Characterization of the direct physical interaction of nc886, a cellular non-coding RNA, and PKR

► First characterization of in vitro interaction between PKR and nc886. ► Direct binding of nc886 to PKR with an affinity comparable to that of dsRNA. ► Two RNA binding domains of PKR recognize the central region of nc886. ► PKR binds equally well to 5′-mono, tri- or de-phosphorylated nc886. ► nc886 sets a threshold for cellular PKR activation. We have recently shown that nc886 (pre-miR-886 or vtRNA2-1) is not a genuine microRNA precursor nor a vault RNA, but a novel type of non-coding RNA that represses PKR, a double-stranded RNA (dsRNA) dependent kinase. Here we have characterized their direct physical association. PKR’s two RNA binding domains form a specific and stable complex with nc886’s central portion, without any preference to its 5′-end structure. By binding to PKR with a comparable affinity, nc886 competes with dsRNA and attenuates PKR activation by dsRNA. Our data suggest that nc886 sets a threshold for PKR activation so that it occurs only during genuine viral infection but not by a minute level of fortuitous cellular dsRNA.