Methods for identifying novel nucleic acid regulatory elements and compounds that affect the regulation

1. A method of identifying one or more candidate compounds having an effect on expression of a gene of interest, said method comprising:

(a) identifying a 5′ or 3′ UTR sequence from a gene of interest;

(b) selecting host cells which express the gene that is endogenously associated with the UTR;

(c) stably transfecting one set of host cells with a test expression vector, said test vector comprising said 5′ or 3′ UTR sequence linked to, and positioned upstream or downstream, respectively, of a reporter gene construct (UTR/reporter), and stably transfecting another set of host cells with a control expression vector, said control vector comprising said reporter gene and lacking said UTR sequence (control/reporter);

(d) identifying whether said UTR sequence has a post-transcriptional regulatory function by assessing whether a first mRNA function of the UTR/reporter transcript is changed compared to the control/reporter transcript;

(e) determining whether the UTR regulatory function identified in step (d) is physiologically relevant by assessing whether said changed first mRNA function of the UTR/reporter transcript corresponds to the first mRNA function of the gene endogenously associated with the UTR;

(f) contacting said compound with an mRNA molecule comprising said UTR sequence; and

(g) measuring whether said compound alters a UTR-mediated effect.

2. The method of claim 1 , wherein said compound is contacted with a cell that expresses said mRNA molecule.

3. The method of claim 1 , wherein said UTR-mediated effect is a change in mRNA function.

4. The method of claim 1 , wherein said compound is contacted with said mRNA molecule in vitro, and further wherein said UTR-mediated effect is an interaction between an mRNA transcript comprising said UTR and an RNA binding protein.

5. The method of claim 2 , wherein the UTR-mediated effect is the expression of a gene linked to said UTR sequence.