RNA-protein interactions play a critical role in the life cycle of many viruses. For example, a wide range of activities including transcription, translation, localization, and stability can be mediated through such interactions. The essential function of some RNA-protein complexes make them attractive targets for anti-viral drugs and inhibitors. Thus, a detailed characterization of the structural and functional relationship involved with these interactions is an essential step towards the design of potential virus inhibitors. A novel class of viral RNAs has been identified that is abundantly expressed, yet non-coding and nuclear localized. Although the functions of these RNAs may vary from virus to virus, little is known about this class or transcription or their role in the viral life cycle. One such RNA called not1 was cloned from Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) and is the most abundantly expressed lytic transcription nut1 forms ribonuclear protein (RNP) complexes, but the identify of the interaction proteins and the function of these complexes is not known. nut1 will be used in two genetic systems that have been designed specifically to identify proteins that bind RNA. The mammalian Tat-hybrid system and the yeast 3- hybrid system. Identification of the proteins that interact with nut1 will be the first step towards understanding its function. Novel nut1- protein interactions will be characterized in detail using biochemical, biophysical, and genetic tests. This analysis should help us better define the functions of nuclear RNAs and may aid in the design of KSHV inhibitors.
