Predicting potential miRNA target sites within gene promoters

Synthetic small duplex RNAs that are complementary to gene promoters can activate or inhibit target gene expression. The potency and robustness of gene modulation by these RNAs suggests that natural mechanisms may exist to facilitate recognition of sequences within gene promoters by endogenous small RNAs. Here, we describe computational methods for identifying potential miRNA target sites within gene promoters. These methods will facilitate investigations of whether miRNAs interact with sequences outside of 3′-untranslated regions and suggest new targets for the design of synthetic modulators of gene expression.