The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr.

Silencing of nuclear DNA is an essential feature of innate immune responses to invading pathogens. Early in infection, unintegrated lentiviral cDNA accumulates in the nucleus yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonizes cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library and identify SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. ATAC-seq demonstrates that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting that the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines its targeting by Vpr as an evolutionarily conserved antagonism. [Display omitted] • Gene expression from unintegrated HIV-1 DNA species is restricted by the host cell • Vpr antagonizes silencing by degrading cellular targets via the CRL4^DCAF1 E3 ligase • A custom "Vpr library" CRISPR-Cas9 knockout screen implicates SLF2 in silencing • SLF2 recruits the SMC5/6 complex to compact and silence unintegrated HIV-1 DNA Unlike integrated HIV-1 DNA, extrachromosomal unintegrated HIV-1 DNA is poorly expressed. Dupont et al. show that the host protein SLF2 recruits the SMC5/6 complex to repress unintegrated HIV-1 DNA. This work implicates the SMC5/6 complex in nuclear immunosurveillance of a wide range of extrachromosomal DNAs leading to DNA compaction-based silencing. [ABSTRACT FROM AUTHOR]