Analysis of transcriptional regulatory sequences in the human endogenous retrovirus W long terminal repeat

The U3 region of the human endogenous retrovirus W long terminal repeat (HERV-W LTR) contains several putative regulatory sequences that might not only regulate transcription of viral genes but also influence the expression of neighbouring cellular genes. In this study, we analysed the U3 region in detail in order to understand the transcriptional regulatory mechanism of HERV-W. Two transcription factor (TF) binding sites for Oct-1 and C/EBP were important as a silencer and an enhancer, respectively, for transcriptional regulation. Furthermore, it was possible to divide the HERV-W LTR isolates into two groups depending on their promoter strength, which might be determined by the integrity of the two TF binding sites. However, neither the Oct-1 binding site nor the CAAT-box was required for the cell type-specific activity of the HERV-W LTR. Instead, the 3′ terminus of U3 from 191 to 260, which includes a TATA box, was sufficient for specificity, suggesting that the efficiency of assembly of basic transcription machinery at the TATA box of HERV-W LTR might determine the cell type specificity.