Lupus autoantigen Ku protein binds HIV-1 TAR RNA in vitro

The control of HIV-1 gene expression depends upon interaction of Tat with the trans-activation responsive (TAR) element present at the 5' end of all HIV-1 transcripts. The TAR sequence forms a stable hair-pin structure that binds Tat and several cellular factors in vitro. In the absence of Tat, TAR acts as a transcription terminator. Tat in conjunction with a cellular factor(s) acts to increase the elongation capacity of the transcription complex. Here we report that Ku protein, the autoantigen in patients with systemic lupus erythematosus, binds TAR RNA in vitro with high affinity and specificity forming a single protein-RNA complex. Ku, a heterodimer of Ku72 and Ku86 that non-specifically binds the ends of DNA fragments, appears to recognize the terminal loop of TAR RNA. UV-crosslinking showed that both subunits of Ku are in proximity to the RNA. Further, Ku shows a 5-fold higher affinity for TAR RNA than for the ends of dsDNA. As Ku is involved in the stimulation of the elongation property of the RNA polymerase II and activation of several transcription factors, the specific interaction of Ku with TAR raises intriguing possibilities for its function in HIV-1 gene expression.