Increasing evidence suggests that allelic variation in gene expression is a widespread phenomenon, an interesting observation because it is likely that such differences may contribute to the phenotypic variation between individuals. One method for detecting the degree of variation in allelic expression at any specific locus is to quantitatively genotype mRNA from individuals heterozygous for an exonic single nucleotide polymorphism (SNP) in the gene of interest. If there is no allelic variation in gene expression then the two alleles of the SNP should be expressed at the same level, but where there is allelic differential expression one allele will be found at a higher level than the other.
A recent study by Krishna Pant and colleagues at Perlegen Sciences, published in the journal Genome Research, looked at allelic differential expression in human white blood cells. They used a dense oligonucleotide array specifically designed to analyse 8046 exonic SNPs in 4102 genes to detect differential allelic expression in mRNA isolated from the white blood cells of 12 unrelated individuals. Of these exonic SNPs, 1983, located in 1389 genes, were found to be expressed in white blood cells and heterozygous in at least one of the 12 individuals, and could thus be examined for differential allelic expression. They found that of these 1389 genes, 731 (53%) demonstrated allele expression differences in at least one individual.
In order to gain additional insight into the regulatory mechanisms controlling these differences, the authors specifically analysed a subset of 60 genes for which all heterozygotes demonstrated differential expression. They found evidence for three patterns of allelic expression, suggesting different underlying regulatory mechanisms. Exonic SNPs in three of the 60 genes were monoallelically expressed in the human white blood cells, and when examined in families demonstrated expression of only the maternal copy, consistent with regulation by imprinting. Approximately one-third of the genes were found to have the same allele expressed more highly in all heterozygotes, suggesting that their regulation is predominantly influenced by cis-elements in strong linkage disequilibrium with the assayed exonic SNP. In the remaining genes the researchers found different alleles expressed more highly in different heterozygotes, suggesting that their expression differences are influenced by factors not in strong linkage disequilibrium with the assayed exonic SNP.
The finding that that three out of the 60 genes are regulated by imprinting is surprising, given that there are only <50 human genes with evidence of imprinting and parent-of-origin effects in the Imprinted Gene Catalogue, and it is generally believed that the number of imprinted genes in mammals is low. The authors conclude that experiments using exonic SNPs for genotyping and expression analysis across multiple tissues at different developmental stages may result in the identification of many more genes regulated by genomic imprinting.
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