Global effects on gene and retroelement expression upon HUSH function abrogation in ERVK3-1 knockout cells

ERVK3-1 is a ubiquitously expressed 109-amino acid endogenous retroviral Rec microprotein. We hereby report its physical and functional interaction with the HUSH complex via PPHLN1. Deletion of the ERVK3-1 coding sequence in HEK293T cells resulted in significant upregulation of ZNF genes and pseudogenes - established classes of HUSH targets. Increased expression of genes involved in immune recognition and signaling - especially the MAGE family - was also noted, consistent with the current knowledge on HUSH depletion increasing L1 expression and consequently, interferon signaling. Analysis of ERV expression from the same RNA-Seq dataset shows widespread dysregulation as well. Overall design: RNA-Seq analysis (rRNA depletion) of wild-type HEK293T cells (WT), ERVK3-1 knockout HEK293T cells (ERVK3-1 KO2), and HEK293T cells transiently expressing Cas9 with a non-target guide RNA to look at differential gene expression with spike-in controls.