Fig. 1.
Investigation of regulatory polymorphism: allele-specific analysis of mRNA. Strategy: This approach uses the presence of an exonic transcribed SNP (shown here as G/A) to resolve the allelic origin of transcribed mRNA [18]. By analysis of mRNA from cells derived from an individual heterozygous for the marker SNP, an internally controlled system is established in which relative allele-specific gene expression can be estimated. Uses: Allele-specific quantification of mRNA is a useful in vivo approach to resolving functionally important haplotypes using transcribed marker SNPs. It provides a direct assessment of the relative abundance of allele-specific transcript in a natural chromosomal context in which the normal regulatory machinery and chromatin environment are operating. Limitations: The assay requires accurate and sensitive quantification of relative transcript abundance, typically based on primer extension methods. A major limitation is that for many genes and for the majority of haplotypes no exonic marker is present to allow resolution of transcript origin. Some information may be achieved by using intronic SNPs to study relative expression of unspliced RNA; a further approach is to use a different indirect measure of gene expression, namely phosphorylated Pol II loading by haploChIP in living cells [80]. The allele-specific density of Pol II loading can be used in the same way as transcript abundance except that as the Pol II is being measured in situ by crosslinking it to DNA, any SNP marker can be used within 2 kb 5′ or 3′ to the gene including promoter and 3′UTR SNPs which considerably expands the number of haplotypes that can be interrogated