Characterization of dsRNA Binding Proteins through Solubility Analysis Identifies ZNF385A as a dsRNA Homeostasis Regulator

Double-stranded RNA (dsRNA) binding proteins (dsRBPs) play crucial roles in various cellular processes, especially in the innate immune response. Comprehensive characterization of dsRBPs is essential to understand the intricate mechanisms for dsRNA sensing and response. Traditional methods have predominantly relied on affinity purification, favoring the isolation of strong dsRNA binders. Here, we adopted the proteome integral solubility alteration (PISA) workflow for characterizing dsRBPs, resulting in the observation of 18 known dsRBPs and the identification of 200 novel potential dsRBPs. Next, we focused on zinc finger protein 385A (ZNF385A) and discovered that its knockout activated the transcription of interferon-ß in the absence of immunogenic stimuli. The knockout of ZNF385A elevated the level of endogenous dsRNAs, especially transcripts associated with retroelements, such as short interspersed nuclear element (SINE), long interspersed nuclear element (LINE), and long terminal repeat (LTR). Moreover, loss of ZNF385A enhanced the bioactivity of 5-Aza-2'-deoxycytidine (5-AZA-CdR) and tumor-killing effect of NK cells. Our findings greatly expand the dsRBP reservoir and contribute to the understanding of cellular dsRNA homeostasis. Overall design: dsRIP-seq profiling of wild type HeLa cells and ZNF385A knockout cells.