Functional characterization of the human hypoxanthine phosphoribosyltransferase gene promoter: evidence for a negative regulatory element

Complementation of replication origin function in mouse embryonic stem cells by human DNA sequences

A functional origin of replication was mapped to the transcriptional promoter and exon 1 of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene in the mouse and human genomes. This origin was lost in mouse embryonic stem (ES) cells with a spontaneous deletion (approximately 36 kb) at the 5' end of the HPRT locus. Restoration of HPRT activity by homologous recombination with human/mouse chimeric sequences reconstituted replication origin activity in two independent ES cell lines. Quantitative PCR analyses of abundance of genetic markers in size-fractionated nascent DNA indicated that initiation of DNA replication coincided with the site of insertion in the mouse genome of the 335 bp of human DNA containing the HPRT exon 1 and a truncated promoter. The genetic information contained in the human sequence and surrounding mouse DNA was analyzed for cis-acting elements that might contribute to selection and functional activation of a mammalian origin of DNA replication.

Evidence that silencing of the HPRT promoter by DNA methylation is mediated by critical CpG sites

The strong correlation between promoter hypermethylation and gene silencing suggests that promoter methylation represses transcription. To identify methylation sites that may be critical for maintaining repression of the human HPRT gene, we treated human/hamster hybrid cells containing an inactive human X chromosome with the DNA demethylating agent 5-azadeoxycytidine (5aCdr), and we then examined the high resolution methylation pattern of the HPRT promoter in single cell-derived lines. Reactivation of HPRT correlated with complete promoter demethylation. In contrast, the 61 5aCdr-treated clones that failed to reactivate HPRT exhibited sporadic promoter demethylation. However, three specific CpG sites remained methylated in all unreactivated clones, suggesting these sites may be critical for maintaining transcriptional silencing of the HPRT gene. Re-treatment of partially demethylated (and unreactivated) clones with a second round of 5aCdr did not increase the frequency of HPRT reactivation. This is consistent with mechanisms of methylation-mediated repression requiring methylation at specific critical sites and argues against models invoking overall levels or a threshold of promoter methylation. Treatment of cells with the histone deacetylase inhibitor, trichostatin A, failed to reactivate HPRT on the inactive X chromosome, even when the promoter was partially demethylated by 5aCdr treatment, suggesting that transcriptional repression by DNA methylation is unlikely to depend upon a trichostatin A-sensitive histone deacetylase.

Regulation of hypoxanthine phosphoribosyltransferase, glyceraldehyde-3-phosphate dehydrogenase and beta-actin mRNA expression in porcine immune cells and tissues

Various "housekeeping" genes are often used as endogenous controls in gene expression experiments. We have cloned from swine, three genes commonly used as endogenous controls in other species and have characterized their relative levels of expression in various porcine tissues and their response to various cell activators. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin were readily detected by northern hybridization in various tissues and in alveolar macrophages. The expression of hypoxanthine phosphoribosyltransferase (HPRT) was detected only by northern hybridization of poly-A+ enriched RNA and by reverse transcriptase-polymerase chain reaction (RT-PCR), making it more suitable for highly sensitive detection methods. Expression of GAPDH varied less among tissues than did beta-actin, making it more useful control for comparisons of gene expression between tissues with northern hybridizations. Various treatments of cultured alveolar macrophages differentially affected levels of beta-actin and GAPDH, while HPRT expression was unchanged in alveolar macrophages or spleen cells similarly treated. Therefore, while HPRT can be used as the endogenous control with sensitive detection methods such as RT-PCR, less sensitive detection methods require a more abundant gene such as GAPDH.

Structure, organization, and expression of the human band 7.2b gene, a candidate gene for hereditary hydrocytosis

Band 7.2b is an integral membrane phosphoprotein absent from the erythrocyte membranes of patients with hereditary hydrocytosis, a hemolytic anemia inherited in an autosomal dominant fashion and characterized by stomatocytic red blood cells with abnormal permeability to Na+ and K+. The precise role of band 7.2b is unknown, but it may interact with other proteins of the junctional complex of the membrane skeleton. To gain additional insight into the structure and function of this protein and to provide the necessary tools for further genetic studies of hydrocytosis patients, we determined the sequence of the full-length human band 7.2b cDNA, characterized the genomic structure of the band 7.2b gene, studied its pattern of expression in different tissues, and characterized the promoter of the gene. The composite band 7.2b gene cDNA was 3047 base pairs in length. Northern blot analysis revealed a wide tissue distribution of expression of the band 7.2b gene, with utilization of alternative polyadenylation signals generating transcripts of 2.2 and 3.1 kilobases. Cloning of the band 7.2b chromosomal gene revealed that it is composed of seven exons distributed over 40 kilobases of DNA. The band 7.2b gene promoter was identified as a TATA-less, (G+C)-rich promoter with a typical InR recognition sequence and a single transcription initiation site. It directed high level expression of a reporter gene in both erythroid and nonerythroid cells. An imperfect simple sequence repeat polymorphism was identified in the 5'-flanking DNA, and an assay was developed for its analysis by PCR.

HSV as a gene transfer vector for the nervous system

Gene therapy for diseases of the nervous system requires vectors capable of delivering the therapeutic gene into postmitotic cells in vivo. Herpes simplex virus type 1 is a neurotropic virus that naturally establishes latency in neurons of the peripheral nervous system. Replication defective HSV vectors have been developed; these are deleted for at least one essential immediate early regulatory gene, rendering the virus less cytotoxic, incapable of reactivation, but still capable of establishing latency. Foreign genes can be vigorously expressed from an HSV-based vector in a transient manner in brain and other tissues. Long-term but weak foreign gene expression may be achieved in the nervous system by exploiting the transcriptional control mechanisms of the natural viral latency active promoter. To meet the needs of specific applications, either highly active long-term or regulatable transgene expression will be needed, requiring further studies in order to design the appropriate latency-based promoter systems.

Promoter function of the human glucose-6-phosphate dehydrogenase gene depends on two GC boxes that are cell specifically controlled

Human glucose-6-phosphate dehydrogenase is expressed in all cells by a housekeeping gene whose regulatory 5'-flanking sequence includes at least nine GC boxes. By transient transfection of HeLa and HepG2 cells with constructs containing glucose-6-phosphate dehydrogenase gene regions linked to a reporter gene, we have now delineated the core promoter and have located upstream stimulatory and inhibitory sequences. By mutational analysis, we demonstrate that the activity of the core promoter requires two out of seven GC boxes. We show that stimulatory protein 1 (Sp1)-related factors and activator protein 2 (AP-2)-related proteins bind to these two boxes in band-shift experiments. One point mutation that affects the binding of only the Sp1-related factors to one or both boxes causes a marked decrease of promoter activity in HepG2 cells but not in HeLa cells. We conclude that (a) two out of many seemingly redundant GC boxes are necessary to drive a G+C-rich housekeeping promoter; (b) factors that bind to GC boxes may exert cell-type-specific regulation of housekeeping gene promoter activity; (c) point mutations in the promoter of the glucose-6-phosphate dehydrogenase gene can inhibit its transcription.

5'-flanking sequences of the human HPRT gene direct neuronal expression in the brain of transgenic mice

Total deficiency of hypoxanthine phosphoribosyltransferase (HPRT) in humans causes the neurological disorder Lesch-Nyhan syndrome. The HPRT gene is expressed at basal levels in all tissues but at higher levels in the brain, the relevance and mechanism of which is unknown. To determine if cis-acting DNA elements play a role in the tissue-differential pattern of expression, we generated transgenic mice carrying different sequences of the human HPRT (hHPRT) promoter fused to the bacterial lacZ gene. We show that a 1.6 kb fragment of the hHPRT promoter contains essential information to direct beta-galactosidase expression preferentially to the basal ganglia, cerebral cortex, hippocampus, and several other areas of the forebrain. At least two elements within the 1.6 kb fragment appear to be required for neuronal expression. A 182 bp element (hHPRT-NE) represents one of these sequences and is involved not only in conferring neuronal specificity but also in repressing transgene expression in non-neuronal tissues. These studies provide molecular insight into the mechanism of increased HPRT expression in the brain.

Characterization of regulatory sequences and nuclear factors that function in cooperation with the promoter of the human thymidylate synthase gene

To identify the essential sequence of the promoter of the human thymidylate synthase (hTS) gene, deletion mutants were constructed and assayed for promoter activity. The essential sequence was located within 65 bp upstream from the major cap site and a sequence that reduces the promoter activity was found in a region upstream from the essential promoter sequence. We previously identified two DNA-binding nuclear factors, NF-TS2 and NF-TS3, that bind to a region around the site of initiation of translation of the hTS gene. In this study, we confirmed the binding site of these factors by gel mobility shift analysis and found that NF-TS2 is the major factor that binds to the hTS gene in HeLa cells, whereas NF-TS3 is the major factor in the TIG-1 line of human fibroblast cells. To clarify the function of these factors, we examined the effects of the binding of these factors on the promoter activity. Our findings suggest that the binding of NF-TS2 enhances the promoter activity of the hTS gene in HeLa cells, whereas the binding of NF-TS3 represses the activity of the same promoter in TIG-1 cells.

Hepatitis B virus C gene promoter is under negative regulation

The regulation of the core promoter of Hepatitis B virus (HBV) was investigated using the chloramphenicol acetyltransferase (CAT) reporter system. Deletional analysis of sequences 5' to the HBV core promoter indicated the presence of a negative regulatory element (NRE) located within a 282-bp BamHI-HincII DNA fragment. The NRE was functional in hepatic as well as nonhepatic cells. Results of in vivo competition experiments suggest a role for cellular transacting repressor protein(s) in the functioning of the NRE. The HBV NRE, positioned 5' to the SV40 early promoter, inhibited the activity of the heterologous promoter in an orientation-independent, but position-dependent manner. These data indicate that the HBV NRE is a silencer element, which functions to downregulate the activity of the core promoter.