TY - JOUR TI - Identification of host proteins differentially associated with HIV-1 RNA splice variants AU - Knoener, Rachel AU - Evans, Edward, III AU - Becker, Jordan T AU - Scalf, Mark AU - Benner, Bayleigh AU - Sherer, Nathan M AU - Smith, Lloyd M A2 - Sundquist, Wesley I A2 - Weigel, Detlef VL - 10 PY - 2021 DA - 2021/02/25 SP - e62470 C1 - eLife 2021;10:e62470 DO - 10.7554/eLife.62470 UR - https://doi.org/10.7554/eLife.62470 AB - HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs, each playing distinct roles in viral replication. Elucidating their host protein ‘interactomes’ is crucial to understanding virus-host interplay. Here, we present HyPR-MSSV for isolation of US, PS, and CS transcripts from a single population of infected CD4+ T-cells and mass spectrometric identification of their in vivo protein interactomes. Analysis revealed 212 proteins differentially associated with the unique RNA classes, including preferential association of regulators of RNA stability with US and PS transcripts and, unexpectedly, mitochondria-linked proteins with US transcripts. Remarkably, >80 of these factors screened by siRNA knockdown impacted HIV-1 gene expression. Fluorescence microscopy confirmed several to co-localize with HIV-1 US RNA and exhibit changes in abundance and/or localization over the course of infection. This study validates HyPR-MSSV for discovery of viral splice variant protein interactomes and provides an unprecedented resource of factors and pathways likely important to HIV-1 replication. KW - HIV KW - splicing KW - proteomics KW - RNA binding proteins KW - RNA imaging KW - interactome JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -