The bidirectional promoter of the divergently transcribed mouse Surf-1 and Surf-2 genes

Tissue-specific processing of the Surf-5 and Surf-4 mRNAs

The mouse surfeit locus is an unusually tight cluster of at least six "housekeeping" genes that do not share any sequence homology and whose gene organization may play a role in gene expression. The transcription of each of the five well-characterized genes (Surf-1 to -5) alternates with respect to its neighbor(s) and no more than 159 bp separates any two adjacent genes with the Surf-4 and Surf-2 genes overlapping at their 3' ends by 133 bp. In this work, the expression of the Surf-5 and Surf-4 genes has been examined in various mouse tissues. In addition to the ubiquitously expressed 3.5-kb Surf-5 mRNA, a second alternatively spliced Surf-5 mRNA, Surf-5b, was discovered that was highly expressed in the brain, heart, testis, and skeletal muscle. The alternative splice donor site of the Surf-5b mRNA is similar to splice donor sites found in neuron-specific mRNAs. Surf-5b encodes a unique protein, which, like the ubiquitous Surf-5 protein, has been found to be primarily located in the soluble fraction of the cytoplasm. The expression of the Surf-5b protein was also found to increase in embryonal carcinoma cells differentiated into neuronal cultures. Although the Surf-5 gene is highly conserved through evolution, the presence of the Surf-5b alternative splice may be restricted to higher vertebrates. The Surf-4 gene was ubiquitously expressed in eight different mouse tissues; however, the ratios of the three previously reported Surf-4 mRNAs (two of which are known to derive from different sites of polyadenylation) altered dramatically between tissues. The use of different forms of mRNA processing for regulation of tissue-specific expression of ubiquitously expressed genes is discussed.

Intergenic region between TATA-box binding protein and proteasome subunit C3 genes of Medaka function as the bidirectional promoter in vitro and in vivo

In the genome of eukaryotic organisms, each protein-coding gene has the unique promoter in the 5'-flanking region, and the direction of the promoter is usually controlled unidirectional. In this study, we revealed that the intergenic region between TATA-box binding protein (tbp) and proteasome subunit C3 (psmc3) genes in Medaka functions as bidirectional promoter in vitro and in vivo. The tbp and psmc3 genes were allocated as a head-to-head configuration with a 719bp intergenic region. A comparative analysis of gene arrangement surrounding loci of tbp in vertebrates also illustrated that it was unique in Acanthopterygii lineage. The transcription activities were about 1.2 times for tbp direction and 0.7 times for psmc3 direction against that of SV40 promoter in Medaka fibroblasts, respectively. A dual fluorescent reporter assay directly showed that the bidirectional promoter could express two divergent genes concurrently without disruption of RNA polymerase II elongation. In addition, an analysis of sequential deletion of this promoter suggested that the ETS binding site was necessary for maximum expression of downstream gene, and only the ETS binding site was shared from fish to mammals. In mammals, high correlation with CpG islands was observed in such bidirectional promoters, no association was found in the tbp/psmc3 bidirectional promoter in Medaka. These results suggest that molecular machineries of fish bidirectional promoter may be somehow different from those of mammals but the cis-acting element for binding ETS transcription factors is essential for divergent gene expression.

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs

Background

Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence composition, functional association and regulatory motif discovery.

Results

We identified 1210 bi-directional gene pairs based on the GRCh37 assembly data, accounting for 11.6% of all the human genes owning RNAs. CpG islands were detected in 98.42% of bi-directional promoters and 61.07% of unidirectional promoters. Functional enrichment analysis in GO and GeneGO both revealed that bi-directional genes tend to be associated with housekeeping functions in metabolism pathways and nuclear processes, and 46.84% of the pair members are involved in the same biological function. By fold-enrichment analysis, we characterized 73 and 43 putative transcription factor binding sites(TFBS) that preferentially occur in bi-directional promoters from TRANSFAC and JASPAR database respectively. By text mining, some of them were verified by individual experiments and several novel binding motifs were also identified.

Conclusions

Bi-directional promoters feature a significant enrichment of CpG-islands as well as a high GC content. We provided insight into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities. We hypothesized that the functional association underlies the co-expression of bi-directional genes. Furthermore, we proposed a set of putative regulatory motifs in the bi-directional promoters for further experimental studies to investigate transcriptional regulation of bi-directional genes.

Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism

We have previously shown that in the chicken major histocompatibility complex, the two transporters associated with antigen processing genes (TAP1 and TAP2) are located head to head between two classical class I genes. Here we show that the region between these two TAP genes has transcription factor-binding sites in common with class I gene promoters. The TAP genes are also up-regulated by interferon-gamma in a similar way to mammalian TAP genes and in a way that suggests they are both transcribed from a bi-directional promoter. The gene structures of TAP1 and TAP2 differ from that of human TAPs in that TAP1 has a truncated exon 1 and TAP2 has fused exons, resulting in a much smaller gene size. The truncation of TAP1 results in the loss of approximately 150 amino acids, which are thought to be involved in endoplasmic reticulum retention, heterodimer formation and tapasin binding, compared to human TAP1. Most of the protein sequence features involved in binding ATP are conserved, with two exceptions: chicken TAP1 has a glycine in the switch region where other TAPs have glutamine or histidine, and both chicken TAP genes have serines in the C motif where mammalian TAP2 has an alanine. Lastly, the chicken TAP genes are highly polymorphic, with at least as many TAP alleles as there are class I alleles, as seen by investigating nine inbred lines of chicken. The close proximity of the TAP genes to the class I genes and the high level of polymorphism may allow co-evolution of the genes, allowing TAP molecules to transport peptides specifically for the class I molecules of that haplotype.

DNA supercoiling and transcription control: a model from the study of suppression of the leu-500 mutation in Salmonella typhimurium topA- strains

DNA supercoiling is known to modulate gene expression. The functional relationship between DNA supercoiling and transcription initiation has been established genetically and biochemically. The molecular mechanism whereby DNA supercoiling regulates gene expression remains unclear however. Quite commonly, the same gene responds to the same DNA supercoiling change differently when the gene is positioned at different locations. Such strong positional effects on gene expression suggest that rather than the overall DNA supercoiling change, the variation of DNA supercoiling at a local site might be important for transcription control. We have started to understand the local DNA supercoiling dynamic on the chromosome. As a primary source of local DNA supercoiling fluctuation, transcription-driven DNA supercoiling is important in determining the chromosome supercoiling dynamic and theoretically, therefore, for transcription control as well. Indeed, by studying the coordinated expression of genes in the ilvIH-leuO-leuABCD gene cluster, we found that transcription-driven DNA supercoiling governs the expression of a group of functionally related genes in a sequential manner. Based on the findings in this model system, we put forward the possible mechanisms whereby DNA supercoiling plays its role in transcription control.

The Pxmp2 and PoleI genes are linked by a bidirectional promoter in an evolutionary conserved fashion

Pxmp2 is the most abundant peroxisomal membrane protein in higher eukaryotes. Its expression is tissue-specific with highest levels of expression in liver, kidney and heart tissue. We have analysed the 5'-flanking genomic region of the murine Pxmp2 gene and we found, that the first exon of the gene encoding the DNA polymerase epsilon (PoleI) was localized adjacent to the first exon of the Pxmp2 gene in head to head orientation. Both genes were separated by only 393 bp containing a CpG island with numerous binding sites for Sp1. A TATA box, however, was lacking. Northern blot analysis revealed that both genes were expressed differently, indicating that their expression was regulated independently. We have analysed the promoter activity of the small genomic fragment separating the Pxmp2 and PoleI genes using luciferase as a reporter molecule in transient transfection assays. The small genomic fragment was a functional promoter, controlling gene expression regardless of its orientation. Promoter activity was 60-70% compared with the activity of the strong CMV promoter. The Pxmp2 and PoleI genes were also linked on the human and rat genome. Furthermore, the sequence of the intergenic fragment was highly conserved among these species. Thus, the small intergenic fragment is probably the common basic element of two independently regulated promoters.

Transcription of Leishmania major Friedlin chromosome 1 initiates in both directions within a single region

Almost nothing is known about the sequences involved in transcription initiation of protein-coding genes in the parasite Leishmania. We describe here the transcriptional analysis of chromosome 1 (chr1) from Leishmania major Friedlin (LmjF) which encodes the first 29 genes on one DNA strand, and the remaining 50 on the opposite strand. Strand-specific nuclear run-on assays showed that a low level of nonspecific transcription probably takes place over the entire chromosome, but an approximately 10-fold higher level of coding strand-specific RNA polymerase II (Pol II)-mediated transcription initiates within the strand-switch region. 5' RACE studies localized the initiation sites to a <100 bp region. Transfection studies support the presence of a bidirectional promoter within the strand-switch region, but suggest that other factors are also involved in Pol II transcription. Thus, while in most eukaryotes each gene possesses its own promoter, a single region seems to drive the expression of the entire chr1 in LmjF.

Two overlapping divergent transcription units in the human genome: the FEN1/C11orf10 locus

Flap endonuclease 1 (FEN-1) is a nuclear enzyme involved in DNA metabolism, such as replication, repair, and recombination. Here, we report the comparative genomic organization of the chicken, mouse, and human FEN1 genes as well as the comparative organization of a small gene (C11orf10) located immediately upstream of the FEN1 gene in reverse orientation. Immunostaining revealed that the C11orf10 protein, unlike FEN-1, is located in the cytoplasm, suggesting that these two proteins do not form a physical complex. Importantly, in the human genome, the two mRNAs are overlapping (14 bp) in their 5' ends. Thus, the FEN1/C11orf10 locus is a new example of two overlapping, divergent transcription units in the human genome.

Mutation of a nuclear respiratory factor 2 binding site in the 5' untranslated region of the ADSL gene in three patients with adenylosuccinate lyase deficiency

Adenylosuccinate lyase (ADSL; also called "adenylosuccinase") catalyzes two steps in the synthesis of purine nucleotides: (1) the conversion of succinylaminoimidazolecarboxamide ribotide into aminoimidazolecarboxamide ribotide and (2) the conversion of adenylosuccinate into adenosine monophosphate. ADSL deficiency, a recessively inherited disorder, causes variable-but most often severe-mental retardation, frequently accompanied by epilepsy and/or autism. It is characterized by the accumulation, in body fluids, of succinylaminoimidazolecarboxamide riboside and succinyladenosine, the dephosphorylated derivatives of the two substrates of the enzyme. Analysis of the ADSL gene of three unrelated patients with ADSL deficiency, in whom one of the ADSL alleles displayed a normal coding sequence, revealed a -49T-->C mutation in the 5' untranslated region of this allele. Measurements of the amount of mRNA transcribed from the latter allele showed that it was reduced to approximately 33% of that transcribed from the alleles mutated in their coding sequence. Further investigations showed that the -49T-->C mutation provokes a reduction to 25% of wild-type control of promoter function, as evaluated by luciferase activity and mRNA level in transfection experiments. The mutation also affects the binding of nuclear respiratory factor 2 (NRF-2), a known activator of transcription, as assessed by gel-shift studies. Our findings indicate that a mutation of a regulatory region of the ADSL gene might be an unusually frequent cause of ADSL deficiency, and they suggest a role for NRF-2 in the gene regulation of the purine biosynthetic pathway.

The human homologue of the mouse Surf5 gene encodes multiple alternatively spliced transcripts

Hu-Surf5 is included within the Surfeit locus, a cluster of six genes originally identified in mouse. In the present study, we have cloned and characterized the Hu-Surf5 gene and its mRNA multiple transcripts. Comparison of the most abundant cDNA and genomic sequence shows that the Hu-Surf5 is spread over a region of approximately 7.5 kb and consists of five exons separated by four introns. The nucleotide sequence of the genomic region flanking the 3'-end of the Hu-Surf5 gene revealed the presence of a processed pseudogene of human ribosomal protein L21 followed by Hu-Surf6 gene. Only 110 bp separate the transcription start site of Hu-Surf5 and Hu-Surf3/L7a gene and the transcription direction is divergent. Earlier studies defined the 110 bp region essential for promoter activity of Hu-Surf3/L7a. Here, we show that this region stimulates transcription with a slightly different efficiency in both directions. The bidirectional promoter lacks an identifiable TATA box and is characterized by a CpG island that extends through the first exon into the first intron of both genes. These features are characteristic of housekeeping genes and are consistent with the wide tissue distribution observed for Hu-Surf5 expression. Hu-Surf5 encodes three different transcripts, Surf-5a, Surf-5b, and Surf-5c, which result from alternative splicing. Two protein products, SURF-5A and SURF-5B have been characterized. Production of chimaeras between the full-length SURF-5A or SURF-5B and the green fluorescent protein (GFP) allowed to localize both proteins in the cytoplasm.

Cloning and functional analysis of pyruvate kinase promoter region from Drosophila melanogaster

Pyruvate kinase (PK; EC 2.7.1.40) is a key glycolytic enzyme of Drosophila melanogaster. It catalyzes the conversion of phosphoenolpyruvate into pyruvate with the transfer of a phosphate group to ADP to form ATP. The ATP provides energy for cell growth and metabolism, and pyruvate participates in many metabolic reactions. Therefore, PK plays an important role in cell metabolism. Southern blot analysis, PCR, and sequencing were used to determine the content of a Drosophila pyruvate kinase (Pyk) genomic clone, lambdaPK61. The results indicated that the insert of lambdaPK61 comprised 8330 bp upstream of and 7186 bp downstream of the transcription start point of the Pyk gene. The size of the insert was 15,516 bp in total, which contained six genes including Pyk. Deletion mapping was applied to identify the promoter region and cis-acting elements 5' of PyK. Ten serial deletions produced by PCR were inserted upstream of the reporter gene (LacZ) to form recombinant plasmids, which were then transfected into Drosophila S2 cells. The results revealed that the regions -1475 approximately -1033 and -1033 approximately -534 of the 5' end of PyK possessed positive regulatory function for Pyk expression; i.e., increased gene expression. There were redundant putative cis-acting elements, including ecdysone response element (EcRE), E74A, and broad complex zinc finger (BRCZ) binding sites. Both E74A and BRCZ belong to the early genes regulated by ecdysone. This result suggested that Pyk might be regulated by ecdysone, directly or indirectly. However, the results of the developmental profile of Pyk expression by Northern blot analysis suggested that the effects of ecdysone on Pyk were repressive, not inductive. In addition, it was found that in these regions, there were many cis-acting elements related to egg and embryo development. Both -258 approximately -254 and -167 approximately -163 contained a CAAT box, and deletion of these regions decreased reporter gene expression. Therefore, it is suggested that both CAAT boxes are functional and that the promoter of Pyk might be located in the region of -258 approximately +109. No TATA box or downstream promoter element were identified around the transcription start site of Pyk. Additionally, PyK might share a regulatory region with an unknown neighboring gene. It was concluded that Pyk has the characteristics of a housekeeping gene.

Expression and functional analysis of SURF1 in Leigh syndrome patients with cytochrome c oxidase deficiency

Leigh syndrome (LS) associated with cytochrome c oxidase (COX) deficiency is an autosomal recessive neurodegenerative disorder caused by mutations in SURF1. Although SURF1 is ubiquitously expressed, its expression is lower in brain than in other highly aerobic tissues. All reported SURF1 mutations are loss of function, predicting a truncated protein (hSurf1) product. Western blot analysis with anti-hSurf1 antibodies demonstrated a specific 30 kDa protein in control fibroblasts, but no protein in LS patient cells. Steady-state levels of both nuclear- and mitochondrial-encoded COX subunits were also markedly reduced in patient cells, consistent with a failure to assemble or maintain a normal amount of the enzyme complex. An epitope (FLAG)-tagged hSurf1 was targeted to mitochondria in COS7 cells and a mitochondrial import assay showed that the hSurf1 precursor protein (35 kDa) was imported and processed to its mature form (30 kDa) in a membrane potential-dependent fashion. The protein was resistant to alkaline carbonate extraction and susceptible to proteinase K digestion in mitoplasts. Mutant proteins in which the N-terminal transmembrane domain or central loop were deleted, or the C-terminal transmembrane domain disrupted, did not accumulate and could not rescue COX activity in patient cells. Co-expression of the N- and C-terminal transmembrane domains as independent entities also failed to rescue the enzyme deficiency. These data demonstrate that hSurf1 is an integral inner membrane protein with an essential role in the assembly or maintenance of the COX complex and that insertion of both transmembrane domains in the intact protein is necessary for function.

Genes for the human mitochondrial trifunctional protein alpha- and beta-subunits are divergently transcribed from a common promoter region

Human HADHA and HADHB genes encode the subunits of an enzyme complex, the trifunctional protein, involved in mitochondrial beta-oxidation of fatty acids. Both genes are located in the same region of chromosome 2p23. We isolated genomic clones, including 5' flanking regions, for HADHA and HADHB. Sequencing revealed that both of these genes are linked in a head-to-head arrangement on opposite strands and have in common a 350-bp 5' flanking region. The 5' flanking region has bidirectional promoter activity within this region; two cis elements proved critical for the activity. Transcription factor Sp1 functions as an activator for the bidirectional promoter by binding to both elements. Therefore, expression of trifunctional protein subunits are probably coordinately regulated by a common promoter and by Sp1.

SURF1, encoding a factor involved in the biogenesis of cytochrome c oxidase, is mutated in Leigh syndrome

Leigh Syndrome (LS) is a severe neurological disorder characterized by bilaterally symmetrical necrotic lesions in subcortical brain regions that is commonly associated with systemic cytochrome c oxidase (COX) deficiency. COX deficiency is an autosomal recessive trait and most patients belong to a single genetic complementation group. DNA sequence analysis of the genes encoding the structural subunits of the COX complex has failed to identify a pathogenic mutation. Using microcell-mediated chromosome transfer, we mapped the gene defect in this disorder to chromosome 9q34 by complementation of the respiratory chain deficiency in patient fibroblasts. Analysis of a candidate gene (SURF1) of unknown function revealed several mutations, all of which predict a truncated protein. These data suggest a role for SURF1 in the biogenesis of the COX complex and define a new class of gene defects causing human neurodegenerative disease.

The human Surfeit locus

The organization of the human Surfeit locus containing the six sequence-unrelated housekeeping genes Surf-1 to Surf-6 (HGMW-approved symbols SURF1-SURF6) has been determined. The human surfeit locus occupies about 60 kb of DNA, and the tightly clustered gene organization and the juxtaposition of the human genes are similar to the mouse and chicken surfeit loci with the 5' end of each gene associated with a CpG-rich island. Whereas in the mouse the Surf-2 and Surf-4 genes overlap at their 3' ends, the human Surf-2 and Surf-4 genes have been found to be separated by 302 bp due to a much shorter 3' untranslated region in the human Surf-2 gene. The distance between the 3' ends of the human Surf-1 and Surf-3 genes is 374 bp, and the distance between the 5' ends of the human Surf-3 and Surf-5 genes is only 112 bp. Unusually the human Surf-5 gene contains an intron in its 5' untranslated region not found in the mouse or rat Surf-5 genes. This additional intron is also found in the Surf-5 gene of both Old and New World monkeys, being generated before the divergence of human and prosimians but after the divergence of primates and rodents. A contig of 200 kb containing the human Surfeit locus has been constructed from overlapping cosmid, P1, and PAC clones. Approximately 40 kb proximal to the 3' end of the Surf-6 gene, the 5' region of the ABO glycosyltransferase gene has been detected. This allows us to determine the orientation of the Surfeit and ABO loci with respect to each other and to the telomere and centromere of human chromosome 9.

Evidence for a bidirectional promoter complex within the X gene of woodchuck hepatitis virus

The genetic organization of hepadnaviruses is unusual in that all cis-acting regulatory sequences are located within genes. Thus, in the mammalian hepadnavirus genome, the presurface, surface, and X transcript promoters reside within the polymerase gene while the pregenome transcript promoter is located within the X gene. In this study we have identified two additional promoters within the woodchuck hepatitis virus (WHV) X gene that stimulate production of transcripts in vitro. First, we cloned regions of the WHV X gene into a promoterless expression vector (pGL2) to examine their ability to promote expression of firefly luciferase and mapped a previously unidentified promoter to positions 1475-1625 of the WHV8 genome. Deletion analysis revealed that the essential domain of this promoter, termed the ORF5/deltaX transcript promoter, mapped to nucleotides 1525-1625. Analysis revealed that this transcript initiated at nucleotide 1572 in both human (HuH-7) and woodchuck (WLC-3) hepatoma cell lines. Consistent with this finding, DNA footprinting analysis revealed protection of nucleotides 1567-1578 on the positive strand of the WHV8 genome. The function of this transcript in vivo is unclear, however, it may be used to produce a truncated form of the X protein that initiates at an AUG codon at position 1743-1745 on the WHV8 genome. Next, a second promoter was identified at positions 1625-1975 that was responsible for production of an antisense transcript. The activity of this promoter was comparable to that of the previously characterized surface transcript promoter of WHV in the absence of an enhancer. The antisense transcript promoter resides immediately upstream of open reading frame (ORF) 6, a previously identified ORF on the strand opposite of the known WHV protein-encoding sequences, that is thought to represent a vestigial gene. Analysis indicates that the antisense transcript had multiple start sites: nucleotides 1683 and 1762 on the WHV8 genome when assayed in HuH-7 cells, and nucleotide 1786 when assayed in WLC-3 cells. These data are consistent with footprinting analysis of supercoiled WHV DNA that revealed that the regions encompassing nucleotides 1696-1685, 1781-1766, and 1801-1787 on the negative sense DNA strand were protected from nuclease degradation. It is possible that such a transcript was once used in protein expression in an ancestral virus and may now be used for genetic control of WHV replication and/or gene expression. Overall, these data are consistent with the presence of a bidirectional promoter complex within the WHV X gene.

A bidirectional promoter connects the p14.5 gene to the gene for RNase P and RNase MRP protein subunit hPOP1

We have identified the functional promoter of the translational inhibitor p14.5, the human homologue to a rat perchloric acid-soluble protein (PSP), a mouse heat-responsive protein (Hrp12) and a goat tumor antigen (UK114). Sequence analysis revealed a GC-rich promoter with several consensus sequences for transcription factors, but no TATA- and CAAT-box. To confirm promoter activity, DNA fragments of the p14.5 5'-flanking region were ligated in front of the luciferase gene and were transfected into HeLa and HepG2 cells. A minimal promoter between nt -104 and nt +88 relative to the transcription start site was responsible for basal activity. Furthermore, we observed a head-to-head orientation of p14.5 to the gene for the protein subunit of RNase P and MRP ribonucleoproteins (hPOP1). Luciferase assays with fragments of the hPOP1 5'-flanking region revealed a minimal promoter between nt -20 and nt +98 relative to the start of transcription. These data indicate that the 102 bp region between p14.5 and hPOP1 can act as a bidirectional promoter. The p14.5-hPOP1-cluster was mapped to chromosome 8q22 using in situ hybridization technique.

Organisation of regulatory elements in two closely spaced Drosophila genes with common expression characteristics

Sperm tail proteins that are components of a specific structure formed late during spermatid elongation have been found to be encoded by the Mst(3)CGP gene family. These genes have been demonstrated to be regulated both at the transcriptional as well as at the translational level. We report here on the dissection of the regulatory regions for two members of the gene family, Mst84Da and Mst84Db. While high level transcription and negative translational control of Mst84Da is mediated by a short gene segment of 205 nt (-152/+53), Mst84Db expression is controlled by a number of distinct regulatory elements with different effects that all reside within the gene itself. We identify a transcriptional control element between +154 and +216, a translational repression element around +216 to +275 and an RNA stability element within the 3'UTR. Irrespective of the final common expression characteristics, correct regulation for any individual member of the gene family seems to be achieved by very different means. This confirms earlier observations that did not detect any other sequence elements in common apart from the TCE (translational control element).

A functional YY1 binding site is necessary and sufficient to activate Surf-1 promoter activity in response to serum growth factors

The human Surf-1 and Surf-2 housekeeping genes are divergently transcribed and share a bi-directional, TATA-less promoter. Housekeeping promoters typically contain complex arrays of transcription factor binding sites and several studies have suggested that many of these sites might be functionally redundant. The Surf-1/Surf-2 promoter region contains four factor binding sites; members of the ETS family of transcription factors bind to two of these sites whilst YY1 binds to a third site immediately downstream of the major Surf-1 transcription start point. Here we show that Sp1 binds to the fourth transcription factor binding site. Although YY1 and Sp1 have previously been shown to interact both in vitro and in vivo, these proteins function independently at the Surf-1/Surf-2 promoter. The binding of Sp1 alone is sufficient to bring about full promoter activity in the Surf-2 direction. In contrast, both Sp1 and ETS proteins are required to bring about full promoter activity in the Surf-1 direction. The YY1 binding site is not required for basal transcription in either direction. The YY1 binding site is, however, both necessary and sufficient to confer growth factor inducibility on transcription in the Surf-1 direction. Our data suggest that functionally redundant transcription factor binding sites might not be a general feature of housekeeping promoters.

The genes encoding mammalian chaperonin 60 and chaperonin 10 are linked head-to-head and share a bidirectional promoter

Chaperonins are a class of stress-inducible molecular chaperones involved in protein folding. We report the cloning, sequencing and characterisation of the rat mitochondrial chaperonin 60 and chaperonin 10 genes. The two genes are arranged in a head-to-head configuration and together comprise 14 kb and contain 14 introns. The genes are linked together by a region of approximately 280 bp, which constitutes a bidirectional promoter and includes a common heat-shock element. Insertion of the shared promoter region between two reporter genes is sufficient to drive their expression under both constitutive and heat-shock conditions. The arrangement of the mammalian chaperonin genes suggests the potential to provide the coordinated regulation of their products in a manner that is mechanistically distinct from, yet conceptually similar to, that employed by the bacterial chaperonin (groE) operon.

Role of NRF-1 in bidirectional transcription of the human GPAT-AIRC purine biosynthesis locus

GPAT and AIRC encode enzymes for steps one and six plus seven respectively in the pathway for de novo purine nucleotide synthesis in vertebrates. The human GPAT and AIRC genes are divergently transcribed from a 558 bp intergenic promoter region. Cis-acting sites and transcription factors important for bidirectional expression were identified. A cluster of sites between nt 215 and 260 are essential, although not sufficient, for expression of both genes. Two proteins from HepG2 cell nuclear extract, identified as NRF-1 and Sp1, bound to the promoter at sites within the 215-260 region. NRF-1 was required for stable binding of Sp1. Deletion of a 5'promoter region including nt 215-260 resulted in decreased expression of GPAT and AIRC in transfected HepG2 cells. The decreased expression was accounted for by point mutations in an NRF-1 site and either of two flanking sites for Sp1. These transcription factors account in part for the coordinated expression of human GPAT and AIRC.

Regulation of vascular smooth muscle soluble guanylate cyclase activity, mRNA, and protein levels by cAMP-elevating agents

Although the biochemical properties of soluble guanylate cyclase (sGC) have been extensively studied, little is known about the regulation of gene expression of sGC subunits by second messengers. cAMP analogues and elevating agents have been previously shown to alter gene expression in vascular cells. The aim of the present study was to investigate the effects of cAMP-elevating agents on sodium nitroprusside-stimulated sGC activity and to correlate activity changes with mRNA and protein levels in cultured rat aortic smooth muscle cells. Pretreatment of cells with 50 to 1000 mumol/L isobutylmethyl-xanthine or 0.01 to 10 mumol/L forskolin led to a time- and concentration-dependent decrease in sodium nitroprusside-induced cGMP accumulation, first evident after 3 hours of pretreatment with forskolin and 6 hours of pretreatment with isobutylmethylxanthine. Incubation of cells with a protein kinase A-selective inhibitor (H89 or KT 5720) partially or fully prevented the downregulation in sodium nitroprusside-induced cGMP accumulation caused by cAMP-elevating agents. Quantification of reverse transcriptase-polymerase chain reaction products by high-performance liquid chromatography revealed that mRNA for both alpha1- and beta1-subunits of sGC were decreased in cells pretreated with isobutylmethylxanthine and forskolin but not with dideoxyforskolin (inactive analogue). Moreover, protein levels for the sGC alpha1 subunit of cells pretreated with isobutylmethylxanthine and forskolin but not with dideoxyforskolin were decreased as indicated by Western blot analysis. These data indicate that cAMP-elevating agents decrease sGC activity, possibly by decreasing mRNA or protein levels or both.

CpG methylation and the binding of YY1 and ETS proteins to the Surf-1/Surf-2 bidirectional promoter

The divergently transcribed Surf-1 and Surf-2 genes are separated by a bi-directional, TATA-less promoter which contains three important factor-binding sites, Su1, Su2 and Su3. The transcription initiation factor YY1 binds to the Su1 site and stimulates transcription in the direction of Surf-1 and, to a lesser extent, Surf-2. Members of the ETS family of transcription factors bind to the Su2 and Su3 sites. Here we show that in transient transfection assays, transcription in both the Surf-1 and the Surf-2 direction is severely reduced by CpG methylation. Although the Su1 site contains three CpG dinucleotides, the binding of YY1 is not affected by CpG methylation. In contrast, the binding of two ETS factors (ETS-2 and PEA-3) to the Su2 site (which also contains three CpG dinucleotides) is totally abolished by CpG methylation. Finally, we show that methylation of a single C within the Su2 site is sufficient to prevent ETS factor binding.

The surf-4 gene encodes a novel 30 kDa integral membrane protein

The mouse surfeit locus is a tight cluster of at least six genes (surf-1 to -6), unrelated by sequence homology, whose unique organization is conserved in vertebrates. We show that the surf-4 coding sequence is conserved between mouse and human. Primary sequence analysis predicts that the mouse surf-4 protein contains seven transmembrane domains and a double lysine endoplasmic reticulum (ER) retrieval motif on the carboxyl terminus. Translation of the mouse surf-4 cDNA in vitro resulted in the production of a 30 kDa membrane protein. Salt and detergent extraction procedures showed that the surf-4 protein associated tightly with the microsomal membranes. Proteolysis protection of 14 and 3 kDa fragments indicates that the surf-4 protein contains at least two membrane spanning domains: this is consistent with the proposed topology. Addition of the c-Myc epitope into three different regions of the surf-4 protein resulted in transfectants that expressed a myc-tagged protein. Immunofluorescence analysis of the three surf-4 myc chimeras yielded a cytoplasmic staining pattern. Consistent with the presence of the ER retrieval motif, the surf-4 myc protein was not detected at the plasma membrane. A model for the proposed structure of the surf-4 protein is presented.

The Surf-1 and Surf-2 genes and their essential bidirectional promoter elements are conserved between mouse and human

The organization of the Surfeit locus and the juxtaposition of at least five of the Surfeit genes (Surf-1 to -5) are conserved between mouse and human (Williams et al., 1988; Yon et al., 1993). In the mouse, the heterogeneous transcription start sites of the divergent Surf-1 and Surf-2 genes are separated by a maximum of only 73 bp (Williams and Fried, 1986). This region contains a bidirectional promoter composed of three major factor binding sites required for the efficient expression of both the Surf-1 and Surf-2 genes (Lennard and Fried, 1991). Here we report the isolation and characterization of the human Surf-1 and Surf-2 genes and their intergenic region. Although the major Surf-1 and Surf-2 transcription start sites are separated by 97 bp in the human and there are multiple differences in the mouse and human sequence between and around the transcriptional start sites, there is high conservation of the sequence specifying the three major factor binding sites of the bidirectional promoter. The three factor binding sites (HSu1, 2, and 3) present within the human promoter bind nuclear factors, of which the binding of HSu1 and HSu2 are competed by oligonucleotides carrying the corresponding mouse factor binding sites. The HSu3 site binds factors that are similar but apparently not direct homologs of those that bind to the equivalent mouse sequences. Human Surf-1 and Surf-2 cDNAs have been cloned and sequenced. The putative human Surf-1 and Surf-2 proteins are 77% and 69% identical to the corresponding mouse proteins.

In vitro transcription of the TATAA-less mouse thymidylate synthase promoter: multiple transcription start points and evidence for bidirectionality

The mouse thymidylate synthase (TS) promoter (pTS) lacks a TATAA box and an initiator element, and has multiple transcription start points (tsp) located across a 90-bp region. We have developed an in vitro transcription system for pTS using circular templates and nuclear extracts from HeLa cells or mouse 3T6 fibroblasts. The amount of RNA synthesized and the locations of the tsp were determined by S1 nuclease protection assays. The transcription system reproduced the complex pattern of in vivo tsp, except that the downstream tsp were used preferentially. The reaction temperature, concentrations of DNA template and MgCl2, and incubation time were optimized. The pTS core region contains binding sites for the Sp1 and Ets transcription factors. Inactivation of the Sp1-binding element led to a twofold reduction in transcription and a preferential use of upstream tsp. Inactivation of the Ets-binding element, which reduced promoter activity tenfold in vivo, had only a minor effect in vitro. Addition of a strong initiator element introduced a new tsp, but did not eliminate the complex tsp pattern. To determine if pTS had bidirectional promoter activity, the promoter was inverted and analyzed for transcriptional activity. The inverted promoter was found to initiate transcription at multiple tsp and had approximately the same strength as the normal pTS.

YY1 is involved in the regulation of the bi-directional promoter of the Surf-1 and Surf-2 genes

The Surfeit locus is an unusual cluster of at least 6 housekeeping genes whose organisation is conserved between birds and mammals. We have previously shown that the divergently transcribed Surf-1 and Surf-2 genes are separated by a bi-directional, TATA-less promoter. In mouse, the Surf-1/Surf-2 promoter contains three important factor binding sites: Su1, Su2, and Su3. These sites are conserved between the mouse and human Surf-1/Surf-2 promoters, bind nuclear factors in vitro, and are required for accurate and efficient expression of Surf-1 and Surf-2 in vivo. Using gel retardation assays, methylation interference experiments, and specific antibodies we demonstrate that the Su1 binding factor is the initiator protein YY1. Over-expression of YY1 results in a major stimulation of transcription in the Surf-1 direction and a minor stimulation of transcription in the Surf-2 direction.

Bidirectional transcription from actin promoters in Dictyostelium

Numerous transformation vectors for Dictyostelium discoideum have been constructed by fusing actin 6 and 15 promoters to selectable markers such as G418 and hygromycin. Strand specific probing of RNAs from transformed cells demonstrates that cells containing these vectors accumulate transcripts representing both strands of the vector. The evidence is consistent with bidirectional transcription initiating in the truncated actin promoter fragments. A larger fragment of the actin 15 promoter largely eliminates this problem.

Transcriptional analyses of the gene region that encodes human histidyl-tRNA synthetase: identification of a novel bidirectional regulatory element

A recombinant phage clone containing the 5' end of the gene HRS encoding human histidyl-tRNA synthetase (HRS) has been isolated. Primer extension analyses indicated that there are two types of HRS transcripts. The longer transcripts were initiated from a single transcription start point (tsp) located approximately 455 bp upstream and the shorter transcripts were initiated from multiple tsp located approximately 38 to 82 bp upstream from the HRS ATG start codon. Functionally, we have identified two regions (+1 to -122; -185 to -502), each of which when placed 5' of a promoterless cat construct can initiate transcription in both orientations after transfection into HeLa cells. A pair of imperfect inverted repeats (IIR) was located within the region +1 to -122. Using mobility shift assays, we have identified a nuclear factor that binds specifically to each half of the IIR. However, this pair of IIR (-73 to -110) was not sufficient for bidirectional transcription activity. At least one copy of a 27-bp oligodeoxyribonucleotide (oligo), which spans -94 to -120, was required in order to facilitate bidirectional transcription activity. From mobility shift assays using HeLa cell nuclear extracts and this 27-bp oligo, we have identified two DNA-protein complexes, both of which are presumably required to initiate bidirectional transcription.

Differential effects of DNA-binding proteins on bidirectional transcription from the common promoter region of human collagen type IV genes COL4A1 and COL4A2

Expression of the heterotrimeric collagen IV (alpha 1(IV))2 alpha 2(IV) is essential for the structural integrity and functional properties of basement membranes. The genes COL4A1 and COL4A2 coding for both subunits are located close to each other on the same chromosome and are transcribed from a common bidirectional promoter element. Binding of at least three different nuclear proteins could be detected within this promoter, a CCAAT-binding protein, Sp1 and a newly identified factor, designated 'CTCBF'. Mutagenesis of binding sites proved that these factors are essential for the efficient transcription of both genes, but revealed differential gene-specific effects. Therefore, the common promoter region of collagen IV does not represent an equally functional bidirectional element, but may be better understood as two overlapping gene-specific promoters with shared elements.

Colocalization of the genes coding for the alpha 3 and beta 3 subunits of soluble guanylyl cyclase to human chromosome 4 at q31.3-q33

We have determined the chromosomal location of the human genes coding for the alpha 3 and beta 3 subunits of soluble guanylyl cyclase (GC-S). The study was performed by in situ hybridization of human metaphase spreads with two human cDNA probes, containing the coding sequences of the GC-S alpha 3 and beta 3 subunits, respectively. Each probe gave a strong specific signal on chromosome 4 at the 4q31.3-4q33 region, with the maximal signal in the 4q32 band. The colocalization of both genes in 4q32 represents an interesting feature for the coordinated regulation of expression of both GC-S subunits.

Evidence for a third transcript from the human factor VIII gene

Intron 22 of the human factor VIII gene was recently found to contain a gene, associated with a CpG island, which is transcribed in the direction opposite to factor VIII. We now report that another transcript emanates from the island and is transcribed in the same direction as factor VIII. The divergent transcripts originate within 122 bases of each other. The newly identified 5' exon in intron 22 potentially codes for eight amino acids and is spliced to exons 23-26, with the factor VIII reading frame maintained. The protein encoded by this transcript would include the factor VIII C2 domain, responsible for phospholipid binding and essential for coagulant activity.

The UAS(MAL) is a bidirectional promotor element required for the expression of both the MAL61 and MAL62 genes of the Saccharomyces MAL6 locus

Maltose fermentation in Saccharomyces yeasts requires one of five unlinked MAL loci: MAL1, 2, 3, 4, or 6. Each locus consists of three genes encoding maltose permease, maltase and the MAL activator. At MAL6 the genes are called MAL61, MAL62 and MAL63, respectively. Transcription of MAL61 and MAL62 is coordinately induced by maltose and repressed by glucose and this regulation is mediated by the MAL activator. By deletion analysis of the MAL61-MAL62 intergenic region, we show that a 68-basepair region, from base pairs -515 to -582 upstream of the MAL61 start codon, contains a sequence necessary for the maltose-induced expression of MAL61 and MAL62, the UAS(MAL). This sequence contains two copies of an 11-basepair dyad which may be the active elements of the UAS(MAL). Using heterologous gene plasmid constructs, we demonstrate that the UAS(MAL) sequence is sufficient for maltose inducibility of MAL62 and that this regulated expression requires a functional MAL activator. Our results suggest that the MAL61-MAL62 intergenic region contains additional distinct elements which function to precisely regulate MAL61 and/or MAL62 expression. Among these are repressing sequences, including a glucose-responsive element located between base pairs -583 and -638, which is partially responsible for mediating glucose-repression of MAL62 expression.

Regulation of Aspergillus nidulans penicillin biosynthesis and penicillin biosynthesis genes acvA and ipnA by glucose

Expression of the Aspergillus nidulans penicillin biosynthesis genes acvA and ipnA, encoding delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase and isopenicillin N synthetase, respectively, was analyzed. The intergenic region carrying the divergently oriented promoters was fused in frame in both orientations to Escherichia coli lacZ and E. coli uidA reporter genes. Each construct permits simultaneous expression studies of both genes. Transformants of A. nidulans carrying a single copy of either plasmid integrated at the chromosomal argB locus were selected for further investigations. Expression of both genes was directed by the 872-bp intergenic region. ipnA- and acvA-derived gene fusions were expressed from this region at different levels. ipnA had significantly higher expression than did acvA. Glucose specifically reduced the production of penicillin and significantly repressed the expression of ipnA but not of acvA gene fusions. The specific activities of isopenicillin N synthetase, the gene product of ipnA, and acyl coenzyme A:6-aminopenicillanic acid acyltransferase were also reduced in glucose-grown cultures.