ncRNA targeted excision of HIV-1 from human cells

Scripps Research Institute, The, La Jolla CA

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Abstract

Human immunodeficiency virus type 1 (HIV-1) emerged as a major human disease approximately 25 years ago, with roughly 70% of the current cases in sub-Saharan Africa and little hope for an efficacious vaccine in the near future. Alternative strategies to inhibit HIV-1 replication or purge viral reservoirs are tremendously desirable. One innovative strategy proposed here involves the use of small hairpin RNAs (shRNAs, 21-26bp in length) to guide a humanized protein complex capable of targeting the excision of integrated forms of HIV-1. In both human cells and the ciliated protozoa Tetrahymena thermophila, shRNAs are used to guide histone 3 Lysine 9 di-methylation (H3K9me2) to homology containing target loci in the genome. In Tetrahymena the result of this shRNA targeted epigenetic effect is the recruitment of the programmed DNA degradation protein (Pdd1p) to the target loci;ultimately resulting in the targeted excision of the germ line DNA coinciding with the H3K9me2 mark. We have recently developed a humanized variant of Pdd1p that is capable of targeting the excision of DNA in an shRNA dependant manner. We hypothesize that integrated forms of HIV-1 are also susceptible to shRNA/Pdd1p programmed excision. To test this hypothesis we propose to (1) determine the ability of humanized Pdd1p to target deletions of HIV-1, (2) characterize the function and mechanism of action of Pdd1p in HIV-1 infected human cells, and (3) Identify off-target sites of Pdd1p localization. The completion of this project will better develop our understanding of this complex molecular pathway while simultaneously examining the potential of utilizing a humanized version of the Pdd1p pathway and shRNAs to target the specific deletion of HIV-1 from the human genome.