Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5′-UTR region

SSRs (simple sequence repeats) have been shown to have a variety of effects on an organism. In this study, we compared SSRs in housekeeping and tissue-specific genes in human and mouse, in terms of SSR types and distributions in different regions including 5′-UTRs, introns, coding exons, 3′-UTRs, and upstream regions. Among all these regions, SSRs in the 5′-UTR show the most distinction between housekeeping genes and tissue-specific genes in both densities and repeat types. Specifically, SSR densities in 5′-UTRs in housekeeping genes are about 1.7 times higher than those in tissue-specific genes, in contrast to the 0.8–1.2 times differences between the two classes of genes in other regions. Tri-SSRs in 5′-UTRs of housekeeping genes are more GC rich than those of tissue-specific genes and CGG, the dominant type of tri-SSR in 5′-UTR, accounts for 74–79% of the tri-SSRs in housekeeping genes, as compared to 42–57% in tissue-specific genes. 75% of the tri-SSRs in the 5′-UTR of housekeeping genes have 4–5 repeat units, versus the 86–90% in tissue-specific genes. Taken together, our results suggest that SSRs may have an effect on gene expression and may play an important role in contributing to the different expression profiles between housekeeping and tissue-specific genes.