The human endogenous retrovirus K Rev response element coincides with a predicted RNA folding region

Human endogenous retrovirus K (HERV-K) is the name given to an similar to 3 0-million-year-old family of endogenous retroviruses present at >50 copies per haploid human genome, Previously, the HERV-K were shown to encode a nuc lear RNA export factor, termed K-Rev, that is the functional equivalent of the H-Rev protein encoded by human immunodeficiency virus type 1, HERV-K wa s also shown to contain a cis-acting target element, the HERV-K Rev respons e element (K-RRE), that allowed the nuclear export of linked RNA transcript s in the presence of either K-Rev or H-Rev. Here, we demonstrate that the f unctionally defined K-RRE coincides with a statistically highly significant unusual RNA folding region and present a potential RNA secondary structure for the similar to 416-nt K-RRE, Both in vitro and in vivo assays of seque nce specific RNA binding were used to map two primary binding sites for K-R ev, and one primary binding site for H-Rev, within the K-RRE. Of note, all three binding sites map to discrete predicted RNA stem-loop subdomains with in the larger K-RRE structure, Although almost the entire 416-nt K-RRE was required for the activation of nuclear RNA export in cells expressing K-Rev , mutational inactivation of the binding sites for K-Rev resulted in the se lective loss of the K-RRE response to K-Rev but not to H-Rev. Together, the se data strongly suggest that the K-RRE, like the H-RRE, coincides with an extensive RNA secondary structure and identify specific sites within the K- RRE that can recruit either K-Rev or H-Rev to HERV-K RNA transcripts.