Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression

Genetic changes that help explain the differences between two individuals might include those that create or disrupt sites complementary to microRNAs1,2, but the extent to which such polymorphic microRNA sites mediate repression is unknown. Here, we develop a method to measure mRNA allelic imbalances associated with a regulatory site found in mRNA from one allele but not in that from the other. Applying this method, called allelic-imbalance sequencing (AI-Seq), to sites for three microRNAs (miR-1, miR-133, and miR-122) provided quantitative measurements of repression in vivo, without altering either the microRNAs or their targets. A significant fraction of polymorphic sites mediated repression in tissues that expressed the cognate microRNA, with downregulation depending on site type and site context. Extrapolating these results to the other broadly conserved microRNAs suggests that when comparing two mouse strains (or two human individuals), polymorphic microRNA sites cause expression of many (often hundreds) of genes to differ.