Vertebrate U6 small nuclear RNA (snRNA) gene promoters are among the founding members of those recognized by RNA polymerase III in which all control elements for initiation are located in the 5'-flanking region. Previously, one human U6 gene (U6-1) has been studied extensively. We have identified a total of nine full-length U6 loci in the human genome. Unlike human U1 and U2 snRNA genes, most of the full-length U6 loci are dispersed throughout the genome. Of the nine full-length U6 loci, five are potentially active genes (U6-1, U6-2, U6-7, U6-8 and U6-9) since they are bound by TATA-binding protein and enriched in acetylated histone H4 in cultured human 293 cells. These five all contain OCT, SPH, PSE and TATA elements, although the sequences of these elements are variable. Furthermore, these five genes are transcribed to different extents in vitro or after transient transfection of human 293 cells. Of the nine full-length U6 loci, only U6-7 and U6-8 are closely linked and contain highly conserved 5'-flanking regions. However, due to a modest sequence difference in the proximal sequence elements for U6-7 and U6-8, these genes are transcribed at very different levels in transfected cells.

To determine if the cellular factors La autoantigen (La) and polypyrimidine tract-binding protein (PTB) are required for hepatitis C virus (HCV) replication, we used siRNAs to silence these factors and then monitored their effect on HCV replication using quantitative RT-PCR. In addition, we determined the influence of PTB on the activity of the 3' noncoding region (NCR) of HCV and investigated its interaction with the components of the HCV replicase complex. We found that La is essential for efficient HCV replication while PTB appears to partially repress replication. PTB does, however, block the binding of HCV RNA-dependent RNA polymerase (RdRp, NS5B) to the 3'NCR. Indirect immunofluorescence microscopy showed co-localization of cytoplasmic PTB with the HCV RdRp in hepatoma cells (Huh-7) expressing HCV proteins, while in vitro translation of viral proteins from the HCV replicon revealed the interaction of PTB isoforms with NS5B polymerase and NS3.

Host genes involved in lipid metabolism are differentially regulated during the early stages of hepatitis C virus (HCV) infection. The majority of lipids synthesized in the liver are exported to other tissues in the form of lipoproteins. The formation of these lipoproteins is dependent upon the association of triglycerides with apolipoprotein B100. Using the HCV subgenomic replicon expression system, we show that secretion of apoB100 is significantly reduced. Inhibition of apoB100 degradation by ALLN did not improve secretion. Triglyceride levels as well as microsomal triglyceride transfer protein mRNA and activity levels were reduced in replicon-expressing cells, indicating potential reasons for the observed decrease. Further evidence is presented for the interaction between the HCV nonstructural protein 5A and apoB100. These results provide further insight into the alteration of lipid metabolism by HCV. Hepatitis C virus (HCV)3 infection is a major health problem worldwide. HCV infection causes chronic hepatitis in up to 60 -80% of infected adults (1) and is associated with steatosis, cirrhosis, and hepatocellular carcinoma (2). The HCV viral genome consists of a positive sense single-stranded RNA 9.6 kb in length and encodes a polyprotein precursor of ϳ3000 amino acids (3). The resulting polyprotein is cleaved into at least three structural proteins (the core protein and the envelope proteins E1 and E2) and a variety of nonstructural proteins (p7 through NS5A/B) (3, 4). Many of the nonstructural proteins are essential for productive viral replication (5).The development of selectable subgenomic HCV RNA replicons has led to important advances in the field of HCV. Recently, several groups have reported the full-length infectious tissue culture system (6 -8), which is likely to further our understanding of the infectious process. The subgenomic replicons are bicistronic constructs composed of the HCV internal ribosomal entry site (IRES), the neomycin phosphotransferase (neo) gene, and the encephalomyocarditis IRES, which mediates the translation of the HCV nonstructural proteins NS3 through NS5, followed by the 3Ј-noncoding region (9).Chronic HCV is characterized by several histological features of the liver such as bile duct damage, lymphoid follicles, low serum cholesterol levels, and, in ϳ50 -60% of the cases, steatosis (10, 11). Recently, genomic analysis conducted on the livers of HCV-infected chimpanzees revealed that the transcript levels of genes involved in lipid metabolism and homeostasis are altered (12, 13).The liver is a major site of lipid synthesis. Many of the synthesized lipids are exported from the liver in the form of apolipoprotein-containing particles known as very low density lipoproteins (VLDLs), precursors of low-density lipoproteins. The VLDLs are composed of a nonpolar core of triglycerides and cholesteryl esters surrounded by a monolayer amphipathic coating of protein, phospholipids, and cholesterol (14, 15). VLDLs are formed in the luminal space within the endoplasmic reticulum (ER), ...

Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the transcription of the RNA polymerase III-directed gene encoding the RNA subunit (TER1) of this enzyme. A chimeric gene containing the Glaucoma chattoni TER1 transcribed region flanked by 5' and 3' Tetrahymena regions was used to identify promoter elements following transformation of Tetrahymena cells. Disruption of a conserved proximal sequence element (PSE) located at -55 in the Tetrahymena TER1 5' flanking region eliminated expression of the chimeric gene. In addition, mutation of an A/T-rich element at -25 decreased expression markedly. A gel mobility shift assay and protein-DNA cross-linking identified a PSE-binding polypeptide of 50-60 kDa in Tetrahymena extracts. Gel filtration analysis revealed a native molecular mass of approximately 160 kDa for this binding activity. Our results point to a similar architecture between ciliate telomerase RNA and metazoan U6 small nuclear RNA promoters.