Mice and humans have sequences that create or destroy microRNA binding sites
By Charles Q. Choi | June 5, 2006
Mutations that create or destroy microRNA binding sites in genes appear abundant in humans and mice and could affect genetic function, scientists report in the June 4 online edition of Nature Genetics.
The study "is going to suggest to people that a lot of variation in phenotypes in mammals may be due to these target sites," James Womack at Texas A&M University in College Station, who did not participate in the study, told The Scientist.
Study author Michel Georges, of the University of Liège in Belgium, and colleagues began the work to investigate why Texel sheep are exceptionally meaty. They crossed Texel sheep with another breed to generate offspring representing a range of 37 phenotypes with respect to muscularity, fat deposition and body composition. They mapped the locus to an interval encompassing the myostatin gene GDF8, loss of function of which causes double-muscling in mice, cattle and humans.
The investigators found no polymorphism differences between the coding regions of GDF8 from Texel and control sheep. Of 20 single nucleotide polymorphisms (SNPs) the researchers did find, one, dubbed g+6723G-A was found in 99% of Texels versus 1% of controls. This SNP creates an eight-nucleotide-long octamer motif in the 3' untranslated region (UTR) that three miRNAs are known to target. PCR analysis found that sheep highly expressed two of these miRNAs, miR-1 and miR-206, in their skeletal muscle.
In monkey kidney cells transfected with GDF8 linked to bioluminescent luciferase reporters, miR-1 and miR-206 expression cut luminescence of cells with g+6723G-A in their GDF8 down to 70% of cells with wild-type GDF8. This suggests the SNP boosts meatiness by inhibiting translation of the myostatin gene, according to the authors. Georges and his colleagues found Texel sheep apparently had one third the amount of circulating myostatin that other sheep did.
To see how often point mutations may affect the genes of other species in a similar manner, the researchers searched among 73,497 SNPs in the 3' UTR of 13,621 human genes that might create or destroy known miRNA target octamers. To determine which alleles might be ancestral, the researchers looked at chimpanzee sequences. Georges and his colleagues identified 2,490 SNPs that created and 2,597 that destroyed putative miRNA target sites. Of the latter, 483 affect octamers conserved between primates and rodents. Analyses performed for the mouse using rat sequences to infer the ancestral states for 77,283 SNPs in the 3' UTR of 10,200 genes identified 1,182 SNPs creating and 1,321 destroying putative miRNA target sites, 234 of the latter are evolutionary conserved.
"If the sites are conserved, they are probably functional, so destroying them would have a higher likelihood of destroying a phenotype," said Georges, who along with colleagues has developed Patrocles, a database to help scientists identify such interactions between microRNAs (miRNAs) and gene polymorphisms.
Future research should understand the function of these motifs systematically, "either through SNPs, animal models, or in vitro assays," Manolis Kellis at the Massachusetts Institute of Technology in Cambridge, who was not a study author, told The Scientist.
Experiments could immunoprecipitate RNA-induced silencing complex proteins (RISCs), the enzymes mediating microRNA inhibition of messenger RNAs, from sheep expressing both the mutant and wild-type alleles of a gene and see if their RISC complexes pull down more of the mutant allele. "If we are able to see that, that would be a method that could probably also open the way for systematic tests of these mutations," Georges said.
Charles Q. Choi
Links within this article
D. Steinberg. "MicroRNA target practice." The Scientist, June 20, 2005
A. Clop et al. "A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep." Nature Genetics, published online June 4, 2006.
J. Weitzman. "Blocking myostatin." The Scientist, November 28, 2002.