Effect of increased ART-CPT uptake on tuberculosis outcomes and associated factors, Burundi, 2009-2013

We retrospectively examined 3579 records of human immunodeficiency virus infected tuberculosis (TB) patients diagnosed from January 2009 to June 2013 in 55 TB treatment facilities in Burundi, to demonstrate whether improvement of combined cotrimoxazole preventive therapy and antiretroviral therapy (ART) uptake was accompanied by improvement of treatment outcomes, and to describe associated factors. Treatment success rates increased from 71% to 80% (P < 0.001). While loss to follow-up and transfer-out rates declined significantly, death rates decreased modestly, and remained high, at 14%. ART uptake was worse in suburban areas and private for-profit institutions. World Health Organization targets could be achieved if peripheral health facilities were prioritised.

Treatment of nonunion in neglected long bone shaft fractures by osteoperiosteal decortication

In emerging countries, nonunion in the shaft of fractured long bones is common.

PATIENTS AND METHODS

In a 3-year long prospective study, 50 patients (38 men, 12 women) with an average age of 40.9 years (range 17-60) were treated for neglected diaphyseal nonunion an average of 11 months (range 6-48) after the fracture event. The femur was involved 14 times, tibia 22 times, humerus eight times and forearm bones six times. All of these patients had consulted initially with a traditional bone setter at the time of fracture. The surgical procedure consisted of osteoperiosteal decortication followed by repermeabilization of the medullary canal and then internal fixation. Compression plating was used for the humerus, radius and ulna. Nonunion of the middle-third of the femur and tibia was treated by intramedullary nailing and nonunion of the proximal third of the femur with an inverted DCS screw-plate. Patients were reviewed clinically and with X-rays on postoperative days 21, 45, 90 and 120.

RESULTS

Bone union was obtained in under 90 days in the upper limb and under 120 days in the lower limb. No additional grafting was needed. There were only two cases of leg length differences.

DISCUSSION

Osteoperiosteal decortication is a reliable technique that leads to predictable, satisfactory results, given the limited materials required to treat long bone nonunion in emerging countries.

User fees and access to ARV treatment for persons living with HIV/AIDS: implementation and challenges in Burkina Faso, a limited-resource country

Access to antiretroviral (ARV) treatment remains a crucial problem for patients living with HIV/AIDS (PLWHA) in limited-resources countries. Some African countries have adopted the principle of providing ARV free of charge, but Burkina Faso opted for a direct out-of-pocket payment at the point of care delivery, with subsidized payments and mechanisms for the poorest populations to receive these services free of charge. Our objectives were to determine the proportion of PLWHA who pay for ARV and to identify the factors associated with ARV access in Burkina Faso. A cross-sectional study was performed in 13 public health facilities, 10 Nongovernmental Organizations and association health facilities, and three faith-based health facilities. In each facility, 20 outpatients receiving ARV were interviewed during a routine clinic visit. A multivariate analysis by logistic regression was performed. Among the expected 520 patients receiving ARV, 499 (96.0%) were surveyed. The majority of patients (79%) did not pay for their ARV treatment, thereby limiting cost recovery from patient payments. In a multivariate analysis, level of education and income were associated with free access to ARV. Patients with no education more frequently received free ARV than those who had received some level of education (OR 2.7, 95% CI [1.3-5.6]). Patients without any income or with less than US$10 per month were more likely to receive free ARV (OR 2.6 [95% CI 1.3-5.2]) than those who earned more than US$10 per month. However, 16% of patients without any income and 21% of those without employment paid for ARV, and the costs of drugs for opportunistic infections, food, and transport remained a burden for 85%, 91%, and 74%, respectively, of those who did not pay for ARV. Free access to a minimum care package for every PLWHA would enhance access to ARV.

[Genetic diversity of P. falciparum and pathogenesis of the severe malarial anaemia in children under 5 years old in the province of Boulgou, Burkina Faso]

The clinical presentation of malaria mainly the severe form may be related to Plasmodium falciparum msp-2 (merozoite surface protein 2) specific family To verify this hypothesis, during the high malaria transmission season in 2001; we analyzed the allelic polymorphism of the msp-2 gene of P. falciparum in children under 5 years old with different presentation of malaria in the regional Hospital and at community level in the Boulgou Province (Burkina Faso). A total of 405 children (107 severe malarial anaemia cases, 102 severe malaria cases without severe anaemia and 196 non severe malaria cases) were enrolled in the study. The frequencies of the FC27 were 89.2% in severe malarial anaemia children group, then 89.7% and 86.9% respectively in severe malaria non anaemic children cases and non severe malaria cases (P = 0.4). The frequencies of the 3D7 were 72.5%; 84.1% and 77% respectively severe malaria non anaemic children, severe malarial anaemia cases and non severe malaria cases (P = 0.7). The complexity of the FC27 genotypes was significantly higher in children with severe malaria (with and without severe anaemia) compared to the non severe malarial children (P << 0.001). No significant difference was pointed up in the complexity of the 3D7 genotypes.

Tumor-suppression function of transcription factor USF2 in prostate carcinogenesis

Although the transcription factor USF2 has been implicated in the regulation of cellular growth and proliferation, it is unknown whether alterations in USF2 contribute to tumorigenesis and tumor development. We examined the role of USF2 in prostate tumorigenesis. Western blot analysis revealed markedly decreased USF2 levels in three androgen-independent prostate cancer cell lines, PC-3, DU145, and M12, as compared to nontumorigenic prostate epithelial cells or the androgen-dependent cell line, LNCaP. Ectopic expression of USF2 in PC-3 cells did not affect the cell proliferation rate of PC-3 cells on plastic surfaces. However, it dramatically decreased anchorage-independent growth of PC-3 cells in soft agar (90-98% inhibition) and the invasion capability (80% inhibition) of PC-3 cells in matrix gel assay. Importantly, expression of USF2 in PC-3 cells inhibited the tumorigenicity of PC-3 cells in an in vivo nude mice xenograft model (80-90% inhibition). These results suggest that USF2 has tumor-suppression function. Consistent with its function in tumor suppression, we found that the USF2 protein is present in normal prostate epithelial cells but absent in 18 of 42 (43%) human prostate cancer tissues (P = 0.015). To further examine the functional role of USF2 in vivo, we generated mice with genetic deletion of USF2 gene. We found that USF2-null mice displayed marked prostate hyperplasia at a young age, suggesting that USF2 is involved in the normal growth and differentiation of prostate. Together, these studies demonstrate that USF2 has tumor-suppressor function and plays a role in prostate carcinogenesis.

[Plasma lipids profile of non treated HIV infected adults in Ouagadougou (Burkina Faso)]

Many authors reported metabolic perturbations in connection with HIV infection. The aim of this studies was to determinate plasma lipids profile in non treated HIV infected adults in Ouagadougou (Burkina Faso). The results obtain with 187 HIV infected patients showed a significative (p < 10(-6)) high level of LDL, triglycerid, atherogenic indice; HDL was decreased. The atherogenic risk is increased with lymphocytes CD4 depletion. Plasma lipids levels must be consider in the choice of antiretroviral treatment.

[Neonatal screening of glucose-6-phosphate dehydrogenase deficiency in umbilical cord blood]

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most frequent enzyme deficiency. It is a sex-linked genetic disease concerning mostly african, mediterranean and far-eastern populations. The main clinical expression is a hemolytic anemia which can be acute or chronic. During the neonatal period the disease may manifest as neonatal jaundice. We have been asked by the neonate department to set up a blood screening test for this deficiency. We have therefore developed a test using umbilical cord blood. The assay of G6PD has been automatised and red blood cell aspartate-amino-transferase (ASAT) chosen as a reference enzyme to evaluate the age of red blood cells. Normal values of G6PD, ASAT and G6PD/ASAT ratio have been calculated from 235 cord samples. Genetic frequency of this deficiency in 2002 was 6% in male and 1% in female newborns.

The USF proteins regulate transcription of the follicle-stimulating hormone receptor but are insufficient for cell-specific expression

Expression of the FSH receptor (FSHR) is limited to granulosa cells of the ovary and Sertoli cells of the testis. Previous studies showed that an E box in the proximal promoter of the FSHR gene is required for transcription and that the predominant E box binding proteins are the ubiquitous transcription factors, upstream stimulatory factor 1 (USF1) and USF2. Through cotransfection analysis, we have shown that both wild-type and dominant negative forms of the USF proteins regulate the rat FSHR promoter and that transcriptional activation of FSHR required several domains within the amino-terminal portion of the USF proteins. Analysis of the FSHR promoter region using in vivo genomic footprinting indicated that the E box is occupied by proteins in Sertoli cells but not in cells that fail to express the receptor, despite the presence of the USF proteins. To help delineate the regions of the rat FSHR gene required for correct spatial and temporal expression, transgenic mice harboring two constructs containing variable amounts of 5'-flanking sequence (5,000 bp and 100 bp) were generated. Examination of 16 different transgenic lines revealed varied transgene expression profiles with multiple lines having different amounts of ectopic expression and two lines failing to express the transgene. In addition, little or no expression was observed in Sertoli cells. These studies indicate that additional regulatory sequences outside the region from -5,000 to +123 bp are needed for proper expression in Sertoli cells.

Spatial organization of RNA polymerase II transcription in the nucleus

In eukaryotic cells, mRNA synthesis is carried out by large, multifunctional complexes that are also involved in coordinating transcription with other nuclear processes. This survey focuses on the distribution and structural arrangement of these complexes within the nucleus, in relationship with the discrete positioning of particular chromosomal loci. To better understand the link between the spatial organization of the nucleus and the regulation of gene expression, it is necessary to combine information from biochemical studies with results from microscopic observations of preserved nuclear structures. Recent experimental approaches have made this possible. The subnuclear locations of specific chromosome loci, RNA transcripts, RNA polymerases, and transcription and pre-mRNA-processing factors can now be observed with computer-assisted microscopy and specific molecular probes. The results indicate that RNA polymerase II (RNAPII) transcription takes place at discrete sites scattered throughout the nucleoplasm, and that these sites are also the locations of pre-mRNA processing. Transcribing polymerases appear to be grouped into clusters at each transcription site. Cell cycle-dependent zones of transcription and processing factors have been identified, and certain subnuclear domains appear specialized for expression or silencing of particular genes. The arrangement of transcription in the nucleus is dynamic and depends on its transcriptional activity, with the RNAPII itself playing a central role in marshalling the large complexes involved in gene expression.

Loss of USF transcriptional activity in breast cancer cell lines

USF is a family of transcription factors that are structurally related to the Myc oncoproteins and also share with Myc a common DNA-binding specificity. USF overexpression can prevent c-Myc-dependent cellular transformation and also inhibit the proliferation of certain transformed cells. These antiproliferative activities suggest that USF inactivation could be implicated in carcinogenesis. To explore this possibility, we compared the activities of the ubiquitous USF1 and USF2 proteins in several cell lines derived from either normal breast epithelium or breast tumors. The DNA-binding activities of USF1 and USF2 were present at similar levels in all cell lines. In the non-tumorigenic MCF-10A cells, USF in general, and USF2 in particular, exhibited strong transcriptional activities. In contrast, USF1 and USF2 were completely inactive in three out of six transformed breast cell lines investigated, while the other three transformed cell lines exhibited loss of USF2 activity. Analyses in cells cultured from healthy tissue confirmed the transcriptional activity of USF in normal human mammary epithelial cells. These results demonstrate that a partial or complete loss of USF function is a common event in breast cancer cell lines, perhaps because, like Myc overexpression, it favors rapid proliferation.

Upstream stimulatory factor regulates major histocompatibility complex class I gene expression: the U2DeltaE4 splice variant abrogates E-box activity

The tissue-specific expression of major histocompatibility complex class I genes is determined by a series of upstream regulatory elements, many of which remain ill defined. We now report that a distal E-box element, located between bp -309 and -314 upstream of transcription initiation, acts as a cell type-specific enhancer of class I promoter activity. The class I E box is very active in a neuroblastoma cell line, CHP-126, but is relatively inactive in the HeLa epithelial cell line. The basic helix-loop-helix leucine zipper proteins upstream stimulatory factor 1 (USF1) and USF2 were shown to specifically recognize the class I E box, resulting in the activation of the downstream promoter. Fine mapping of USF1 and USF2 amino-terminal functional domains revealed differences in their abilities to activate the class I E box. Whereas USF1 contained only an extended activation domain, USF2 contained both an activation domain and a negative regulatory region. Surprisingly, the naturally occurring splice variant of USF2 lacking the exon 4 domain, U2DeltaE4, acted as a dominant-negative regulator of USF-mediated activation of the class I promoter. This latter activity is in sharp contrast to the known ability of U2DeltaE4 to activate the adenovirus major late promoter. Class I E-box function is correlated with the relative amount of U2DeltaE4 in a cell, leading to the proposal that U2DeltaE4 modulates class I E-box activity and may represent one mechanism to fine-tune class I expression in various tissues.

Cell-type-dependent activity of the ubiquitous transcription factor USF in cellular proliferation and transcriptional activation

USF1 and USF2 are basic helix-loop-helix transcription factors implicated in the control of cellular proliferation. In HeLa cells, the USF proteins are transcriptionally active and their overexpression causes marked growth inhibition. In contrast, USF overexpression had essentially no effect on the proliferation of the Saos-2 osteosarcoma cell line. USF1 and USF2 also lacked transcriptional activity in Saos-2 cells when assayed by transient cotransfection with USF-dependent reporter genes. Yet, there was no difference in the expression, subcellular localization, or DNA-binding activity of the USF proteins in HeLa and Saos-2 cells. Furthermore, Gal4-USF1 and Gal4-USF2 fusion proteins activated transcription similarly in both cell lines. Mutational analysis and domain swapping experiments revealed that the small, highly conserved USF-specific region (USR) was responsible for the inactivity of USF in Saos-2 cells. In HeLa, the USR serves a dual function. It acts as an autonomous transcriptional activation domain at promoters containing an initiator element and also induces a conformational change that is required for USF activity at promoters lacking an initiator. Taken together, these results suggest a model in which the transcriptional activity of the USF proteins, and consequently their antiproliferative activity, is tightly controlled by interaction with a specialized coactivator that recognizes the conserved USR domain and, in contrast to USF, is not ubiquitous. The activity of USF is therefore context dependent, and evidence for USF DNA-binding activity in particular cells is insufficient to indicate USF function in transcriptional activation and growth control.

Multiple rounds of transcription by RNA polymerase II at covalently cross-linked templates

An important control point for gene regulation is the frequency of initiations leading to different numbers of RNA polymerases simultaneously transcribing the same gene. To date, the only direct assay for multiple-round transcription by RNA polymerase II in vitro required G-free cassette-containing templates and GTP-free conditions and was thus restricted in application. Here we used instead templates containing a triplex-directed interstrand psoralen-DNA cross-link to block RNA polymerase II elongation at a specific location. Covalently cross-linked templates allowed simultaneous detection of both specific initiation and reinitiation with any combination of promoter and transcribed sequence. In reconstituted systems, identical stacking of RNA polymerases was observed when the first polymerase was halted by GTP deprivation at the end of a G-free cassette or by a covalent cross-link downstream of different transcribed sequences. In contrast to transcription of G-free cassettes, reinitiation was unaffected by the transcription factor SII on sequences containing all four nucleotides. In crude nuclear extracts, transcription of covalently cross-linked templates yielded a reinitiation pattern with a wider spacing than in more purified fractions, indicating that the elongation complexes from nuclear extract contained a different form of RNA polymerase II or a different complement of associated factors.

Plasmids for the in vitro analysis of RNA polymerase II-dependent transcription based on a G-free template

Described are a series of plasmids containing combinations of adenovirus-2 major late promoter elements, including consensus TATA box and initiator, upstream of G-free transcription cassettes of various lengths. These provide an assortment of tools for investigating both basal and regulated transcription mechanisms by in vitro transcription methods.

Overlapping roles and asymmetrical cross-regulation of the USF proteins in mice

USF1 and USF2 are ubiquitously expressed transcription factors implicated as antagonists of the c-Myc protooncoprotein in the control of cellular proliferation. To determine the biological role of the USF proteins, mutant mice were generated by homologous recombination in embryonic stem cells. USF1-null mice were viable and fertile, with only slight behavioral abnormalities. However, these mice contained elevated levels of USF2, which may compensate for the absence of USF1. In contrast, USF2-null mice contained reduced levels of USF1 and displayed an obvious growth defect: they were 20-40% smaller at birth than their wild-type or heterozygous littermates and maintained a smaller size with proportionate features throughout postnatal development. Some of the USF-deficient mice, especially among the females, were prone to spontaneous epileptic seizures, suggesting that USF is important in normal brain function. Among the double mutants, an embryonic lethal phenotype was observed for mice that were homozygous for the Usf2 mutation and either heterozygous or homozygous for the Usf1 mutation, demonstrating that the USF proteins are essential in embryonic development.

Autoactivation of Xenopus MyoD transcription and its inhibition by USF

Members of the MyoD family of muscle-specific transcription factors play central roles in the formation and differentiation of skeletal muscle; however, steps involved in the initiation and subsequent regulation of myogenic factor expression are poorly understood. To investigate mechanisms underlying muscle cell type-specific MyoD gene expression, the functions of regulatory elements that control Xenopus MyoDa gene transcription were analyzed. We show that E boxes in the XMyoDa promoter have dual functions. These sites bind myogenic basic helix-loop-helix proteins and serve as target sites for direct autoactivation. In addition, these regulatory elements bind other, more widely expressed proteins that repress promoter activity. In particular, the binding of the transcriptional regulatory protein USF to a conserved site in the XMyoDa promoter decreased basal activity of the promoter and inhibited MyoD-dependent autoactivation. The results suggest that XMyoD transcription and myogenic factor activity is governed by a competition between muscle-specific, positive-acting factors and widely expressed repressors for binding to common regulatory sites.

Functional domains of the transcription factor USF2: atypical nuclear localization signals and context-dependent transcriptional activation domains

USF is a family of basic helix-loop transcriptional factors that recognizes DNA-binding sites similar to those of the Myc oncoproteins. Here, various functional domains in the mouse USF2 protein were identified and characterized. Indirect immunofluorescence studies with transiently transfected cells revealed that both the basic region and the highly conserved USF-specific region (USR) are involved in the nuclear localization of USF2. Cotransfection assays with deletion mutants containing the DNA-binding domain of either USF2 or GAL4 identified two distinct transcriptional activation domains in USF2, the USR and the exon 5-encoded region. Activity of the exon 5 activation domain was detectable in both assay systems. Within USF2, however, its potency varied with the conformation induced by the surrounding regions, especially that encoded by alternatively spliced exon 4. In contrast, the USR activated transcription only in its natural context upstream of the USF2 basic region and only with reporter constructs containing the adenovirus major late minimal promoter but not the E1b minimal promoter. However, insertion of an initiator element downstream of the TATA box rescued the activity of the USR on the E1b-driven reporters. The USR therefore represents a new type of activation domain whose function depends very strongly on the core promoter context.

Antiproliferative properties of the USF family of helix-loop-helix transcription factors

USF is a family of transcription factors characterized by a highly conserved basic-helix-loop-helix-leucine zipper (bHLH-zip) DNA-binding domain. Two different USF genes, termed USF1 and USF2, are ubiquitously expressed in both humans and mice. The USF1 and USF2 proteins contain highly divergent transcriptional activation domains but share extensive homologies in the bHLH-zip region and recognize the same CACGTG DNA motifs. Although the DNA-binding and transcriptional activities of these proteins have been characterized, the biological function of USF is not well understood. Here, focus- and colony-formation assays were used to investigate the potential involvement of USF in the regulation of cellular transformation and proliferation. Both USF1 and USF2 inhibited the transformation of rat embryo fibroblasts mediated by Ras and c-Myc, a bHLH-zip transcription factor that also binds CACGTG motifs. DNA binding was required but not fully sufficient for inhibition of Myc-dependent transformation by USF, since deletion mutants containing only the DNA-binding domains of USF1 or USF2 produced partial inhibition. While the effect of USF1 was selective for Myc-dependent transformation, wild-type USF2 exerted in addition a strong inhibition of E1A-mediated transformation and a strong suppression of HeLa cell colony formation. These results suggest that members of the USF family may serve as negative regulators of cellular proliferation in two ways, one by antagonizing the transforming function of Myc, the other through a more general growth-inhibitory effect.

Murine chromosomal location of five bHLH-Zip transcription factor genes

The genes for the bHLH-Zip transcription factors Tfap4, Mxi1, Tcfeb, Usf1, and Usf2 have been mapped in mouse by interspecific backcross analysis. Mxi1, Usf1, and Usf2 have been mapped previously by in situ hybridization, but their positions on the meiotic linkage map had not been determined. The other two genes have not previously been mapped in mouse. These transcription factors belong to a growing family of transcriptional regulators, some of which are known to form a complex network of interacting proteins that control cell proliferation and apoptosis. As expected, based on mapping studies of other bHLH-Zip genes, these loci were well distributed among mouse chromosomes. In addition, some of the probes used in this study detected multiple, independently segregating loci, suggesting the possible existence of additional family members or species-specific pseudogenes.

Autoregulation of the human C/EBP alpha gene by stimulation of upstream stimulatory factor binding

The human C/EBP alpha gene promoter shares significant sequence homology with that of the mouse but has a different mechanism of autoregulation. Activation of the murine promoter by direct binding of C/EBP alpha to a site within 200 bp of the transcriptional start was shown to elevate activity by approximately threefold (R. J. Christy, K. H. Kaestner, D. E. Geiman, and M. D. Lane, Proc. Natl. Acad. Sci. USA 88:2593-2597, 1991; K. Legraverend, P. Antonson, P. Flodby, and K. G. Xanthapoulos, Nucleic Acids Res. 21:1735-1742, 1993). Unlike its murine counterpart, the human C/EBP alpha gene promoter does not contain a cis element that binds the C/EBP alpha protein. Neither C/EBP alpha nor C/EBP beta (NF-Il-6) binds the human C/EBP alpha promoter within 437 bp. However, cotransfection studies show that C/EBP alpha stimulates transcription of a reporter gene driven by 437 bp of the C/EBP alpha promoter. Our studies show that the human C/EBP alpha protein stimulates USF to bind to a USF consensus element within C/EBP alpha promoter and activates it by two- to threefold. We propose that the human gene employs the ubiquitously expressed DNA-binding protein factor USF to carry out autoregulation. Autoregulation of the human C/EBP alpha promoter was abolished by deletion of the USF binding site, CACGTG. Expression of human C/EBP beta following transfection did not stimulate USF binding. These studies suggest a mechanism whereby tissue-specific autoregulation can be achieved via a trans-acting factor that is expressed in all cell types. Thus, direct binding of the C/EBP alpha protein to the promoter of the C/EBP alpha gene is not required for autoregulation.

Sarkosyl block of transcription reinitiation by RNA polymerase II as visualized by the colliding polymerases reinitiation assay

There are indications that different concentrations of Sarkosyl can block transcription initiation by RNA polymerase II in vitro at different functional steps [Hawley and Roeder (1985) J. Biol. Chem. 260, 8163-8172]. Consequently, this reagent could be a very useful tool for mechanistic studies. So far, however, evidence for the selectivity of Sarkosyl effects on RNA polymerase II transcription has been only indirect. To directly investigate the effect of Sarkosyl on transcription initiation and reinitiation by RNA polymerase II, we employed the reinitiation assay based on utilization of templates containing G-free cassettes (colliding polymerases reinitiation assay, or CoPRA). These experiments showed unambiguously that, under the appropriate conditions, Sarkosyl can be used to block transcription reinitiation by RNA polymerase II while allowing a first round of initiations from preassembled initiation complexes. This inhibition is not due to a disruption of the SII-dependent elongation of the reinitiated transcripts, and the levels of Sarkosyl that prevent transcription reinitiation coincide with the levels that block preinitiation complex assembly. However, Sarkosyl addition to transcription reactions reconstituted with partially purified transcription factors was found to have several undesirable side effects. The usefulness and limitations of the Sarkosyl-based and CoPRA assays for measurements of transcription reinitiation are discussed.

Role of the leucine zipper in the kinetics of DNA binding by transcription factor USF

USF is a transcription factor characterized by a helix-loop-helix (HLH) DNA-binding domain that has been highly conserved through evolution. Vertebrate USFs contain an additional C-terminal leucine zipper (LZ) immediately adjacent to the HLH domain. This LZ is essential for efficient DNA binding by human USF. However, sea urchin has a USF family member that lacks a LZ and yet binds DNA efficiently. To clarify the role of the LZ in DNA binding by USF, we compared the properties of human and sea urchin USFs and found that the two proteins interacted with their specific sites on the DNA with identical affinities but very different kinetics. Association and dissociation rate constants of sea urchin USF were about 10-fold those of human USF. Domain-swapping experiments revealed that the LZ was responsible for the slower kinetics of human USF. USF heterodimers containing a single LZ displayed rates intermediate between those of dimers containing either two or no LZ, indicating that zipper-zipper interactions within USF dimers were not important for DNA binding. Temperature effects on DNA-binding parameters revealed a very high energy barrier for binding of human USF to DNA. Presence of a LZ increased the activation energy of the reaction.

The basic helix-loop-helix protein upstream stimulating factor regulates the cardiac ventricular myosin light-chain 2 gene via independent cis regulatory elements

Previous studies have documented that 250 bp of the rat cardiac ventricular myosin light-chain 2 (MLC-2v) promoter is sufficient to confer cardiac muscle-specific expression on a luciferase reporter gene in both transgenic mice and primary cultured neonatal rat myocardial cells. Utilizing ligation-mediated PCR to perform in vivo dimethyl sulfate footprinting, the present study has identified protein-DNA interaction within the position from -176 to -165. This region, identified as MLE1, contains a core sequence, CACGTG, which conforms to the consensus E-box site and is identical to the upstream stimulating factor (USF)-binding site of the adenovirus major late promoter. Transient assays of luciferase reporter genes containing point mutations of the site demonstrate the importance of this cis regulatory element in the transcriptional activation of this cardiac muscle gene in ventricular muscle cells. The protein complex that occupies this site is capable of binding to HF-1a and PRE B sites which are known to be required for cardiac muscle-specific expression of rat MLC-2v and alpha-myosin heavy-chain genes, respectively. This study provides direct evidence that USF, a member of the basic helix-loop-helix leucine zipper family, binds to MLE1, HF-1a, and PRE B sites and suggests that it is a component of protein complexes that may coordinately control the expression of MLC-2v and alpha-myosin heavy-chain genes. The current study also provides evidence that USF can positively and negatively regulate the MLC-2v gene via independent cis regulatory elements.

The cellular transcription factor USF cooperates with varicella-zoster virus immediate-early protein 62 to symmetrically activate a bidirectional viral promoter

The mechanisms governing the function of cellular USF and herpesvirus immediate-early transcription factors are subjects of considerable interest. In this regard, we identified a novel form of coordinate gene regulation involving a cooperative interplay between cellular USF and the varicella-zoster virus immediate-early protein 62 (IE 62). A single USF-binding site defines the potential level of IE 62-dependent activation of a bidirectional viral early promoter of the DNA polymerase and major DNA-binding protein genes. We also report a dominant negative USF-2 mutant lacking the DNA-binding domain that permits the delineation of the biological role of both USF-1 and USF-2 in this activation process. The symmetrical stimulation of the bidirectional viral promoter by IE 62 is achieved at concentrations of USF-1 (43 kDa) or USF-2 (44 kDa) already existing in cells. Our observations support the notion that cellular USF can intervene in and possibly target promoters for activation by a herpesvirus immediate-early protein.

Archaic structure of the gene encoding transcription factor USF

The upstream stimulatory factor (USF) is a helix-loop-helix transcription factor that interacts with specific sites on the DNA that are also recognized by the MYC oncoproteins. We isolated genomic clones to the murine 44-kDa form of USF (USF2 gene). This unique gene spans 13 kilobases of DNA and is composed of 10 exons. The gene seems to have maintained its archaic structure, since many of the exons encode discrete functional domains of the transcription factor originally identified by protein sequence comparisons. A particularly striking HpaII tiny fragment island, extending over nearly 2,000 base pairs, surrounds the USF2 translation initiation site. This region, which includes the USF2 promoter and the first four exons, is characterized by an overall GC content greater than 74%. Analysis by S1 mapping and transient transfection assays revealed that the USF2 transcripts originate from an initiator element located within a highly GC-rich region that is surrounded by two long polyadenylate stretches and functions as a bidirectional promoter. Different forms of USF2 messages result from the presence or absence of the fourth exon in the processed USF2 mRNA. Alternative splicing correlates with the lack of a consensus lariat branch point in the third intron. Transient cotransfection assays revealed that the presence or absence of the amino acid sequences encoded by exon 4 affects considerably the transcription activation properties of the USF2 protein.

Ubiquitous expression of the 43- and 44-kDa forms of transcription factor USF in mammalian cells

USF is a helix-loop-helix transcription factor that, like Myc, recognizes the DNA binding motif CACGTG. Two different forms of USF, characterized by apparent molecular weights of 43,000 and 44,000, were originally identified in HeLa cells by biochemical analysis. Clones for the 43-kDa USF were first characterized, but only partial clones for the human 44-kDa USF (USF2, or FIP) have been reported. Here we describe a complete cDNA for the 44-kDa USF from murine cells. Analysis of this clone has revealed that the various USF family members are quite divergent in their N-terminal amino acid sequences, while a high degree of conservation characterizes their dimerization and DNA-binding domains. Interestingly, the 3' noncoding region of the 44-kDa USF cDNAs displayed an unusual degree of conservation between human and mouse. In vitro transcription/translation experiments indicated a possible role for this region in translation regulation. Alternative splicing forms of the 44-kDa USF messages exist in both mouse and human. Examination of the tissue and cell-type distribution of USF by Northern blot and gel retardation assays revealed that while expression of both the 43- and 44-kDa USF species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cells.

Synthesis of reinitiated transcripts by mammalian RNA polymerase II is controlled by elongation factor SII

Previous studies have revealed that the in vitro synthesis of reinitiated transcripts by RNA polymerase II requires an additional activity, designated reinitiation transcription factor (RTF), which is distinct from all of the general class II initiation factors. While further characterizing this activity, it was found that RTF displays properties indistinguishable from those of the RNA polymerase II elongation factor SII. In addition, Western blot analysis using SII-specific antibodies revealed that human SII is a major component in purified RTF preparations. The functional equivalence of the two proteins was established using recombinant SII, which proved fully capable of substituting for RTF in the reinitiation assay. In these reconstituted reactions, transcription complexes resulting from reinitiation events required SII to proceed through a 400 bp G-free cassette, while complexes resulting from the first round of initiations were SII-independent. Reinitiations can take place in the absence of SII; however, addition of the elongation factor is essential for full extension of the reinitiated transcripts. These results suggest that events taking place at the promoter (e.g. first-round initiations versus reinitiations) can create marked differences in the properties of RNA polymerase II elongation complexes.

Protein-protein interaction studies using immobilized oligohistidine fusion proteins

Using a human transcription factor, upstream stimulatory factor, as a model system, we developed a method for the rapid and efficient purification of proteins that interact with a cloned polypeptide expressed as a fusion with an oligohistidine domain. The complex between the oligohistidine fusion protein and its interacting partner was loaded onto a column of chelating resin charged with Ni2+. The bound complex could be eluted as a whole with high concentrations of imidazole. Alternatively, the secondary protein could be released separately using appropriate elution conditions. This procedure is both simple and efficient, and it presents distinct advantages over other affinity purification methods. In addition, this same method can be used to study protein-protein interactions.

Single-step purification of bacterially expressed polypeptides containing an oligo-histidine domain

Plasmid expression vectors have been constructed that direct the synthesis in Escherichia coli of fusion proteins containing a stretch of six histidine residues at either the N or C terminus. This oligo-histidine domain allows the single-step purification of the fusion proteins, under nondenaturing conditions, by immobilized metal affinity chromatography on Ni2+ bound to iminodiacetic acid-agarose. Several eukaryotic transcription factors (e.g., the upstream stimulatory factor for the adenovirus major late promoter) have been successfully purified, in an active state, by this method.

Members of the USF family of helix-loop-helix proteins bind DNA as homo- as well as heterodimers

We have isolated human cDNA clones for USF2, a new member of the upstream stimulatory factor (USF) family of transcription factors. Analysis of these clones revealed the existence of highly conserved elements in the C terminal region of all USF proteins. These include the basic region, helix-loop-helix (HLH) motif, and, in the case of the human proteins, the C-terminal leucine repeat (LR). In addition, a highly conserved USF-specific domain is located immediately upstream of the basic region. Using in vitro translated proteins, we found that all members of the USF family bound DNA as dimers. The N-terminal portion of USF, including the USF-specific domain, was entirely dispensable for dimer formation and DNA-binding. However, deletion mutants of USF2 lacking the LR were deficient in DNA-binding activity. Interestingly, each of the USF proteins could form functional heterodimers with the other family members, including the sea urchin USF, which does not have a LR motif. This indicates that the conserved LR in human USF is not required for dimer formation, and influences only indirectly DNA-binding.

Sea urchin USF: a helix-loop-helix protein active in embryonic ectoderm cells

We previously characterized a DNA-binding factor in nuclear extracts of Strongylocentrotus purpuratus embryos that bound Spec gene promoters, was ectoderm specific, and had properties similar to the vertebrate transcription factor USF. Here we describe a cDNA clone, suUSF, isolated from an S. purpuratus cDNA library, with sequence homology to human USF. Spec gene promoter fragments formed sequence-specific complexes with suUSF, and antibodies against suUSF inhibited binding activity in nuclear extracts. Reaction of USF-site containing probes with filter-bound nuclear proteins demonstrated that suUSF binding activity was enriched in ectoderm cells, and immunoblotting showed a similar ectoderm enrichment. These data demonstrated that suUSF was responsible for the ectoderm-specific activity observed in sea urchin extracts.

Transcription factor requirement for multiple rounds of initiation by human RNA polymerase II

We have investigated conditions that allow multiple rounds of transcription initiation from the adenovirus major late promoter in an in vitro system derived from HeLa cell nuclear extracts. Templates containing guanine-free cassettes provided a direct assay for discriminating between reinitiated transcripts and transcripts generated by a first-round of transcription initiations. When reactions were reconstituted with the previously characterized class II transcription factors (TFIIA, TFIIB, TFIID, TFIIE/F), transcription by human RNA polymerase II from the adenovirus major late promoter was essentially restricted to a single round of initiations. Reinitiations at previously transcribed major late templates required an additional activity, designated reinitiation transcription factor (RTF). The RTF activity could be separated from the required transcription initiation factors. Semipurified human RTF also promoted transcription reinitiations at minimal promoters derived from the human c-myc, histone H4, and heat shock 70-kDa protein genes, indicating that the same reinitiation factor may be utilized by many, if not all, genes. The possible role of RTF in regulating the transcription rate of various class II genes is discussed.

The murine adenosine deaminase promoter requires an atypical TATA box which binds transcription factor IID and transcriptional activity is stimulated by multiple upstream Sp1 binding sites

We have explored the template and factor requirements for in vitro transcription of the GC-rich promoter of the murine adenosine deaminase gene. The core promoter consists of an A-rich sequence (TAAAAAA) 27 base pairs upstream of the initiation site which binds transcription factor IID (TFIID) and a high affinity Sp1 binding site located 27 base pairs further upstream. Multiple upstream elements increased core promoter activity 20-fold and correspond to protected regions in DNase I footprinting assays with purified Sp1 protein. Internal deletion of the TA6 element alone eliminated transcription in spite of the presence of all other promoter elements including four Sp1 binding sites. Recombinant human TFIID supported weak basal transcription in heat-treated nuclear extracts whereas a partially purified TFIID fraction from HeLa cells reconstituted a maximal level of transcription. Inclusion of 12 base pairs immediately adjacent to the proximal Sp1 site resulted in a 5-fold boost in transcriptional activity and corresponds to a second Sp1 binding site. These results serve as a basis for further exploration of the factors involved in the developmental and selective high level tissue expression of the murine adenosine deaminase gene.

The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer

We isolated full-length cDNAs encoding the 43-kD form of human upstream stimulatory factor (USF), a cellular factor required for efficient transcription of the adenovirus major late (AdML) promoter in vitro. Sequence analysis showed USF to be a member of the c-myc-related family of DNA-binding proteins. Using proteins translated in vitro, we identified a DNA-binding domain near the carboxyl terminus, which includes both a helix-loop-helix motif and a leucine repeat. We show that USF interacts with its target DNA as a dimer. The leucine repeat is required for efficient DNA binding of the intact protein and for interactions between full-length and truncated USF proteins. Interestingly, it is not required for DNA binding of the isolated helix-loop-helix domain. The structure of different cDNA clones indicates that USF RNA is differentially spliced, and alternative exon usage may regulate the levels of functional USF protein.

DNA-binding and transcriptional properties of human transcription factor TFIID after mild proteolysis

The existence of separable functions within the human class II general transcription factor TFIID was probed for differential sensitivity to mild proteolytic treatment. Independent of whether TFIID was bound to DNA or free in solution, partial digestion with either one of a variety of nonspecific endoproteases generated a protease-resistant protein product that retained specific DNA recognition, as revealed by DNase I footprinting. However, in contrast to native TFIID, which interacts with the adenovirus major late (ML) promoter over a very broad DNA region, partially proteolyzed TFIID interacted with only a small region of the ML promoter immediately surrounding the TATA sequence. This novel footprint was very similar to that observed with the TATA factor purified from yeast cells. Partially proteolyzed human TFIID could form stable complexes that were resistant to challenge by exogenous templates. It could also nucleate the assembly of transcription complexes on the ML promoter with an efficiency comparable to that of native TFIID, yielding similar levels of transcription initiation. These results suggest a model in which the human TFIID protein is composed of at least two different regions or polypeptides: a protease-resistant "core," which by itself is sufficient for promoter recognition and basal transcriptional levels, and a protease-sensitive "tail," which interacts with downstream promoter regions and may be involved in regulatory processes.

Stability of transcription complexes on class II genes

Commitment of a TATA box-driven class II gene to transcription requires binding of only one transcription factor, TFIID. Additional factors (TFIIB, TFIIE, and RNA polymerase II) do not remain associated with the TFIID-promoter complex during the course of transcription. This indicates that there are two intermediates along the transcription reaction pathway which may be potential targets for the regulation of gene expression.

Physical analysis of transcription preinitiation complex assembly on a class II gene promoter

Transcription of protein-encoding genes by human RNA polymerase II requires multiple ancillary proteins (transcription factors). Interactions between these proteins and the promoter DNA of a viral class II gene (the major late transcription unit of adenovirus) were investigated by enzymatic and chemical footprinting. The experiments indicated that the assembly of functionally active RNA polymerase II-containing transcription preinitiation complexes requires a complete set of transcription factors, and that both specific protein-DNA and protein-protein interactions are involved. This allows individual steps along the transcription reaction pathway to be tested directly, thus providing a basis for understanding basic transcription initiation mechanisms as well as the regulatory processes that act on them.

Multiple forms of the human gene-specific transcription factor USF. II. DNA binding properties and transcriptional activity of the purified HeLa USF

The gene-specific upstream stimulatory transcription factor (USF) is required for maximal expression of the adenovirus major late promoter in vivo as well as in vitro. We have examined the DNA binding and transcriptional properties of USF purified to near-homogeneity from HeLa cell nuclei (Sawadogo, M., Van Dyke, M. W., Gregor, P. D., and Roeder, R. G. (1988) J. Biol. Chem. 263, 11985-11993). The 44-and 43,000-dalton forms of USF displayed identical affinities for the major late promoter upstream sequence. Specific binding parameters were greatly influenced by neighboring sequences, but not by the topological state of the DNA. The dissociation rate was highly dependent upon the concentration of competitor DNA, indicating that USF can efficiently transfer from one binding site to another by passing through a doubly bound intermediate state (direct transfer mechanism). Transcription stimulation by purified USF showed titration curves identical to those observed with cruder preparations of the transcription factor. However, the overall stimulation observed at saturating USF concentration was significantly lower with the purified protein. By contrast, interaction with TATA box-binding RNA polymerase II transcription factor D was observed with both USF-containing fractions. This could suggest the existence of two different mechanisms for upstream sequence-dependent transcription stimulation, where one critical component (or some necessary modification of the upstream factor itself) may be missing in reactions reconstituted with purified USF.

Multiple forms of the human gene-specific transcription factor USF. I. Complete purification and identification of USF from HeLa cell nuclei

The human gene-specific upstream stimulatory transcription factor (USF) is required, both in vivo and in vitro, for maximal expression of the major late promoter (MLP) of adenovirus. We report here the complete purification and identification of USF from HeLa cell nuclei. The protein was followed throughout its purification using a quantitative filter binding assay. With a combination of classical purification techniques and fast-flow protein liquid chromatography, USF can be purified to homogeneity starting either with a standard HeLa cell nuclear extract or with a higher salt extract from (lysed) HeLa cell nuclei (nuclear pellet extract). Approximately 20,000-fold purification from the nuclear pellet extract and 80,000-fold from the nuclear extract are necessary to obtain homogeneous preparations of the transcription factor. A maximum of 20,000 molecules of USF appear to be present in HeLa cells. Two major forms of the USF protein can be distinguished both by their slightly different mobilities in sodium dodecyl sulfate gel electrophoresis (apparent molecular weights 44,000 and 43,000, respectively) and by different electrophoretic mobilities of the corresponding protein-DNA complexes. Both forms of USF are heat-stable and interact with the MLP as monomers. Antibodies elicited against purified HeLa USF interact with the transcription factor bound to the MLP upstream element.

The gene-specific initiation factor USF (upstream stimulatory factor) bound at the adenovirus type 2 major late promoter: mass and three-dimensional structure

The gene-specific transcription initiation factor USF (upstream stimulatory factor) binds at a palindromic sequence that extends from -52 to -63 relative to the start site of the adenovirus type 2 major late promoter; USF enhances in vitro transcription 10- to 20-fold. By analysis of digital micrographs from the Brookhaven scanning transmission electron microscope, we have identified a sample of 29 proteins (mass, 55 +/- 5 kDa) specifically bound at the palindrome. The individual protein digital images show extensive homology, which permits modeling a three-dimensional structure at a relatively low resolution, which is nonetheless significant for the study of protein-protein interactions in initiation. Non-sequence-specific competitor DNA at high mass excess can be used in reactions for microscopy, enabling characterization of specific binding for proteins present at 1% of total protein or less.

Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region

A gene-specific transcription factor, called USF, has been partially purified from HeLa cell nuclear extracts. Addition of USF results in a 10 to 20 fold increase in transcription from the adenovirus major late promoter in an in vitro system reconstituted with transcription factors TFIIB, TFIID, TFIIE, and RNA polymerase II. Binding of USF to the promoter inhibits DNAase I cleavages over a 20 base pair region just upstream of the -45 to +35 region shown previously to interact with TFIID. More discriminating footprint analyses using methidiumpropyl-EDTA-Fe(II) as the cleaving agent indicate that USF interacts primarily with the small palindromic DNA sequence GGCCACGTGACC located between positions -63 and -52 of the major late promoter, while TFIID interacts primarily with a 10 base pair DNA region centered on the consensus TATA sequence. Dissociation rate measurements indicate a cooperative interaction between USF and TFIID when simultaneously bound to the promoter DNA.

Factors involved in specific transcription by human RNA polymerase II: analysis by a rapid and quantitative in vitro assay

We describe a new assay system that allows a rapid, direct, and quantitative detection of promoter-dependent in vitro transcription by RNA polymerase II. The template used is a hybrid plasmid containing the adenovirus major late promoter linked to a synthetic 400-base-pair DNA fragment that lacks cytidine residues on the transcribed strand--i.e., generates a transcript with no guanosine residues. In vitro transcriptions are carried out in the absence of GTP or, if the reactions contain GTP, in the presence of RNase T1 and the chain terminator 3'-0-methyl-GTP. Under these conditions the only RNAs that can accumulate, whether from a circular or linearized DNA template, are the 400-nucleotide RNase T1-resistant transcripts resulting from accurate initiation at the major late promoter. Thus, specific transcription can be directly monitored by conventional RNA quantitation methods. Using this fast assay, we show that three basic transcription factors, TFIIB, TFIID, and TFIIE, are absolutely required, in addition to the RNA polymerase II, for specific transcription initiation from the adenovirus major late promoter. Units of activity can be defined for each of these individual components. The applicability of this kind of assay to other systems is discussed.

Energy requirement for specific transcription initiation by the human RNA polymerase II system

The energy requirement for specific transcription initiation and elongation by the human RNA polymerase II system was studied in vitro using partially purified transcription factors from HeLa cell nuclear extracts. The synthesis of the 536-nucleotide long run-off transcript resulting from initiation at the adenovirus major late promoter was found to be dependent upon the presence of either ATP or dATP (with the imido derivative adenyl-5'-yl imidodiphosphate being used as the substrate for the RNA polymerase elongation reaction). An identical requirement for hydrolysis of the phosphate bond in an adenosine nucleotide was observed for the synthesis of the decanucleotide transcribed from the major late promoter in the absence of the GTP substrate. In contrast, the nonhydrolyzable analog adenyl-5'-yl imidodiphosphate fully substitutes for ATP during the subsequent elongation of these short transcripts, which demonstrates that the energy requirement occurs at an earlier step of the transcription reaction. Thus the particular transcription factor that requires ATP (or dATP) hydrolysis for its function must act prior to, or concomitant with, formation of the first few phosphodiester linkages by the RNA polymerase II.