293T cells transfected with HIV-1 proviral plasmids

The HIV-1 Gag protein orchestrates all steps of virion genesis, including RNA recruitment into virions. However, the identities of specific RNA sequences recognized by Gag in cells and virions are largely unknown. Using crosslinking-immunoprecipitation (CLIP) sequencing, we uncover dramatic changes in the RNA binding specificity of Gag during virion genesis that are induced by its membrane binding, multimerization and proteolytic maturation. Prior to assembly, and also in mature virions, the nucleocapsid domain of Gag preferentially binds to psi and Rev Response elements in the viral genome, and GU-rich mRNA sequences. However, during assembly of immature virions, this specificity changes in a manner that facilitates genome packaging, as nucleocapsid binds to many sites on the viral genome and mRNA sequences with a similar A-rich nucleotide composition. Additionally, we find that the matrix domain of Gag binds almost exclusively to specific tRNAs in the cytosol, and this association regulates Gag binding to cellular membranes. CLIP-seq data sets from 293T cells