrosin 1 UTR with other mammals. With the exception of primates, all mammalian fibrosin 1 UTRs examined had an SR in the same position within the UTR. The rodent lineage replaced (GT)n with (AC)n. Although the flanking sequences present in other mammals were still present in human and other primates, the SR was lost, one of few SR losses observed.
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Evolutionary Genomics | Molecular Evolution | Human Evolution
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Article Title: Simple Sequence Repeats in the Human Genome: Evolution
 
How to Cite close
Riley, Donald E, and Krieger, John N(May 2008) Simple Sequence Repeats in the Human Genome: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020839]