Department of Microbiology and Physiological Systems; Department of Quantitative Health Sciences
Adaptor Proteins, Vesicular Transport; Algorithms; Carrier Proteins; Cell Cycle Proteins; HEK293 Cells; HIV-1; HeLa Cells; High-Throughput Screening Assays; *Host-Pathogen Interactions; Humans; Jurkat Cells; Nuclear Proteins; *RNA Interference; *Virus Replication
Amino Acids, Peptides, and Proteins | Biochemistry | Cellular and Molecular Physiology | Computational Biology | Genetics and Genomics | Virology
RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene's phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1-host cell interactions.
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Citation: Cell Rep. 2014 Oct 23;9(2):752-66. doi: 10.1016/j.celrep.2014.09.031. Epub 2014 Oct 16. Link to article on publisher's site.
DOI of Published Version
Zhu, Jian; Perreira, Jill; Chin, Christopher R.; Baker, Richard E.; Maranda, Louise; Elledge, Stephen J.; and Brass, Abraham L., "Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents" (2014). Open Access Articles. 2582.
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