Compilation and analysis of eukaryotic POL II promoter sequences

Pathogenic Tau Causes a Toxic Depletion of Nuclear Calcium

Synaptic activity-induced calcium (Ca2+) influx and subsequent propagation into the nucleus is a major way in which synapses communicate with the nucleus to regulate transcriptional programs important for activity-dependent survival and memory formation. Nuclear Ca2+ shapes the transcriptome by regulating cyclic AMP (cAMP) response element-binding protein (CREB). Here, we utilize a Drosophila model of tauopathy and induced pluripotent stem cell (iPSC)-derived neurons from humans with Alzheimer's disease to study the effects of pathogenic tau, a pathological hallmark of Alzheimer's disease and related tauopathies, on nuclear Ca2+. We find that pathogenic tau depletes nuclear Ca2+ and CREB to drive neuronal death, that CREB-regulated genes are over-represented among differentially expressed genes in tau transgenic Drosophila, and that activation of big potassium (BK) channels elevates nuclear Ca2+ and suppresses tau-induced neurotoxicity. Our studies identify nuclear Ca2+ depletion as a mechanism contributing to tau-induced neurotoxicity, adding an important dimension to the calcium hypothesis of Alzheimer's disease.

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesus monkey, rat, dog, chicken and Plasmodium falciparum.

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers. Finally, we present a new data access tool, ChIP-Extract, which enables computational biologists to extract diverse types of promoter-associated data in numerical table formats that are readily imported into statistical analysis platforms such as R.

The Transcription Factor ATF5 Mediates a Mammalian Mitochondrial UPR

Mitochondrial dysfunction is pervasive in human pathologies such as neurodegeneration, diabetes, cancer, and pathogen infections as well as during normal aging. Cells sense and respond to mitochondrial dysfunction by activating a protective transcriptional program known as the mitochondrial unfolded protein response (UPR(mt)), which includes genes that promote mitochondrial protein homeostasis and the recovery of defective organelles [1, 2]. Work in Caenorhabditis elegans has shown that the UPR(mt) is regulated by the transcription factor ATFS-1, which is regulated by organelle partitioning. Normally, ATFS-1 accumulates within mitochondria, but during respiratory chain dysfunction, high levels of reactive oxygen species (ROS), or mitochondrial protein folding stress, a percentage of ATFS-1 accumulates in the cytosol and traffics to the nucleus where it activates the UPR(mt) [2]. While similar transcriptional responses have been described in mammals [3, 4], how the UPR(mt) is regulated remains unclear. Here, we describe a mammalian transcription factor, ATF5, which is regulated similarly to ATFS-1 and induces a similar transcriptional response. ATF5 expression can rescue UPR(mt) signaling in atfs-1-deficient worms requiring the same UPR(mt) promoter element identified in C. elegans. Furthermore, mammalian cells require ATF5 to maintain mitochondrial activity during mitochondrial stress and promote organelle recovery. Combined, these data suggest that regulation of the UPR(mt) is conserved from worms to mammals.

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

We present an update of EPDNew (http://epd.vital-it.ch), a recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally characterized eukaryotic POL II promoters, which are conceptually defined as transcription initiation sites or regions. EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD. This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments. We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.

Conserved short sequences in promoter regions of human genome

Recognition of promoter elements by the transcription factors is one of the early initial and crucial steps in gene expression and regulation. In prokaryotes, there are clear signals to identify the promoter regions like TATAAT at around -10 and TTGACA at -35 positions from transcription start site (TSS). In eukaryotes the promoter regions are structurally more complex and there are no conserved or consensus sequences similar to the ones found in prokaryotic promoters. We have located a set of GC rich short sequences (< 8 nt) that are relatively common in human promoter sequences around the TSS (+/- 100 relative to TSS). These sequences were sorted based on their frequency of occurrence in the database and the most common 50 sequences were used for further studies. Sigmoidal behavior of the high end of the frequency distribution of these sequences suggests presence of some internal co-operativity. These short sequences are distributed on both sides of TSS, suggesting that probably the transcription factors recognize these sequences on both upstream and downstream of TSS. As eukaryotic promoters lack any conserved sequences, we expect that these short sequences may help in recognition of promoter regions by relevant transcription factors prior to the initiation of transcription process. We postulate that a cluster of genes with common short sequences in the promoter region can be recognized by a particular transcription factor. We also found that most of these short sequences are fairly common within miRNA (both mature and stem-loop sequences). Our studies indicate that eukaryotic transcription is more complex than currently believed.

Promoting developmental transcription

Animal growth and development depend on the precise control of gene expression at the level of transcription. A central role in the regulation of developmental transcription is attributed to transcription factors that bind DNA enhancer elements, which are often located far from gene transcription start sites. Here, we review recent studies that have uncovered significant regulatory functions in developmental transcription for the TFIID basal transcription factors and for the DNA core promoter elements that are located close to transcription start sites.

Identification of promoter regions and regulatory sites

Promoter sequences are the main regulatory elements of gene expression. Their recognition by computer algorithms is fundamental for understanding gene expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.

Transcriptional control of SET DOMAIN GROUP 8 and CAROTENOID ISOMERASE during Arabidopsis development

Carotenoids are pigments required for photosynthesis, photoprotection and the production of carotenoid-derived hormones such as ABA and strigolactones. The carotenoid biosynthetic pathway bifurcates after lycopene to produce epsilon- and beta-carotenoids and this branch is critical for determining carotenoid composition. Here, we show how the branch point can be regulated by the chromatin-modifying histone methyltransferase, Set Domain Group 8 (SDG8) targeting the carotenoid isomerase (CRTISO). SDG8 is required to maintain permissive expression of CRTISO during seedling development, in leaves, shoot apex, and some floral organs. The CRTISO and SDG8 promoters show overlapping tissue-specific patterns of reporter gene activity. Interestingly, CRTISO showed atypical reporter gene expression in terms of greater variability between different lines compared to the Cauliflower Mosaic Virus 35S promoter (CaMV35s) and epsilonLCY promoters, potentially due to chromosomal position effects. Regulation of the CRTISO promoter was dependent in part upon the presence or absence of SDG8. Knockouts of SDG8 (carotenoid and chloroplast regulation (ccr1)) and CRTISO (ccr2) result in altered carotenoid composition and this could be restored in ccr2 using the CaMV35s or CRTISO promoters. In contrast, varying degrees of GUS expression and carotenoid complementation by CRTISO overexpression using CaMV35S or CRTISO promoters in the ccr1 background demonstrated that both the CRTISO promoter and open reading frame are necessary for SDG8-mediated expression of CRTISO.

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.

Background

Transcription initiation is a key component in the regulation of gene expression. mRNA 5' full-length sequencing techniques have enhanced our understanding of mammalian transcription start sites (TSSs), revealing different initiation patterns on a genomic scale.

Results

To identify TSSs in Drosophila melanogaster, we applied a hierarchical clustering strategy on available 5' expressed sequence tags (ESTs) and identified a high quality set of 5,665 TSSs for approximately 4,000 genes. We distinguished two initiation patterns: 'peaked' TSSs, and 'broad' TSS cluster groups. Peaked promoters were found to contain location-specific sequence elements; conversely, broad promoters were associated with non-location-specific elements. In alignments across other Drosophila genomes, conservation levels of sequence elements exceeded 90% within the melanogaster subgroup, but dropped considerably for distal species. Elements in broad promoters had lower levels of conservation than those in peaked promoters. When characterizing the distributions of ESTs, 64% of TSSs showed distinct associations to one out of eight different spatiotemporal conditions. Available whole-genome tiling array time series data revealed different temporal patterns of embryonic activity across the majority of genes with distinct alternative promoters. Many genes with maternally inherited transcripts were found to have alternative promoters utilized later in development. Core promoters of maternally inherited transcripts showed differences in motif composition compared to zygotically active promoters.

Conclusions

Our study provides a comprehensive map of Drosophila TSSs and the conditions under which they are utilized. Distinct differences in motif associations with initiation pattern and spatiotemporal utilization illustrate the complex regulatory code of transcription initiation.

A transcription factor affinity-based code for mammalian transcription initiation

The recent arrival of large-scale cap analysis of gene expression (CAGE) data sets in mammals provides a wealth of quantitative information on coding and noncoding RNA polymerase II transcription start sites (TSS). Genome-wide CAGE studies reveal that a large fraction of TSS exhibit peaks where the vast majority of associated tags map to a particular location ( approximately 45%), whereas other active regions contain a broader distribution of initiation events. The presence of a strong single peak suggests that transcription at these locations may be mediated by position-specific sequence features. We therefore propose a new model for single-peaked TSS based solely on known transcription factors (TFs) and their respective regions of positional enrichment. This probabilistic model leads to near-perfect classification results in cross-validation (auROC = 0.98), and performance in genomic scans demonstrates that TSS prediction with both high accuracy and spatial resolution is achievable for a specific but large subgroup of mammalian promoters. The interpretable model structure suggests a DNA code in which canonical sequence features such as TATA-box, Initiator, and GC content do play a significant role, but many additional TFs show distinct spatial biases with respect to TSS location and are important contributors to the accurate prediction of single-peak transcription initiation sites. The model structure also reveals that CAGE tag clusters distal from annotated gene starts have distinct characteristics compared to those close to gene 5'-ends. Using this high-resolution single-peak model, we predict TSS for approximately 70% of mammalian microRNAs based on currently available data.

Using CorePromoter to find human core promoters

The CorePromoter program is very useful for identification of transcriptional start sites (TSS) and core promoter regions when 5'-upstream genomic DNA sequences of human genes are available. It is very simple to use and can be accessed either through the Web or after downloading to a local computer. The protocols in this unit introduce its basic methodology and discuss how to apply it to a sample problem in conjunction with other gene-finding programs.

Hepatocellular expression of glutamine synthetase: an indicator of morphogen actions as master regulators of zonation in adult liver

Glutamine synthetase (GS) has long been known to be expressed exclusively in pericentral hepatocytes most proximal to the central veins of liver lobuli. This enzyme as well as its peculiar distribution complementary to the periportal compartment for ureogenesis plays an important role in nitrogen metabolism, particularly in homeostasis of blood levels of ammonium ions and glutamine. Despite this fact and intensive studies in vivo and in vitro, many aspects of the regulation of its activity on the protein and on the genetic level remained enigmatic. Recent experimental advances using transgenic mice and new analytic tools have revealed the fundamental role of morphogens such as wingless-type MMTV integration site family member signals (Wnt), beta-catenin, and adenomatous polyposis coli in the regulation of this particular enzyme. In addition, novel information concerning the structure of transcription factor binding sites within regulatory regions of the GS gene and their interactions with signalling pathways could be collected. In this review we focus on all aspects of the regulation of GS in the liver and demonstrate how the new findings have changed our view of the determinants of liver zonation. What appeared as a simple response of hepatocytes to blood-derived factors and local cellular interactions must now be perceived as a fundamental mechanism of adult tissue patterning by morphogens that were considered mainly as regulators of developmental processes. Though GS may be the most obvious indicator of morphogen action among many other targets, elucidation of the complex regulation of the expression of the GS gene could pave the road for a better understanding of the mechanisms involved in patterning of liver parenchyma. Based on current knowledge we propose a new concept of how morphogens, hormones and other factors may act in concert, in order to restrict gene expression to small subpopulations of one differentiated cell type, the hepatocyte, in different anatomical locations. Although many details of this regulatory network are still missing, and an era of exciting new discoveries is still about to come, it can already be envisioned that similar mechanisms may well be active in other organs contributing to the fine-tuning of organ-specific functions.

Characterization of a new densovirus infecting the German cockroach, Blattella germanica

A new DNA virus (Parvoviridae: Densovirinae, Densovirus) was isolated and purified from descendants of field-collected German cockroaches, Blattella germanica. Viral DNA and cockroach tissues infected with B. germanica densovirus (BgDNV) were examined by electron microscopy. Virus particles, about 20 nm in diameter, were observed both in the nucleus and in the cytoplasm of infected cells. Virus DNA proved to be a linear molecule of about 1.2 microm in length. BgDNV isolated from infected cockroaches infected successfully and could be maintained in BGE-2, a B. germanica cell line. The complete BgDNV genome was sequenced and analysed. Five open reading frames (ORFs) were detected in the 5335 nt sequence: two ORFS that were on one DNA strand encoded structural capsid proteins (69.7 and 24.8 kDa) and three ORFs that were on the other strand encoded non-structural proteins (60.2, 30.3 and 25.9 kDa). Three putative promoters and polyadenylation signals were identified. Structural analysis of the inverted terminal repeats revealed the presence of extended palindromes. The genome structure of BgDNV was compared with that of other members of the family Parvoviridae; the predicted amino acid sequences were aligned and subjected to phylogenetic analyses.

A dicistronic gene pair within a cluster of "EF-hand" protein genes in the genomes of Drosophila species

Androcam is a Drosophila melanogaster calmodulin-related protein that functions specifically in the testis. We show that the Acam gene is part of a cluster of three intronless genes arranged in a head-to-tail manner. The additional genes also encode calmodulin-related proteins with testis-specific transcription. Acam and the 5'-most gene (gene1) generate monocistronic transcripts. Surprisingly, the central gene (gene2) is transcribed only as a dicistronic transcript with Acam. A similar cluster is found in D. yakuba. In D. pseudoobscura, the cluster contains four genes: two Acam-type genes downstream of a single gene related to both gene1 and gene2 and a fourth weakly related gene. Nevertheless, the D. pseudoobscura cluster also generates a dicistronic transcript from a gene pair analogous to the gene2-Acam pair. A cotranscribed gene1/2-Acam gene pair may be the founding feature of this locus. Although Acam protein is present in D. melanogaster and D. pseudoobscura testes, cognate proteins for the gene1/2-type ORFs are not detectable by immunoblotting and mass spectrometry techniques.

EPD in its twentieth year: towards complete promoter coverage of selected model organisms

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mapping experiments for individual genes, or, starting from release 73, from mass genome annotation projects. Subsets of promoter sequences with customized 5′ and 3′ extensions can be downloaded from the EPD website. The focus of current development efforts is to reach complete promoter coverage for important model organisms as soon as possible. To speed up this process, a new class of preliminary promoter entries has been introduced as of release 83, which requires less stringent admission criteria. As part of a continuous integration process, new web-based interfaces have been developed, which allow joint analysis of promoter sequences with other bioinformatics resources developed by our group, in particular programs offered by the Signal Search Analysis Server, and gene expression data stored in the CleanEx database. EPD can be accessed at .

Characterization of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta

We report the cloning and characterization in tobacco and Arabidopsis of a Vigna radiata L. (mung bean) promoter that controls the expression of VR-ACS1, an auxin-inducible ACC synthase gene. The VR-ACS1 promoter exhibits a very unusual behavior when studied in plants different from its original host, mung bean. GUS and luciferase in situ assays of transgenic plants containing VR-ACS1 promoter fusions show strong constitutive reporter gene expression throughout tobacco and Arabidopsis development. In vitro quantitative analyses show that transgenic plants harboring VR-ACS1 promoter-reporter constructs have on average 4-6 fold higher protein and activity levels of both reporter genes than plants transformed with comparable CaMV 35S promoter fusions. Similar transcript levels are present in VR-ACS1 and CaMV 35S promoter lines, suggesting that the high levels of gene product observed for the VR-ACS1 promoter are the combined result of transcriptional and translational activation. All tested deletion constructs retaining the core promoter region can drive strong constitutive promoter activity in transgenic plants. This is in contrast to mung bean, where expression of the native VR-ACS1 gene is almost undetectable in plants grown under normal conditions, but is rapidly and highly induced by a variety of stimuli. The constitutive behavior of the VR-ACS1 promoter in heterologous hosts is surprising, suggesting that the control mechanisms active in mung bean are impaired in tobacco and Arabidopsis. The 'aberrant' behavior of the VR-ACS1 promoter is further emphasized by its failure to respond to auxin and cycloheximide in heterologous hosts. VR-ACS1 promoter regulatory mechanisms seem to be different from all previously characterized auxin-inducible promoters.

Databases, models, and algorithms for functional genomics: a bioinformatics perspective

A variety of patterns have been observed on the DNA and protein sequences that serve as control points for gene expression and cellular functions. Owing to the vital role of such patterns discovered on biological sequences, they are generally cataloged and maintained within internationally shared databases. Furthermore,the variability in a family of observed patterns is often represented using computational models in order to facilitate their search within an uncharacterized biological sequence. As the biological data is comprised of a mosaic of sequence-levels motifs, it is significant to unravel the synergies of macromolecular coordination utilized in cell-specific differential synthesis of proteins. This article provides an overview of the various pattern representation methodologies and the surveys the pattern databases available for use to the molecular biologists. Our aim is to describe the principles behind the computational modeling and analysis techniques utilized in bioinformatics research, with the objective of providing insight necessary to better understand and effectively utilize the available databases and analysis tools. We also provide a detailed review of DNA sequence level patterns responsible for structural conformations within the Scaffold or Matrix Attachment Regions (S/MARs).

Osteo-Promoter Database (OPD) -- promoter analysis in skeletal cells

Background

Increasing our knowledge about the complex expression of genes in skeletal tissue will provide a better understanding of the physiology of skeletal cells. The study summarizes transcriptional regulation factors interacting and cooperating at promoter regions that regulate gene expression. Specifically, we analyzed A/T rich elements along the promoter sequences.

Description

The Osteo-Promoter Database (OPD) is a collection of genes and promoters expressed in skeletal cells. We have compiled a new viewer, OPD, as unique database developed and created as an accessible tool for skeletal promoter sequences. OPD can navigate to identify genes specific to skeletal cDNA databases and promoter analysis sites. OPD offers exclusive access to facilitate a dynamic extraction of promoters' gene-specific analyses in skeletal tissue. The data on promoters included in OPD contains cloned promoters or predicted promoters that were analyzed by bioinformatics tools. OPD offers MAR-analysis, which allocates A/T rich elements along these promoter sequences.

Conclusion

The analysis leads to a better insight of proteins that bind to DNA, regulate DNA, and function in chromatin remodeling. The OPD is a distinctive tool for understanding the complex function of chromatin remodeling and transcriptional regulation of specific gene expression in skeletal tissue.

Specific TATAA and bZIP requirements suggest that HTLV-I Tax has transcriptional activity subsequent to the assembly of an initiation complex

Background

Human T-cell leukemia virus type I (HTLV-I) Tax protein is a transcriptional regulator of viral and cellular genes. In this study we have examined in detail the determinants for Tax-mediated transcriptional activation.

Results

Whereas previously the LTR enhancer elements were thought to be the sole Tax-targets, herein, we find that the core HTLV-I TATAA motif also provides specific responsiveness not seen with either the SV40 or the E1b TATAA boxes. When enhancer elements which can mediate Tax-responsiveness were compared, the authentic HTLV-I 21-bp repeats were found to be the most effective. Related bZIP factors such as CREB, ATF4, c-Jun and LZIP are often thought to recognize the 21-bp repeats equivalently. However, amongst bZIP factors, we found that CREB, by far, is preferred by Tax for activation. When LTR transcription was reconstituted by substituting either κB or serum response elements in place of the 21-bp repeats, Tax activated these surrogate motifs using surfaces which are different from that utilized for CREB interaction. Finally, we employed artificial recruitment of TATA-binding protein to the HTLV-I promoter in "bypass" experiments to show for the first time that Tax has transcriptional activity subsequent to the assembly of an initiation complex at the promoter.

Conclusions

Optimal activation of the HTLV-I LTR by Tax specifically requires the core HTLV-I TATAA promoter, CREB and the 21-bp repeats. In addition, we also provide the first evidence for transcriptional activity of Tax after the recruitment of TATA-binding protein to the promoter.

Polymorphic NF-Y dependent regulation of human nicotine C-oxidase (CYP2A6)

OBJECTIVES

In humans, cytochrome P450 2A6 (CYP2A6) constitutes the principal nicotine C-oxidase. Several different polymorphic CYP2A6 gene variants are known which contribute to the highly variable expression of this enzyme among individuals. In this study we report a novel polymorphism located in the 5' flanking region (-745A > G) of the CYP2A6 gene disrupting a CCAAT box.

METHODS AND RESULTS

Electrophoretic mobility shift assays (EMSA) indicated that NF-YA is part of this nuclear protein complex. Chromatin immunoprecipitation revealed that NF-Y recognizes a region of the CYP2A6 5' flanking region located between -932 and -606. EMSA showed that out of the three CCAAT boxes in the CYP2A6 promoter, with CCAAT core sequences located between -839/-835, -748/-744, and -689/-685, only the one at -748/-744 was able to compete with the nuclear protein complex binding to the -748/-744 CCAAT box. Cotransfection experiments indicated that NF-Y acts as a positive regulatory element on CYP2A6 gene regulation. EMSA demonstrated that an NF-Y consensus oligonucleotide but not the -745A > G oligonucleotide competed efficiently with binding of the protein complex to the -748/-744 CCAAT box. Promoter activity of the -745A > G variant was significantly reduced to 78% relative to the wild-type allele in HepG2 cells transfected with luciferase reporter plasmids. Finally, haplotype analysis was carried out comprising the -745A > G variant in combination with all known CYP2A6 3' and 5' flanking single nucleotide polymorphisms: -1013A > G, -48T > G, and the CYP2A6/CYP2A7 3' flank conversion.

CONCLUSION

A new haplotype, CYP2A6*1H was identified, with allele frequencies of 3.1% in Swedish and 5.2% in Turkish populations.

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.

Signal search analysis server

Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large number of precompiled functional site collections. The programs offered allow: (i) the identification of non-random sequence regions under evolutionary constraint; (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site; (iii) the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site; and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif. These programs can be accessed at: http://www.isrec.isb-sib.ch/ssa/.

Expression pattern and biochemical characteristics of a major epidermal retinol dehydrogenase

The biological functions of vitamin A in the epidermis are mediated by all-trans retinoic acid, which is biosynthesized from retinol in two oxidative reactions. The first step involves enzymatic conversion of retinol to retinaldehyde. The physiological significance and relative contributions of the various retinol dehydrogenases to the oxidation of retinol in epidermal cells remain unclear. We report the characterization of a retinol dehydrogenase/reductase of the SDR superfamily, hRoDH-E2, which is abundantly expressed in the epidermis, epidermal appendages and in cultured epidermal keratinocytes. Both in live keratinocytes and in isolated keratinocyte microsomes, where the enzyme normally localizes, hRoDH-E2 functions as a bona fide retinol dehydrogenase. In the prevailing oxidative reaction it recognizes both free- and CRBP-bound retinol, and shows preference toward NADP as a co-substrate. In comparison, hRoDH-E2 retinol dehydrogenase activity in the simple epithelial HEK 293 cells is much lower and in CHO cells is non-existent. hRoDH-E2 transcripts are distributed throughout the epidermal layers but are more abundant in the basal cells. In contrast, the protein is detected predominantly in the basal and the most differentiated living layers. Its synthesis is negatively regulated by retinoic acid. The biochemical properties and the differential expression of hRoDH-E2 in the strata where retinoic acid signaling is critical for epidermal homeostasis support a conclusion that hRoDH-E2 bears the characteristics of the major microsomal retinol dehydrogenase activity in the epidermal keratinocytes in physiological circumstances.

Ribosomal protein S19 expression during erythroid differentiation

The gene encoding ribosomal protein S19 (RPS19) has been shown to be mutated in 25% of the patients affected by Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia. As the role of RPS19 in erythropoiesis is still to be defined, we performed studies on RPS19 expression during terminal erythroid differentiation. Comparative analysis of the genomic sequences of human and mouse RPS19 genes enabled the identification of 4 conserved sequence elements in the 5' region. Characterization of transcriptional elements allowed the identification of the promoter in the human RPS19 gene and the localization of a strong regulatory element in the third conserved sequence element. By Northern blot and Western blot analyses of murine splenic erythroblasts infected with the anemia-inducing strain Friend virus (FAV cells), RPS19 mRNA and protein expression were shown to decrease during terminal erythroid differentiation. We anticipate that these findings will contribute to further development of our understanding of the contribution of RPS19 to erythropoiesis.

Characterization of the human gene encoding the scavenger receptor expressed by endothelial cell and its regulation by a novel transcription factor, endothelial zinc finger protein-2

The scavenger receptor expressed by endothelial cell (SREC), mediates the selective uptake of modified low density lipoprotein (LDL), such as acetylated LDL and oxidized LDL, into endothelial cells. The SREC gene spans 12 kilobase pairs and contains 11 exons. Analysis of full-length cDNA clones of SREC from a peripheral blood leukocyte cDNA library revealed that at least five alternatively spliced cDNAs were present, and two of them encoded soluble forms of SREC. The transcription start site of the SREC gene was mapped, and DNA sequence analysis revealed an Sp1 binding site in its proximal region. Deletion analysis of the 5'-flanking sequence revealed that sequence between base pairs -108 and -98 was critical for the promoter activity. This region contained half of an inverted repeat (IR) sequence with a triple nucleotide spacer (IR-3). A protected sequence between base pairs -268 and +17 was defined by in vitro DNase I footprinting analysis using human umbilical vein endothelial cell (HUVEC) nuclear extract. A novel transcription factor, endothelial zinc finger protein-2 (EZF-2), that binds to the 5'-flanking critical region of the SREC promoter activity was cloned from a HUVEC cDNA library employing a one-hybrid system. Whereas purified recombinant Sp1 alone produced similar protection in in vitro DNase I footprinting analysis, EZF-2 also bound to the 5'-flanking region SREC promoter. Co-transfection of SREC promoter and Sp1 or EZF-2 expression plasmids in HUVEC revealed that EZF-2 but not Sp1 increased SREC promoter activity. On the other hand, the mutation of either the Sp1 motif or IR-3 motif resulted in a decrease in the promoter activity. These results suggest that whereas Sp1 is the major nuclear protein bound to the regulatory region of the promoter, both EZF-2 and Sp1 are responsible for its regulation.

Murine H-rev107 gene encoding a class II tumor suppressor: gene organization and identification of an Sp1/Sp3-binding GC-box required for its transcription

H-rev107, which belongs to class II tumor suppressor genes, is ubiquitously expressed in normal cells, but is downregulated in many carcinomas and tumor cell lines. Sequence analysis showed that the murine H-rev107 gene is composed of five exons and four introns. Transfections revealed that 7.6 kb of the H-rev107 promoter directed a high level expression of the reporter gene. There were no significant differences in promoter activity when various 5'-deletion promoter constructs from -7.6 kb to -113 bp were employed. By further deletion and mutation analysis, we found that the region between -83 and -75 containing a GC-box was essential for promoter activity in NIH3T3 or REF52 fibroblasts expressing H-rev107 at moderate to high levels. Gelshifts demonstrated in vitro binding of Sp1 and Sp3 to this GC-box. Cotransfection of Sp1 and Sp3 functionally stimulated promoter activity in SL2 cells. By chromatin immunoprecipitation assays, we observed in vivo binding of Sp1 and Sp3 to the proximal promoter region in NIH3T3 cells and liver, concluding that the transcription of the H-rev107 gene is dependent on Sp1/Sp3-binding to the -83/-75 GC-box.

Characterization of the mouse aortic carboxypeptidase-like protein promoter reveals activity in differentiated and dedifferentiated vascular smooth muscle cells

The dedifferentiation and proliferation of vascular smooth muscle cells (VSMCs) contribute to the formation of vascular lesions. In this study, the regulation of aortic carboxypeptidase-like protein (ACLP) expression in VSMCs was investigated. After mouse carotid injury, the expression of ACLP increases in the dedifferentiated VSMCs of the neointima in a pattern that differs from that of smooth muscle alpha-actin. To better understand the regulation of ACLP in VSMCs, we characterized the 21-exon mouse ACLP gene and 5'-flanking region and examined its promoter activity. In transient transfection assays, 2.5 kb of the ACLP 5'-flanking sequence directed high levels of luciferase reporter activity in primary cultured rat aortic smooth muscle cells, and this activity was not dependent on serum response factor. We identified a positive element between base pairs -156 and -122 by analysis of 5' deletion and mutant constructs. By use of electrophoretic mobility shift assays with rat aortic smooth muscle cell nuclear extracts, Sp1 and Sp3 transcription factors bound to this region, and transfection assays in D.Mel.2 cells revealed that both Sp1 and Sp3 transactivated the ACLP promoter. Transgenic mice harboring the -2.5-kb ACLP promoter upstream from a nuclear-targeted LacZ gene were generated, and expression was detected in the VSMCs of large blood vessels, arterioles, and veins. Interestingly, ACLP promoter-LacZ reporter activity increased within the neointimal VSMCs of injured carotid vessels, consistent with the expression of the endogenous ACLP protein. The ACLP promoter may provide a novel tool to target gene expression to dedifferentiated VSMCs.

ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences

We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA-protein or DNA-ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented.

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data

The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. World Wide Web-based interfaces have been developed which enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch.

Aedes aegypti glutamine synthetase: expression and gene structure

The peritrophic matrix (PM) is the first natural barrier a mosquito-borne parasite faces when ingested with a blood meal; consequently, understanding the biology of PM formation could provide novel transmission control strategies. Because the PM is composed of chitin (a molecule of repeating units of N-acetyl glucosamine), glycoproteins and glucose, characterizing the regulation of enzymes involved in chitin production should provide information concerning factors that influence PM formation. We previously have shown that glutamine synthetase (GS) provides the glutamine needed in the initial steps of chitin biosynthesis in the yellow fever mosquito, Aedes aegypti. In the present study we show that GS is encoded by a single 4.5 kb gene, designated mGS, containing three exons and two introns. Multiple transcripts are generated from mGS presumably by differential splicing of the introns. Sequences of two cDNAs encoding GS are identical at the protein level, but differ in their 5'-untranslated regions. GS message is constitutively expressed in all developmental stages and in most tissues, with an increase in GS transcription observed in midgut and fat body tissues of female mosquitoes following a blood meal. Transcripts are localized to the apical side of the mosquito midgut epithelium and data suggest that mGS transcription is regulated by an Oct-1 transcription factor.

The human Na(+)/H(+) exchanger NHE2 gene: genomic organization and promoter characterization

The Na(+)/H(+) exchanger (NHE) 2 belongs to a family of plasma membrane transporters involved in intracellular pH and cell volume regulation. We recently reported cloning of human NHE2 (hNHE2) from a colonic cDNA library. Northern blot analysis has identified NHE2 mRNA only in small intestine, prostate, kidney, colon, and skeletal muscle. In this study, we describe the structure and 5'-regulatory region of the hNHE2 gene. The hNHE2 gene spans >90 kb and is organized in 12 exons intervened by 11 introns. All introns contain the conserved GT and AG dinucleotides at the donor and acceptor sites, respectively. The hNHE2 gene was mapped to chromosome 2q11.2. Primer extension analysis revealed a single transcription initiation site in human colonic adenocarcinoma cell lines. Analysis of the DNA nucleotide sequences of a 1.4-kb fragment of the 5'-flanking region shows no canonical TATA or CAAT boxes. However, the promoter region contains several potential cis-regulatory elements such as Sp1, early growth response-1, activator protein-2, MyoD, p300, nuclear factor-kappaB, myeloid zinc finger protein-1, caudal-related homeobox (Cdx) gene A, and Cdx protein-2 binding sites. In transient transfection studies, a reporter construct containing the 1.4-kb promoter region exhibited low luciferase activity levels. However, after deletion upstream of -664, its activity increased approximately threefold. Thus our data suggest that an inhibitory element may exist in the NHE2 promoter 5'-upstream region.

Genomic characterization, localization, and functional expression of FGL2, the human gene encoding fibroleukin: a novel human procoagulant

For diseases in which thrombosis plays a pivotal role, such as virus-induced fulminant hepatitis, fetal loss syndrome, and xenograft rejection, the major procoagulant has remained elusive. Here we describe the isolation and functional expression of a distinct human prothrombinase, termed FGL2. The murine fgl2 gene product has been implicated in the pathophysiology of murine fulminant hepatitis. The predicted ORF corresponds to a 439-amino-acid type II integral membrane protein that contains a carboxy-terminal Fibrinogen-related domain. Functional analysis showed that FGL2-encoded protein is indeed a prothrombinase. This enzyme is a serine protease and directly cleaves prothrombin to thrombin. The FGL2 gene is a single-copy gene in the haploid human genome and has two exons separated by a 2195-bp intron expressing two mRNA transcripts of 1.5 and 5.0 kb. The 5'-flanking region contains putative cis-elements including a TATA box, an AP1 site, CEBP sites, Sp1 site, and Ets binding domains. By both radiation hybrid analyses and fluorescence in situ hybridization, human FGL2 was localized to 7q11.23.

Transcription organization and mRNA levels of the genes for all 12 subunits of the fission yeast RNA polymerase II

The RNA polymerase II (Pol II) of eukaryotes is composed of 12 subunits, of which five are shared among Pol I, Pol II and Pol III. At present, however, little is known about the regulation of synthesis and assembly of the 12 Pol II subunits. To obtain an insight into the regulation of synthesis of these 12 Pol II subunits, Rpb1 to Rpb12, in the fission yeast Schizosaccharomyces pombe, we analysed the transcriptional organization of the rpb genes by use of the oligo capping method, and determined mRNA levels by quantitative competitive PCR assay. The intracellular concentrations of the 12 Rpb subunits in growing S. pombe cells are different, within a range of 15-fold difference between the least abundant Rpb3 and the most abundant Rpb12. The transcription of one group of genes including rpb3, rpb4, rpb5, rpb6, rpb7 and rpb10 is mainly initiated at a single site, while that of the other group of genes for rpb1, rpb2, rpb8, rpb9, rpb11 and rpb12 is initiated at multiple sites. The promoters of the first group of genes contain the TATA box sequence between -26 and -62, while the second group of genes carry TATA-less promoters. Several common sequence segments, tentatively designated 'Rpb motifs', were identified in the promoter regions of the rpb genes. Competitive PCR analysis indicated that mRNAs for Rpb1, Rpb3, Rpb7 and Rpb9 were among the group which had a low abundance, while the levels of Rpb6 and Rpb10 mRNAs were about fivefold, and that of Rpb2 mRNA was about 40-fold higher than the Rpb3 mRNA level. The levels of rpb mRNAs do not correlate with those of Rpb proteins. The protein-to-mRNA ratio or the translation efficiency is low for the rpb1, rpb2, rpb3 and rpb11 genes, encoding the homologues of subunits beta', beta, alpha and alpha, respectively, of the prokaryotic RNA polymerase core enzyme.

Saccharomyces cerevisiae GATA sequences function as TATA elements during nitrogen catabolite repression and when Gln3p is excluded from the nucleus by overproduction of Ure2p

Saccharomyces cerevisiae selectively uses good nitrogen sources (glutamine) in preference to poor ones (proline) by repressing GATA factor-dependent transcription of the genes needed to transport and catabolize poor nitrogen sources, a physiological process designated nitrogen catabolite repression (NCR). We show that some NCR-sensitive genes (CAN1, DAL5, DUR1,2, and DUR3) produce two transcripts of slightly different sizes. Synthesis of the shorter transcript is NCR-sensitive and that of the longer transcript is not. The longer transcript also predominates in gln3Delta mutants irrespective of the nitrogen source provided. We demonstrate that the longer mRNA species arises through the use of an alternative transcription start site generated by Gln3p-binding sites (GATAAs) being able to act as surrogate TATA elements. The ability of GATAAs to serve as surrogate TATAs, i.e. when synthesis of the shorter, NCR-sensitive transcripts are inhibited, correlates with sequestration of enhanced green fluorescent protein (EGFP)-Gln3p in the cytoplasm in a way that is indistinguishable from that seen with EGFP-Ure2p. However, when the shorter, NCR-sensitive DAL5 transcript predominates, EGFP-Gln3p is nuclear. These data suggest that the mechanism underlying NCR involves the cytoplasmic association of Ure2p with Gln3p, an interaction that prevents Gln3p from reaching it is binding sites upstream of NCR-sensitive genes.

Complex interactions between epidermal POU domain and activator protein 1 transcription factors regulate the expression of the profilaggrin gene in normal human epidermal keratinocytes

The human profilaggrin gene is expressed in the granular layer during the late stages of the epidermal differentiation. The proximal promoter region of the gene confers high levels of keratinocyte-specific transcription via interactions with c-Jun/c-Fos heterodimers. Here we provide evidence for another level of complexity in the regulation of the profilaggrin promoter activity. The POU domain proteins Oct1, Skn1a/i, and Oct6, which are abundantly expressed in the epidermal cells, act to both stimulate and repress transcription in a general and a cell type-specific mode. While binding to specific recognition elements within the promoter region, they exert their effects by either stimulating or antagonizing the c-Jun-dependent activity of the promoter. The response of the promoter to forced expression of the POU domain proteins reflects the effect of these transcription factors on the endogenous profilaggrin mRNA synthesis and suggests that the latter requires a fine balance in the amounts and the activities of the individual activator protein 1 and POU domain proteins.

Regulation of DHP receptor expression by elements in the 5'-flanking sequence

The alpha(1)-subunit of the cardiac/vascular Ca(2+) channel, which is the dihydropyridine (DHP)-binding site (the DHP receptor), provides the pore structure for Ca(2+) entry. It contains the binding sites for multiple classes of drugs collectively known as Ca(2+) antagonists. As an initial step toward understanding the mechanisms controlling transcription of the rat cardiac alpha(1C)-subunit gene, we have cloned a 2.3-kb fragment containing the 5'-flanking sequences and identified the alpha(1C)-subunit gene transcription start site. The rat alpha(1C)-subunit gene promoter belongs to the TATA-less class of such basal elements. Using deletion analysis of alpha(1C)-subunit promoter-luciferase reporter gene constructs, we have characterized the transcriptional modulating activity of the 5'-flanking region and conducted transient transfections in cultured neonatal rat cardiac ventricular myocytes and vascular smooth muscle cells. Sequence scanning identified several potential regulatory elements, including five consensus sequences for the cardiac-specific transcription factor Nkx2.5, an AP-1 site, a cAMP response element, and a hormone response element. Transient transfection experiments with the promoter-luciferase reporter fusion gene demonstrate that the 2-kb 5'-flanking region confers tissue specificity and hormone responsiveness to expression of the Ca(2+) channel alpha(1C)-subunit gene. Electrophoretic mobility shift assays identified a region of the alpha(1C)-subunit gene promoter that can bind transcription factors and appears to be important for gene expression.

Development of an effective polyvalent vaccine against both Marek's and Newcastle diseases based on recombinant Marek's disease virus type 1 in commercial chickens with maternal antibodies

An earlier report (M. Sakaguchi et al., Vaccine 16:472-479, 1998) showed that recombinant Marek's disease virus type 1 (rMDV1) expressing the fusion (F) protein of Newcastle disease virus (NDV-F) under the control of the simian virus 40 late promoter [rMDV1-US10L(F)] protected specific pathogen-free chickens from NDV challenge, but not commercial chickens with maternal antibodies against NDV and MDV1. In the present study, we constructed an improved polyvalent vaccine based on MDV1 against MDV and NDV in commercial chickens with maternal antibodies. The study can be summarized as follows. (i) We constructed rMDV1 expressing NDV-F under the control of the MDV1 glycoprotein B (gB) promoter [rMDV1-US10P(F)]. (ii) Much less NDV-F protein was expressed in cells infected with rMDV1-US10P(F) than in those infected with rMDV1-US10L(F). (iii) The antibody response against NDV-F and MDV1 antigens of commercial chickens vaccinated with rMDV1-US10P(F) was much stronger and faster than with rMDV1-US10L(F), and a high level of antibody against NDV-F persisted for over 80 weeks postvaccination. (iv) rMDV1-US10P(F) was readily reisolated from the vaccinated chickens, and the recovered viruses were found to express NDV-F. (v) Vaccination of commercial chickens having maternal antibodies to rMDV1-US10P(F) completely protected them from NDV challenge. (vi) rMDV1-US10P(F) offered the same degree of protection against very virulent MDV1 as the parental MDV1 and commercial vaccines. These results indicate that rMDV1-US10P(F) is an effective and stable polyvalent vaccine against both Marek's and Newcastle diseases even in the presence of maternal antibodies.

The eukaryotic promoter database (EPD)

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch

Analysis of the promoter of the MUC1 gene overexpressed in breast cancer

The MUC1 gene encodes a mucin glycoprotein and is overexpressed in breast cancer. Knowledge of the mechanisms leading to MUC1 overexpression may help in the development of molecular approaches for breast cancer therapy. In order to study the regulation of the MUC1 gene transcription, we analyzed functional activities of various deletion mutants of the MUC1 promoter. We established that transcriptional cis-elements present in the SacI/XmnI fragment of the promoter are competent and sufficient for expression of, at least, tandem repeats containing isoform(s) of the MUC1 protein. CAT transfection analysis showed that both the 3' and 5' regions of the SacI/XmnI fragment possess transcription activities. Promoter activities associated with the SacI/XmnI fragment were confirmed by a RNase protection assay, which demonstrated multiple transcription start sites (TSSs) in the MUC1 gene transcribed in epithelial T47D cells. We show that treatment of the T47D cells with TGFbeta1 leads to activation of additional TSSs in the MUC1 gene. The roles of the structural and functional properties of the MUC1 promoter in MUC1 gene transcription are discussed.

Once-weekly resistance exercise improves muscle strength and neuromuscular performance in older adults

OBJECTIVE

To determine the effect of frequency of resistive training on gain in muscle strength and neuromuscular performance in healthy older adults.

DESIGN

A randomized controlled trial with subjects assigned either to high-intensity resistance training 1 (EX1), 2 (EX2), or 3 (EX3) days per week for 24 weeks or to a control group (CO).

SETTING

An exercise facility at an academic medical center.

SUBJECTS

Forty-six community-dwelling healthy men (n = 29) and women (n = 17) aged 65 to 79 years.

INTERVENTION

Progressive resistance training consisting of three sets of eight exercises targeting major muscle groups of the upper and lower body, at 80% of one-repetition maximum (1-RM) for eight repetitions, either 1, 2, or 3 days per week.

MEASURES

Dynamic muscle strength (1-RM) using isotonic equipment every 4 weeks, bone mineral density and body composition by dual energy X-ray absorptiometry (DXA), and neuromuscular performance by timed chair rise and 6-meter backward tandem walk.

RESULTS

For each of the eight exercises, muscle strength increased in the exercise groups relative to CO (P < .01), with no difference among EX1, EX2 and EX3 groups at any measurement interval. Percent change averaged 3.9 +/- 2.4 (CO), 37.0 +/- 15.2 (EX1), 41.9 +/- 18.2 (EX2), and 39.7 +/- 9.8 (EX3). The time to rise successfully from the chair 5 times decreased significantly (P < .01) at 24 weeks, whereas improvement in the 6-meter backward tandem walk approached significance (P = .10) in the three exercise groups compared with CO. Changes in chair rise ability were correlated to percent changes in quadriceps strength (r = -0.40, P < .01) and lean mass (r = -0.40, P < .01).

CONCLUSIONS

A program of once or twice weekly resistance exercise achieves muscle strength gains similar to 3 days per week training in older adults and is associated with improved neuromuscular performance. Such improvement could potentially reduce the risk of falls and fracture in older adults.

Genomic cloning and promoter analysis of aortic preferentially expressed gene-1. Identification of a vascular smooth muscle-specific promoter mediated by an E box motif

Aortic preferentially expressed gene-1 (APEG-1) was originally identified as a 1.4-kilobase (kb) transcript preferentially expressed in differentiated vascular smooth muscle cells (VSMC). Its expression is markedly down-regulated in de-differentiated VSMC, suggesting a role for APEG-1 in VSMC differentiation. We have now determined that APEG-1 is a single-copy gene in the human, rat, and mouse genomes and have mapped human APEG-1 to chromosome 2q34. To study the molecular mechanisms regulating its expression, we characterized the genomic organization and promoter of mouse APEG-1. APEG-1 spans 4.5 kb in the mouse genome and is composed of five exons. Using reporter gene transfection analysis, we found that a 2. 7-kb APEG-1 5'-flanking sequence directed a high level of promoter activity only in VSMC. Its activity was minimal in five other cell types. A repressor region located within an upstream 685-base pair sequence suppressed the activity of this 2.7-kb promoter. Further deletion and mutation analyses identified an E box motif as a positive regulatory element, which was bound by nuclear protein prepared from VSMC. In conjunction with its flanking sequence, this E box motif confers VSMC-specific enhancer activity to a heterologous SV40 promoter. To our knowledge, this is the first demonstration of an E box motif that mediates gene expression restricted to VSMC.

Cloning and characterization of retinol dehydrogenase transcripts expressed in human epidermal keratinocytes

The normal growth and differentiation of the epidermis require an adequate supply of vitamin A. The active form of vitamin A for normal epidermal homeostasis is retinoic acid (RA). Retinoic acid controls the expression of retinoid-responsive genes via interactions of the retinoic acid/nuclear receptor complexes at specific DNA sequences in their control regions. The message conveyed by RA is likely modulated by the concentration of the ligand available for binding to the receptors. Following the uptake of plasma retinol, epidermal keratinocytes synthesize retinoic acid via two sequential reactions with retinaldehyde as an intermediate. Several retinol dehydrogenase (RDH) enzymes, members of the short-chain dehydrogenase/reductase (SDR) gene superfamily, catalyze the first and rate-limiting step that generates retinaldehyde from retinol bound to cellular retinol-binding protein (holo-CRBP). However, little is known about these enzymes and their genes in the epidermal cells. Our work describes the first member of the RDH family found in epidermis. We show that this gene is expressed predominantly in the differentiating spinous layers and that it is under positive, feed-forward regulation by retinoic acid. It encodes a protein that, using NAD+ as a preferred cofactor, utilizes free and CRBP-bound all-trans-retinol and steroids as substrates.

Structure and promoter region of the surface membrane protein HS9 gene expressed on the thymic epithelial cells

The HS9 gene encoding a surface membrane protein is expressed in thymic epithelial cells. We have isolated the mouse HS9 gene and determined the sequence of all exons. The mouse HS9 gene is composed of 14 exons spanning approx. 31 kb. Primer extension analysis identified two transcription initiation sites 33 bp and 179 bp upstream from the ATG start codon. DNA sequence analysis of the 5'-flanking region of the first exon revealed a number of consensus binding sites for known transcription factors such as GC box, Sp1, NFkappaB, gamma-IRE. Neither typical TATA nor CCAAT boxes were found in this region. These results and the analysis of the luciferase activity showed that transcription of the HS9 gene is regulated at a TATA-less promoter.

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure

Nucleosomes regulate transcriptional initiation when positioned in the promoter area. This may require the transcription factor (TF) sites to be correlated with the nucleosome positions and phased on the nucleosome surface. If this is the case, one would expect a periodical distribution of TF sites in the vicinity of promoters, with the nucleosomal period of 10.1-10.5 bp. We examined the distributions of putative binding sites of 323 different TFs along 1, 057 sequences of the Eukaryotic Promoter Database (release 50) [Cavin Perier, R., Junier, T. & Bucher, P. (1998) Nucleic Acids Res. 26, 353-357] and of 218 TFs on 673 sequences of the Lead Exon Database of human promoter sequences. We obtained a statistically significant overrepresentation of TF sites distributed with the main period of 10.1-10.5 bp in the region -50 to +120 around the transcription start site and in few locations nearby. Correlation of the positioning of the TF sites with the nucleosomes is further reinforced by sequence-directed mapping of the nucleosomes, a method previously developed.

Cloning and characterization of three genes (SUT1-3) encoding glucose transporters of the yeast Pichia stipitis

We have identified and characterized three genes, SUT1, SUT2 and SUT3, that encode glucose transporters of the yeast Pichia stipitis. When expressed in a Saccharomyces cerevisiae hxt null mutant strain that is unable to take up monosaccharides, all three proteins restored growth on glucose. Sequencing of the genes revealed open reading frames coding for 553 amino acids in the case of SUT1, and for 550 amino acids in the case of SUT2 and of SUT3. The derived protein sequences are closely related to one another, and show distinct sequence similarities to the S. cerevisiae hexose transporter family and to monosaccharide transporters of other organisms. The Sut2 and Sut3 proteins are nearly identical and differ only in one amino acid. Determination of substrate specificities and kinetic parameters of the individual Sut proteins expressed in a S. cerevisiae hxt1-7 mutant revealed Sut1, Sut2 and Sut3 as glucose transporters with K(m) values in the millimolar range. The proteins were also able to transport xylose and other monosaccharides, but with a considerably lower affinity. In P. stipitis, transcription of SUT1 was strongly induced by glucose and was independent of the oxygen supply. In contrast, SUT2 and SUT3 were only expressed under aerobic conditions, but independent of the carbon source. Cells disrupted for the SUT1 gene did not show any obvious growth phenotype, however low-affinity glucose uptake was lost. Further investigations suggest that the Sut proteins constitute a subfamily of glucose transporters in P. stipitis, and that other and probably unrelated proteins exist additionally mediating high-affinity glucose and xylose uptake.

Effect of glucocorticoids on the mouse methionine adenosyltransferase A1 gene expression, which is regulated by two promoters

The methionine adenosyltransferase A1 (MATA1) gene encodes the hepatic forms of the enzyme MAT I and III. To determine the molecular mechanisms that regulate MATA1 gene expression, we characterized promoters and the 5'-flanking sequence of MATA1. Transient expression assays demonstrated the presence of two promoters for the MATA1 gene. The p1 promoter is contained in the -57 to -2 nucleotide region, and gives rise to the P1 transcript initiated at +1. The p2 promoter is contained in the -248 to -146 nucleotide region. The -229 to -213 nucleotide region of the MATA1 gene, which contains an Ets-binding-site sequence, was necessary for p2 promoter activity. Sequence analysis of 5'-RACE products indicated that there was a transcript (P2) initiated at -156. The -107 to +145 nucleotide region is missing from the mature P2 transcript, which suggests that the -107 to +145 nucleotide sequence is an intron of the P2 transcript. The p2 promoter may give rise to the P2 transcript. The p1 promoter activity was increased by glucocorticoids, but the p2 promoter activity was not affected by glucocorticoids.