The regulation of TT virus (TTV) gene expression was characterized. Transient-transfection assays using reporter constructs revealed that a 113-nucleotide (nt) sequence within the untranslated region, proximal to the transcription initiation site and containing a TATA box motif, has a basal promoter activity. This sequence is well conserved among different TTV genotypes. Upstream stimulating factor bound to a consensus binding motif within this region and positively regulates TTV transcription. Furthermore, a 488-nt region upstream of the basal promoter exhibited enhancer activity, presumably in a cell type-specific manner. This study illustrates some of the mechanisms involved in the transcriptional regulation of TTV.TT virus (TTV), which was discovered in a patient with acute hepatitis, is an unenveloped, single-stranded, circular DNA virus, with a genome of approximately 3.8 kb (6). TTV is thought to be a new member of the Circoviridae family of viruses, and it was recently proposed that the virus be named Torque Teno virus (6). The TTV genome includes an untranslated region (UTR) of approximately 1.2 kb and a coding region of approximately 2.6 kb, including two major open reading frames which are sandwiched by the TATA box and polyadenylation signal motifs (11,13,15). Analyses of TTV transcripts have revealed three spliced mRNA species of 3.0, 1.2, and 1.0 kb with common 5Ј and 3Ј termini (9, 14). However, the molecular mechanisms controlling TTV transcription are still unknown. In this study, the basal promoter and enhancer of a TTV isolate, SANBAN of genogroup 3 (5, 18), were identified and functionally characterized.First, we determined the transcription initiation sites of the TTV genome by 5Ј rapid amplification of cDNA end (5Ј-RACE) analysis (Marathon cDNA amplification kit; Clontech) using poly(A)-rich RNA from a human hepatocellular carcinoma cell line, HepG2, transfected with a cloned TTV genome. The 5Ј-RACE PCR products were cloned and sequenced. We observed two potential transcription initiation sites, which map at nucleotides (nt) 121 and 110 (numbered according to the sequence deposited in DDBJ/GenBank/ EMBL databases under accession number AB025946). Although transcription may be initiated at both sites, the upper site was designated position ϩ1 in this study.The UTR of the TTV genome contains a TATA box element between positions Ϫ40 and Ϫ35, as well as a number of putative transcription factor-binding motifs (Fig. 1A). Despite considerable genetic diversity throughout the whole genome, the UTR sequence was relatively conserved among the different TTV genotypes, presumably reflecting its functional constraints (15, 16). Thus, we analyzed transcriptional regulation of the UTR sequence.To characterize TTV promoter activity, a firefly luciferase reporter plasmid, p(Ϫ890/ϩ115), was constructed by subcloning the TTV sequence from positions Ϫ890 to ϩ115, which was amplified by PCR using appropriate primers with restriction sites at the 5Ј ends, into the promoterless pGL3-Basic (Promega). Eleven diffe...