Cell based methods and systems for the identification of RNA regulatory sequences and compounds that modulate their functions

A method of identifying a small molecule compound that inhibits an hepatitis C virus-internal ribosome entry site (HCV-IRES) mRNA regulatory sequence transcript fragment encoded by a sequence selected from the group consisting of—SEQ ID NO 20, SEQ ID NO 32, SEQ ID NO 38, SEQ ID NO 41, and SEQ ID NO 44 from inhibiting mRNA translation in a mammalian cell culture comprising

• incubating the mammalian cell expressing a reporter mRNA transcript and the mRNA regulatory sequence transcript fragment in the presence of said small molecule compound, wherein said mRNA regulatory sequence transcript fragment is not attached to said reporter mRNA transcript;
• and wherein said HCV-IRES mRNA regulatory sequence transcript fragment inhibits translation of the reporter mRNA transcript in said mammalian cell in the absence of said molecule compound;
• and
• monitoring a reporter protein signal produced by said reporter mRNA transcript in the presence of said small molecule compound, wherein an increase in the signal of the reporter protein in the presence of said small molecule compound compared to the reporter protein signal in the absence of said small molecule compound indicates said small molecule compound inhibits the ability of said mRNA regulatory sequence transcript fragment to inhibit translation of the reporter mRNA transcript.