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