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The 3' untranslated region (3'UTR) of fem-3 messenger RNA apparently controls the switch in the production of sperm to oocytes for hermaphrodite nematode Caenorhabditis elegans. A cytoplasmic protein FBF binding factor has also been discovered that binds to the fem-3 3'UTR's regulatory region and mediates the switch to oocyte from sperm. There are two short flanking regions and eight tandem repeats in the FBF's RNA-binding domain, with several proteins, such as Drosophila Pumilio, conserving the structural element.

RNA-protein interactions are pivotal in fundamental cellular processes such as translation, mRNA processing, early development, and infection by RNA viruses. However, in spite of the central importance of these interactions, few approaches are available to analyze them rapidly in vivo. We describe a yeast genetic method to detect and analyze RNA-protein interactions in which the binding of a bifunctional RNA to each of two hybrid proteins activates transcription of a reporter gene in vivo. We demonstrate that this three-hybrid system enables the rapid, phenotypic detection of specific RNA-protein interactions. As examples, we use the binding of the iron regulatory protein 1 (IRP1) to the iron response element (IRE), and of HIV trans-activator protein (Tat) to the HIV trans-activation response element (TAR) RNA sequence. The three-hybrid assay we describe relies only on the physical properties of the RNA and protein, and not on their natural biological activities; as a result, it may have broad application in the identification of RNA-binding proteins and RNAs, as well as in the detailed analysis of their interactions.