Genetic, epigenetic, and environmental factors determine phenotypic variability, including susceptibility to disease or treatment outcome. Polymorphisms that change the amino acid sequences in coding regions (cSNPs) are readily detectable. However, regulatory polymorphisms (rSNPs) appear to be more prevalent than functional nonsynonymous cSNPs [1
]. Genome-wide surveys and SNP association analysis with mRNA expression trait mapping [5
] indicate regulatory polymorphisms as major factors in human phenotypic evolution and variability [5
]. A third type of functional polymorphism affects mRNA processing (splicing, maturation, stability, transport) and translation [8
]. We refer to this class of polymorphisms as ‘structural RNA polymorphisms’ (srSNPs). However, the overall role of rSNPs and srSNP still requires systematic evaluation.
Whereas mRNA levels are subject to both cis
- and trans
-acting factors, measuring the relative allelic mRNA expression selectively detects only cis
-acting factors. Allelic expression imbalance (AEI), i.e
., a different number or type of mRNAs generated between alleles, is a robust and quantitative phenotype directly linked to cis
-acting polymorphisms [3
] and epigenetic regulation, including X-inactivation, imprinting, and gene silencing [4
Genome-wide association studies continue to increase the number of candidate genes, while knowledge of the functional genetic variants is lagging. AEI analysis is a powerful tool for finding regulatory polymorphisms, but technical difficulties hamper broad usage. Earlier AEI methods mostly targeted monoallelic expression, while polymorphisms resulting in relatively small changes, although potentially physiologically relevant, are more difficult to measure. Array- and RTPCR-based methods with limited precision or sensitivity have been applied to detect partial regulatory changes, but have mostly been applied to small sets of candidate genes in lymphocytes. Results from these studies suggest that 20-50% of genes show detectable AEI [2
]. Yet, because the impact of rSNPs and srSNPs strongly depends on the tissue context, AEI analysis should be performed in physiologically relevant tissues [27
]. Systematic and accurate surveys of AEI in many genes applied to a variety of human target tissues are lacking. Yet, autopsy tissues present additional difficulties because of partial mRNA degradation.
For rapid detection of regulatory polymorphisms in multiple genes, we have developed a robust and fast methodology applicable to human autopsy tissues, filling an important gap between large-scale candidate gene discovery and resolution of the functional variants. This study surveyed AEI for 42 genes in human autopsy tissues, including brain, heart, liver, intestines, and kidney, as well as peripheral mononuclear cells, revealing frequent AEI in a large fraction of genes. In cardiovascular genes where regulatory polymorphisms had been reported previously, we tested whether the observed AEI ratios were compatible with any effects of these polymorphisms on allelic expression in relevant tissues. We also addressed the question of how srSNPs affect mRNA folding, and point to a number of genes where frequent srSNPs affect mRNA expression. The results provide insight into the prevalence of rSNPs and srSNPs.