Enhancers and transcription factors in the control of gene expression

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

Species-specific, new, or "orphan" genes account for 10%-30% of eukaryotic genomes. Although initially considered to have limited function, an increasing number of orphan genes have been shown to provide important phenotypic innovation. How new genes acquire regulatory sequences for proper temporal and spatial expression is unknown. Orphan gene regulation may rely in part on origination in open chromatin adjacent to preexisting promoters, although this has not yet been assessed by genome-wide analysis of chromatin states. Here, we combine taxon-rich nematode phylogenies with Iso-Seq, RNA-seq, ChIP-seq, and ATAC-seq to identify the gene structure and epigenetic signature of orphan genes in the satellite model nematode Pristionchus pacificus Consistent with previous findings, we find young genes are shorter, contain fewer exons, and are on average less strongly expressed than older genes. However, the subset of orphan genes that are expressed exhibit distinct chromatin states from similarly expressed conserved genes. Orphan gene transcription is determined by a lack of repressive histone modifications, confirming long-held hypotheses that open chromatin is important for new gene formation. Yet orphan gene start sites more closely resemble enhancers defined by H3K4me1, H3K27ac, and ATAC-seq peaks, in contrast to conserved genes that exhibit traditional promoters defined by H3K4me3 and H3K27ac. Although the majority of orphan genes are located on chromosome arms that contain high recombination rates and repressive histone marks, strongly expressed orphan genes are more randomly distributed. Our results support a model of new gene origination by rare integration into open chromatin near enhancers.

Differential oncogene-related gene expressions in myeloma cells resistant to prednisone and vincristine

Multidrug resistance in cancer may arise due to alterations in gene expression. In this study, sublines of drug-resistant multiple myeloma (MM) cells, namely RPMI-8226 and U-266, were examined for their differential oncogene-related gene expression levels and the relations to drug resistance were analyzed. Drug resistance was induced by application of the prednisone or vincristine using stepwise dose increments. XTT cytotoxicity assay was used for determination of resistance levels. Microarray analysis was carried out and the genes up- or downregulated more than two-folds were considered as significantly changed. Different types of oncogenes were altered in different drug-resistant RPMI-8226 and U-266 multiple myeloma sublines. The oncogenes which belong to Ras superfamily, especially Rho family of GTPases, were upregulated in prednisone-resistant MM cell lines whereas they were either downregulated or not changed in vincristine resistance. ETS and NF-κB2 are among transcription factors which were downregulated in prednisone-resistant cells. Transforming growth factor beta receptor (TGFß) was downregulated in prednisone-resistant MM cell lines while it was upregulated in vincristine-resistant cell lines. Different types of interleukin gene expressions were seen to be altered in resistant MM sublines whereas suppressors of cytokine signalling genes such as SOCS2, SOCS4 and WSB2 were all downregulated. In conclusion, it is seen that different drugs can induce totally different pathways leading to resistance in the same cancer cell lines. Every drug resistance should be evaluated separately. These facts must be considered in cancer chemotherapy and reversal of drug resistance.

Site-specific methylation of the promoter alters deoxyribonucleic acid-protein interactions and prevents follicle-stimulating hormone receptor gene transcription

In the male gonad, the FSH receptor (FSHR) gene is expressed only in Sertoli cells. To date, the mechanism(s) responsible for Sertoli cell-specific expression of the FSHR gene are unknown. In this study, DNA methylation at specific sites in the promoter are shown to lead to changes in the DNA-protein interactions at those sites and, subsequently, to transcriptional repression of the gene. The extent of methylation of cytosine residues within the core promoter region of genomic DNA isolated from cells/tissues that expressed, or did not express, the FSHR gene was analyzed by the sodium bisulfite conversion technique. All seven cytosine residues in CpG dinucleotides within the core promoter region were found to be unmethylated in primary cultured rat Sertoli cells that were actively expressing FSHR mRNA. In contrast, in tissues not expressing FSHR the same region of the gene was methylated at each of the CpG dinucleotides examined. In addition, DNA-protein interactions in three primary regulatory regions of the promoter were examined by electrophoretic mobility shift assays (EMSA) with synthetic oligonucleotides containing selectively methylated cytosine residues. Methylation of a CpG sequence within a consensus E box element (CACGTG, -124/-119) decreased the binding affinity of USF1/2 transcription factors for this element. Methylation of the CpG sequence in the Inr region (CCGG, -85/-82) allowed the formation of an additional DNA-protein complex. Methylation at both cytosine residues in the E2F element ((m)CG(m)CG) generated a new methylcytosine-specific DNA-protein complex. The core FSHR promoter region of a mouse Sertoli cell line (MSC-1) that does not express FSHR was shown to be methylated at four CpG dinucleotides. The demethylation of these four sites by treatment of the MSC-1 cells with 5-aza-2'-deoxycytidine (5-azaCdR) activated the transcription of the FSHR gene. Taken together, these results suggest that cytosine methylation is a major factor in the repression of the expression of the FSHR gene.

The estrogen receptor gene: promoter organization and expression

The estrogen receptor (ER) is a ligand-activated transcription factor and a member of a large family of nuclear hormone receptors. As a mediator of estrogen hormone action, the ER is involved in many important physiological processes. ER gene expression has been demonstrated to be restricted to certain tissues and under complex hormonal control. However, the molecular mechanisms involved have remained largely unknown. Due to this lack of knowledge an investigation was undertaken to characterize the promoter organization of ER gene and investigate its expression. Approximately 3 kb of the 5' flanking region of the human ER (hER) gene was isolated and sequenced. By performing RT-PCR and RACE experiments it was shown that the hER gene is transcribed from three different promoters. Transcription of the hER gene from these promoters yields three different mRNA isoforms with unique 5' untranslated regions (5'UTRs), but identical coding regions. The expression pattern of the hER mRNA isoforms was investigated by RT-PCR. Both the A- and B-mRNA isoforms were found to be expressed in breast and uterus, whereas expression of the C-transcript was predominantly detected in liver. In bone cells only expression of the B-mRNA could be detected. The steady-state levels of the A- and B-transcripts in normal breast and uterus were quantified and compared with the hER mRNA levels in established cancer cell lines derived from the same tissues. This demonstrated approximately equal levels of the two transcripts in normal tissues whereas the A-mRNA was the most abundant isoform in the cancer cell lines investigated. Approximately 4.5 kb of the 5' flanking region of the rat ER (rER) gene were sequenced. Sequence analysis and PCR experiments suggested that the promoter organization of the rat and human ER genes is only partially conserved which might indicate species-specific differences in the regulation of ER expression. In conclusion, this work suggests tissue-specific alternative promoter usage as a mechanism in the regulation of human and rat ER gene expression.

Characterization of FMR1 promoter elements by in vivo-footprinting analysis

Fragile X syndrome is associated with silencing of the FMR1 gene. We studied the transcriptional regulation, by analysis of the FMR1 promoter region for the presence of in vivo protein/DNA interactions and for cytosine methylation at the single-nucleotide level. Four protein-binding sites were present in the unmethylated promoter of the active FMR1 gene. In the methylated promoter of inactive genes no footprints were detected, and no evidence of active repression was found in the region investigated. We propose that the silencing of FMR1 gene transcription results from a lack of transcription-factor binding.

An HMG I/Y-containing repressor complex and supercoiled DNA topology are critical for long-range enhancer-dependent transcription in vitro

The 3' enhancer of the T cell receptor alpha-chain (TCR alpha) gene directs the tissue- and stage-specific expression and V(D)J recombination of this gene locus. Using an in vitro system that reproduces TCR alpha enhancer activity efficiently, we show that long-range promoter-enhancer regulation requires a T cell-specific repressor complex and is sensitive to DNA topology. In this system, the enhancer functions to derepress the promoter on supercoiled, but not relaxed, templates. We find that the TCR alpha promoter is inactivated by a repressor complex that contains the architectural protein HMG I/Y. In the absence of this repressor complex, expression of the TCR alpha gene is completely independent of the 3' enhancer and DNA topology. The interaction of the T cell-restricted protein LEF-1 with the TCR alpha enhancer is required for promoter derepression. In this system, the TCR alpha enhancer increases the number of active promoters rather than the rate of transcription. Thus, long-range enhancers function in a distinct manner from promoters and provide the regulatory link between repressors, DNA topology, and gene activity.

Efficient expression of pro-urokinase by human lymphoblastoid Namalwa KJM-1 cells using moloney retroviral promoter

We have compared the level of expression of several enhancer/promoters in human lymphoblastoid Namalwa KJM-1 cells when fused to a common reporter gene. A cassette containing the pro-urokinase (pro-UK) coding sequence followed by the rabbit beta-globin and simian virus 40 (SV40) 3' nontranslated region was used for evaluation of the enhancer activity. Cells containing Moloney murine leukemia virus (Mo-MuLV) promoter had an average of 10-20 fold higher expression levels of pro-UK than those containing other promoters, such as SV40 early gene promoter, human cytomegalovirus (hCMV) major immediate-early gene promoter, Rous sarcoma virus (RSV) promoter, and chicken beta-actin gene promoter. The expression level of pro-UK under the control of Mo-MuLV promoter was 2-3 micrograms/10(6) cells/day and was constant for more than 6 months. Furthermore, the production of a high producer clone, obtained by using dhfr gene coamplification, reached 30-40 micrograms/10(6) cells/day. Thus, Mo-MuLV promoter showed the desired characteristics for efficient expression of foreign genes in Namalwa KJM-1 cells.

A compilation of composite regulatory elements affecting gene transcription in vertebrates

Over the past years, evidence has been accumulating for a fundamental role of protein-protein interactions between transcription factors in gene-specific transcription regulation. Many of these interactions run within composite elements containing binding sites for several factors. We have selected 101 composite regulatory elements identified experimentally in the regulatory regions of 64 genes of vertebrates and of their viruses and briefly described them in a compilation. Of these, 82 composite elements are of the synergistic type and 19 of the antagonistic type. Within the synergistic type composite elements, transcription factors bind to the corresponding sites simultaneously, thus cooperatively activating transcription. The factors, binding to their target sites within antagonistic type composite elements, produce opposing effects on transcription. The nucleotide sequence and localization in the genes, the names and brief description of transcription factors, are provided for each composite element, including a representation of experimental data on its functioning. Most of the composite elements (3/4) fall between -250 bp and the transcription start site. The distance between the binding sites within the composite elements described varies from complete overlapping to 80 bp. The compilation of composite elements is presented in the database COMPEL which is electronically accessible by anonymous ftp via internet.

Transcobalamin II and the membrane receptor for the transcobalamin II-cobalamin complex

Transcobalamin II is a plasma protein that binds vitamin B12 (cobalamin) as it is absorbed in the terminal ileum and distributes it to tissues. The circulating transcobalamin II-cobalamin complex binds to receptors on the plasma membrane of tissue cells and is then internalized by receptor-mediated endocytosis. A number of genetic abnormalities are characterized either by a failure to express transcobalamin II or by synthesis of an abnormal protein. These disorders result in cellular cobalamin deficiency and megaloblastic anaemia. In this chapter we review the structural and functional properties of transcobalamin II, the receptor for the transcobalamin-cobalamin complex and the clinical disorders that are associated with perturbation of circulating transcobalamin II. In addition, we provide emerging data about the molecular genetics of transcobalamin II which has emanated from our own and other laboratories.

TATA-dependent enhancer stimulation of promoter activity in mice is developmentally acquired

Herpes simplex virus (HSV) thymidine kinase (tk) promoter activity depends on four transcription factor binding sites, one of which is a TATA box sequence, and the presence of either a cis-acting enhancer sequence or a transactivator protein. Studies presented here show that this TATA box was required for promoter activity only after cells began to differentiate and then only when promoter activity was stimulated by either an enhancer or a transactivator. When the HSV tk promoter was utilized by mouse embryos from the one-cell to eight-cell stage of development or by undifferentiated mouse embryonic stem cells, disruption of the HSV tk TATA box by site-specific mutations did not reduce promoter activity. This was true even when HSV tk promoter activity was stimulated strongly by either the embryo-responsive polyomavirus F101 enhancer or its natural transactivator, the HSV ICP4 gene product. However, stimulated expression was dependent on a distal Sp1 DNA binding site. Similarly, disruption of the TATA box did not reduce tk promoter activity in primary mouse embryonic fibroblasts or in immortalized 3T3 mouse fibroblasts; in fact, promoter activity was increased up to 2.6-fold. However, in these differentiated cells, stimulation of the HSV tk promoter by either the F101 enhancer or ICP4 protein required the TATA box. HSV tk promoter activity also was dependent on its TATA box in the mouse oocyte, a terminally differentiated cell with an endogenous transactivating activity. These results reveal that the need for a TATA box is developmentally acquired and depends on at least two parameters: the differentiated state of the cell and stimulation of the promoter by either an enhancer or a transactivator.

TATA-dependent enhancer stimulation of promoter activity in mice is developmentally acquired

Herpes simplex virus (HSV) thymidine kinase (tk) promoter activity depends on four transcription factor binding sites, one of which is a TATA box sequence, and the presence of either a cis-acting enhancer sequence or a transactivator protein. Studies presented here show that this TATA box was required for promoter activity only after cells began to differentiate and then only when promoter activity was stimulated by either an enhancer or a transactivator. When the HSV tk promoter was utilized by mouse embryos from the one-cell to eight-cell stage of development or by undifferentiated mouse embryonic stem cells, disruption of the HSV tk TATA box by site-specific mutations did not reduce promoter activity. This was true even when HSV tk promoter activity was stimulated strongly by either the embryo-responsive polyomavirus F101 enhancer or its natural transactivator, the HSV ICP4 gene product. However, stimulated expression was dependent on a distal Sp1 DNA binding site. Similarly, disruption of the TATA box did not reduce tk promoter activity in primary mouse embryonic fibroblasts or in immortalized 3T3 mouse fibroblasts; in fact, promoter activity was increased up to 2.6-fold. However, in these differentiated cells, stimulation of the HSV tk promoter by either the F101 enhancer or ICP4 protein required the TATA box. HSV tk promoter activity also was dependent on its TATA box in the mouse oocyte, a terminally differentiated cell with an endogenous transactivating activity. These results reveal that the need for a TATA box is developmentally acquired and depends on at least two parameters: the differentiated state of the cell and stimulation of the promoter by either an enhancer or a transactivator.

The silencer of mouse Pgk-2 consists of two discrete DNA elements that individually have no effect

Pgk-2 encodes a testis-specific phosphoglycerate kinase isozyme (PGK), and the expression of mouse Pgk-2 is activated during the spermatogenic pathway at the pachytene spermatocyte stage. We previously reported the identification of a silencer-like cis-acting element in a region between nucleotides (nt) -1404 and -685 of mouse Pgk-2, which could be responsible for the repression of Pgk-2 expression in somatic tissues and pre-meiotic testicular germ cells. In the present study, the silencer was precisely located within an 87-bp region between nt -882 and -796. This region contained two distinct sequences that individually bound factors present in nuclear extracts of mouse cultured cells and rat tissues. The two sequences, when aligned in tandem upstream from the Pgk-2 promoter, inhibited cat expression driven by the promoter in mouse erythroleukemia cells, whereas either sequence alone did not show any effect. The results indicate that the Pgk-2 silencer consists of two distinct DNA elements which do not individually influence promoter activity. Binding of distinct nuclear factors to each DNA element appeared to be required for the silencer action.

Mapping and positioning DNA-binding proteins along genomic DNA. Structure of D. melanogaster ribosomal 'Alu-repeats' and 1.688 satellite chromatin

Chromatin structure of so-called 'Alu-repeat' in D. melanogaster ribosomal non-transcribed spacer that contains sequences homologous to the promoter of ribosomal genes has been studied. Using the 'protein image' hybridization assay based on UV-light-induced DNA-protein crosslinking and 2-D gel retardation electrophoresis, two proteins of the molecular mass of 50 kD (rABP50) and 70 kD (rABP70), associated with 'Alu-repeat' DNA have been found. Exo III mapping of crosslinking sites and DNase I footprinting have provided a detailed map of H1, rABP50 and rABP70 contacts within the 'Alu-repeat' and H1 and a non-histone protein contacts on satellite DNA. These data indicate precise positioning of non-histone proteins, histone H1 and nucleosomes within genomic regions studied and account for the presence of unusual 240 bp long nucleosomal particles in 'Alu-repeats'. The same approach can be adapted for successive mapping and positioning proteins on genomic DNA.

Regulation of transcription in eukaryotes by DNA-binding proteins

1. The recognition of DNA by gene regulatory proteins is often mediated by structural motifs that comprise a protein DNA-binding domain. 2. Although binding of these proteins to DNA is not itself sufficient to affect transcription it is a necessary prerequisite. 3. This review summarizes recent studies that define structural motifs for DNA binding function of eukaryotic transcription factors.

Nuclear proteins from Capan-2 cell line form specific complexes with the 17-1A antigen gene promoter

To determine the location of sites important for the function of the 17-1A antigen gene promoter and to characterize the protein factors binding to these sites, fragments of the promoter region were analysed by gel retardation assay with nuclear extracts from Capan 2 cell line. At least two separate regions, which specifically bind nuclear proteins, were identified within the 5'flanking region of the 17-1A antigen gene. These regions have been located between nucleotides -877 to -518 (distal region) and -193 to +3 (proximal region) and presumably participate in regulation of expression of the 17-1A antigen gene.

Multiple cis-acting DNA elements that regulate transcription of the adenovirus 12 E1A gene

To delineate cis-acting elements for adenovirus (Ad) 12 E1A gene transcription, we transfected HeLa and NIH3T3 cells with DNAs having various deletions in the 5'-upstream region linked to the chloramphenicol acetyltransferase gene. Deletions in the regions between nucleotide (nt) positions 54 and 166, and 167 and 200, with respect to the left end of the viral genome at nt position 1, caused a two- to three-fold reduction in transcription. Transcription decreased to an almost undetectable level with loss of the region between nt positions 201 and 282. The effect of these mutations was almost consistent between both cell lines. The region between nt positions 77 and 94 stimulated transcription when situated upstream of the simian virus 40 early promoter in either orientation. Transcription was stimulated about ninefold in the presence of the DNA that encodes the product of the 13S, but not the 12S mRNA of the Ad12 E1A gene. These results indicate that transcription of the Ad12 E1A gene is regulated by multiple cis-acting elements and is stimulated by its own gene product.

The characterization of a mutation of the 3' flanking sequence of the alpha 1-antitrypsin gene commonly associated with chronic obstructive airways disease

A restriction fragment length polymorphism (RFLP) of the 3' flanking region of the alpha 1-antitrypsin (AAT) gene, detected with the restriction enzyme TaqI, occurs in about 17% of patients with chronic obstructive airways disease (COAD). To characterize the mutation the sequence of this region of the normal AAT gene had to be determined. The sequence containing the site of the mutation was amplified by the polymerase chain reaction and the DNA was sequenced in six COAD patients. The mutation is a G to A transition and occurs in a region containing potential regulatory sequences corresponding to enhancer elements. It is as yet unclear if the mutation alters the expression of AAT.

Complex interaction of yeast nuclear proteins with the enhancer/promoter region of SV40

Though highly complex enhancers found in animal cells have not been reported to occur in yeasts they are able to activate the transcription of adjacent genes in yeast cells. Saccharomyces cerevisiae expresses a large number of nuclear proteins that are able to recognize, and specifically bind to, the enhancer sequences of the SV40 animal tumor virus. The complexity of proteins that interact with different elements of the animal enhancers is similar in yeast and animal cell nuclear extracts. Most enhancer motifs, recognized by known trans-acting factors, are protected in footprinting experiments by yeast nuclear proteins.

A short 5' region of the long terminal repeat is required for regulation by hormone and heat shock of Drosophila retrotransposon 1731

1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or deleted Long Terminal Repeats (LTRs) of 1731, we were able to show that a short (28 bp) sequence located in the U3 region of these LTRs was required for 1) the increase in promoter strength, 2) negative regulation by 20-OH and, 3) positive regulation by heat shock.

Regulation of gene expression in preimplantation mouse embryos: effects of the zygotic clock and the first mitosis on promoter and enhancer activities

Previous studies have reported that promoters requiring enhancers for full activity in mammalian somatic cells also require enhancers when injected into mouse two-cell embryos, whereas the same promoters can be expressed just as efficiently in the absence of an enhancer when injected into arrested one-cell embryos. Experiments were designed to determine whether this phenomenon reflected normal developmental changes at the beginning of mammalian development, or simply differences in the physiological states of these cells under the experimental conditions employed. The activity of three different promoters that function in a wide variety of mammalian cells was measured both in embryos whose morphological development was arrested and in embryos that continued development in vitro. Expression of the injected gene was related to the onset of zygotic gene expression ("zygotic clock"), the phase of the cell proliferation cycle, the use of aphidicolin to arrest cell proliferation, and formation of two-cell embryos in vitro and in vivo. The results demonstrated that promoter activity was tightly linked to zygotic gene expression, while the need for enhancers to stimulate promoter activity depended only on formation of a two-cell embryo. These results further support the hypothesis that the first mitosis induces a general repression of promoters prior to initiation of zygotic gene expression that is relieved specifically by enhancers.

Quantitative electron microscopic analysis of DNA-protein interactions

Electron microscopy offers a unique potentiality to visualize individual molecules. For the last 30 years it has been used to study the structure and the interactions of various biological macromolecules. The contribution of electron microscopy is important because of its capacity to demonstrate the existence of conformational structures such as kinks, bents, loops, etc., either on naked DNA, or on DNA associated with various proteins or ligands. Increasing interest was given to such observations when it was found that they provide a direct visualization of interacting molecules involved in DNA metabolism and gene regulation. Technical advances in the preparation of the specimens, their observation in the electron microscope, and the image processing by computers have allowed the shifting from qualitative to quantitative analysis, as illustrated by a few examples from our laboratory.

A set of viral DNA decamers enriched in transcription control signals

We studied the frequency distribution of oligonucleotides 10 bp long in a sample of 620 Kb of viral genomes, containing 102 sequences from GenBank, with the aim of detecting transcription control signals. Two thousand three hundred decamers had a frequency 10 times higher than the mean and were subjected to further statistical analysis. For each of the 2300 decamers (parents), we counted the individual frequencies of the 30 decamers differing from the parent by one base mutation (progeny) and then calculated two variance/mean chi squares for the progeny, with and without the parent. We then studied the distribution of the ratio between the two chi squares. Out of 2300 decamers, 10 times more frequent than average, 479 decamers had a chi square ratio of 1.9 or larger. In this final set, which corresponds to less than 0.05% of all possible decamers, 58 decamers were found to contain viral and eukaryotic transcription control elements, like NF-kB, Sp1 and others. Furthermore, this set contains an excess of signals of length 5, 6, 7, 8, 9 and 10, when compared to 150 random sets, bootstrapped from the same viral genomes.

Cooperation between upstream and downstream elements of the adenovirus major late promoter for maximal late phase-specific transcription

Transcription from the adenovirus major late promoter (MLP) is greatly stimulated during lytic infection, after replication of the viral DNA has started. This replication-dependent activation has previously been shown to be mediated by a positive regulatory cellular protein(s). Binding of this factor(s) to sequence elements (DE1 and DE2), located between positions +76 and +124, with respect to the MLP transcriptional startsite, is detected only after the onset of DNA replication. Using a cell-free transcription system which mimics the late phase induction of the MLP and DNA binding assays, we now present evidence showing that maximal stimulation also depends on the MLP upstream element (UE), without involving increased DNA binding activity of the corresponding factor (UEF) during the lytic cycle. Our results indicate that the upstream and downstream elements act cooperatively on transcription efficiency, although no direct interactions between the cognate factors could be demonstrated. These observations strongly suggest that the elevated rate of transcription originating at the MLP startsite, late in infection, results from the simultaneous action of factors bound at the upstream and downstream elements onto a common target within the basal transcription machinery.

The transcription factor LF-A1 interacts with a bipartite recognition sequence in the promoter regions of several liver-specific genes

The transcription factors LF-A1 and LF-B1 are required for the cell-specific expression of the human alpha 1-antitrypsin gene in hepatocytes. We report here the purification and preliminary characterization of LF-A1. This protein, purified to homogeneity from calf liver nuclei by site-specific DNA affinity chromatography and reverse-phase HPLC, has a molecular mass of 40 kDa. Binding sites of LF-A1 are present in the promoter regions of several genes expressed in the liver (alpha 1-antitrypsin, apolipoproteins A1, B1, A4 and pyruvate kinase). Interestingly, the binding site of LF-A1 is bipartite and consists of two short sequence motifs (consensus: TGGACT/CT/C and TGGCCC) separated by a variable 'spacer' region. Insertion or deletion of 1-4 nucleotides in the 'spacer' region of the site in the alpha 1-antitrypsin promoter does not abolish DNA binding.

The combination of a novel stimulatory element in the first exon of the maize Shrunken-1 gene with the following intron 1 enhances reporter gene expression up to 1000-fold

Both exon 1 and intron 1 of the maize Shrunken-1 (Sh1) gene individually stimulate expression of reporter genes in transient gene expression experiments if present within the transcription unit. The Sh1 exon 1 mediates a 10-fold increase in activity when inserted at the 5' end of the bacterial chloramphenicol transacetylase (CAT) marker gene in both monocot and dicot protoplasts. The Sh1 intron 1 enhances chimeric gene expression in rice and maize protoplasts approximately 100-fold but inhibits CAT expression in tobacco protoplasts. In combination, the stimulatory effects of Sh1 exon 1 and intron 1 are multiplicative in monocot protoplasts resulting in a final enhancement of up to 1000-fold compared to the unmodified CAT or luciferase marker genes.

Multiple cis- and trans-acting elements involved in regulation of the neu gene

A 2.4-kb rat neu genomic DNA fragment that hybridized to the 5'-most coding sequence of the rat neu cDNA was cloned. S1 nuclease mapping identified multiple transcriptional initiation sites. DNA sequence analysis revealed that this fragment contained 64 bp of the first intron, 81 bp of the first exon, and the upstream noncoding sequence of the neu gene. The sequence immediately upstream of the translation start site was G + C rich (greater than 75%) and contained a consensus CCAAT sequence despite the absence of a TATA box. An Sp1-binding site was found, in addition to various sequence motifs common to the promoters of the human neu gene (erbB2), the epidermal growth factor receptor gene, and the simian virus 40 enhancer. A 2.2-kb EcoRI-Narl fragment containing sequences upstream from the 3'-most transcriptional start site was fused to the bacterial chloramphenicol acetyltransferase reporter gene and shown to promote transcription efficiently. A series of promoter deletion constructs was made, and results from transfection and subsequent chloramphenicol acetyltransferase assays suggested the presence of multiple cis-acting elements that contributed either positively or negatively to the transcription activity. Cotransfection competition experiments using subcloned cis-acting elements confirmed the existence of trans-acting factors interacting with these DNA fragments. In addition, a gel retardation assay was performed to demonstrate the physical binding of nuclear factors to certain fragments. The results complemented those of the deletion studies and led us to conclude that transcriptional regulation of the neu proto-oncogene involves at least one negative and three positive trans-acting factors interacting with different cis-acting elements along the neu gene promoter.

Multiple cis- and trans-acting elements involved in regulation of the neu gene

A 2.4-kb rat neu genomic DNA fragment that hybridized to the 5'-most coding sequence of the rat neu cDNA was cloned. S1 nuclease mapping identified multiple transcriptional initiation sites. DNA sequence analysis revealed that this fragment contained 64 bp of the first intron, 81 bp of the first exon, and the upstream noncoding sequence of the neu gene. The sequence immediately upstream of the translation start site was G + C rich (greater than 75%) and contained a consensus CCAAT sequence despite the absence of a TATA box. An Sp1-binding site was found, in addition to various sequence motifs common to the promoters of the human neu gene (erbB2), the epidermal growth factor receptor gene, and the simian virus 40 enhancer. A 2.2-kb EcoRI-Narl fragment containing sequences upstream from the 3'-most transcriptional start site was fused to the bacterial chloramphenicol acetyltransferase reporter gene and shown to promote transcription efficiently. A series of promoter deletion constructs was made, and results from transfection and subsequent chloramphenicol acetyltransferase assays suggested the presence of multiple cis-acting elements that contributed either positively or negatively to the transcription activity. Cotransfection competition experiments using subcloned cis-acting elements confirmed the existence of trans-acting factors interacting with these DNA fragments. In addition, a gel retardation assay was performed to demonstrate the physical binding of nuclear factors to certain fragments. The results complemented those of the deletion studies and led us to conclude that transcriptional regulation of the neu proto-oncogene involves at least one negative and three positive trans-acting factors interacting with different cis-acting elements along the neu gene promoter.

A comparison of BKV, JCV, and SV 40 transcriptional enhancers in primate cells. Application of the two-phase partition assay for chloramphenicol acetyl transferase (CAT)

The activities of the transcriptional enhancers of the prototype human polyomaviruses, BKV (Dun) and JCV (MAD-1), were compared with that of the rhesus virus SV 40 in Old World African green monkey kidney cells (CV-1) and in New World owl monkey kidney cells (OMK). Enhancer activities were tested in CAT-expression plasmids. CAT activity in transfected cell extracts were measured by the novel two-phase partition assay. The activities of the BKV and JCV enhancers were 45% and 20% that of SV 40, respectively, in CV-1 cells. The effectiveness of each viral enhancer was less in OMK cells than in CV-1 cells, as would be expected if the viruses co-evolved with their natural hosts. In CV-1 cells, the BKV enhancer was more active than that of JCV, but in OMK cells the reverse was true. This result is significant in view of the fact that JCV, but not BKV, is oncogenic in owl monkeys.

A sequence-specific DNA-binding factor (VF1) from Anabaena sp. strain PCC 7120 vegetative cells binds to three adjacent sites in the xisA upstream region

A DNA-binding factor (VF1) partially purified from Anabaena sp. strain PCC 7120 vegetative cell extracts by heparin-Sepharose chromatography was found to have affinity for the xisA upstream region. The xisA gene is required for excision of an 11-kilobase element from the nifD gene during heterocyst differentiation. Previous studies of the xisA upstream sequences demonstrated that deletion of this region is required for the expression of xisA from heterologous promoters in vegetative cells. Mobility shift assays with a labeled 250-base-pair fragment containing the binding sites revealed three distinct DNA-protein complexes. Competition experiments showed that VF1 also bound to the upstream sequences of the rbcL and glnA genes, but the rbcL and glnA fragments showed only single complexes in mobility shift assays. The upstream region of the nifH gene formed a weak complex with VF1. DNase footprinting and deletion analysis of the xisA binding site mapped the binding to a 66-base-pair region containing three repeats of the consensus recognition sequence ACATT.

Eukaryotic transcription factors

Many nuclear proteins have been found recently to interact with short conserved sequences which are involved in regulating the transcription of various genes. Nuclear transcription factors may be arbitrarily subdivided into two groups, ubiquitous and tissue-specific. The transcription of one gene is usually regulated by several factors which interact with different sequences located either in the promoter region of the gene or outside it. The appearance or disappearance of transcription factors for some genes corresponds to certain phases of cell differentiation or dedifferentiation and even to individual stages of the cell cycle.

A relational database of transcription factors

Recent advances in the understanding of eukaryotic gene regulation have produced an extensive body of transcriptionally-related sequence information in the biological literature, and have created a need for computing structures that organize and manage this information. The 'relational model' represents an approach that is finding increasing application in the design of biological databases. This report describes the compilation of information regarding eukaryotic transcription factors, the organization of this information into five tables, the computational applications of the resultant relational database that are of theoretical as well as experimental interest, and possible avenues of further development.

Binding of a liver-specific factor to the human albumin gene promoter and enhancer

A segment of 1,022 base pairs (bp) of the 5'-flanking region of the human albumin gene, fused to a reporter gene, directs hepatoma-specific transcription. Three functionally distinct regions have been defined by deletion analysis: (i) a negative element located between bp -673 and -486, (ii) an enhancer essential for efficient albumin transcription located between bp -486 and -221, and (iii) a promoter spanning a region highly conserved throughout evolution. Protein-binding studies have demonstrated that a liver trans-acting factor which interacts with the enhancer region is the well-characterized transcription factor LF-B1, which binds to promoters of several liver-specific genes. A synthetic oligodeoxynucleotide containing the LF-B1-binding site is sufficient to act as a tissue-specific transcriptional enhancer when placed in front of the albumin promoter. The fact that the same binding site functions in both an enhancer and a promoter suggests that these two elements influence the initiation of transcription through similar mechanisms.

Neuropeptide gene expression and neural activity: assessing a working hypothesis in nucleus caudalis and dorsal horn neurons expressing preproenkephalin and preprodynorphin

1. The working hypothesis that neuropeptide gene expression in a neuron is an indicator of that neuron's physiological activity is discussed. 2. Representative examples from the literature are presented to support the hypothesis. 3. Further, we discuss the regulation of expression of two opioid peptides, preproenkephalin and preprodynorphin, in laminae I and II of the spinal cord and in nucleus caudalis of the trigeminal nuclear complex, where they may play a role in pain modulation. 4. The expression of the opioid peptide genes can be induced by both painful and nonnoxious stimuli in neurons in time-dependent and sensory-specific fashions.

Binding of a liver-specific factor to the human albumin gene promoter and enhancer

A segment of 1,022 base pairs (bp) of the 5'-flanking region of the human albumin gene, fused to a reporter gene, directs hepatoma-specific transcription. Three functionally distinct regions have been defined by deletion analysis: (i) a negative element located between bp -673 and -486, (ii) an enhancer essential for efficient albumin transcription located between bp -486 and -221, and (iii) a promoter spanning a region highly conserved throughout evolution. Protein-binding studies have demonstrated that a liver trans-acting factor which interacts with the enhancer region is the well-characterized transcription factor LF-B1, which binds to promoters of several liver-specific genes. A synthetic oligodeoxynucleotide containing the LF-B1-binding site is sufficient to act as a tissue-specific transcriptional enhancer when placed in front of the albumin promoter. The fact that the same binding site functions in both an enhancer and a promoter suggests that these two elements influence the initiation of transcription through similar mechanisms.

Protein binding elements in the human beta-polymerase promoter

The core promoter for human DNA polymerase beta contains discrete binding sites for mammalian nuclear proteins, as revealed by DNasel footprinting and gel mobility shift assays. Two sites correspond to sequences identical with the Sp1 factor binding element, and a third site includes an eight residue palindromic sequence, TGACGTCA, known as the CRE element of several cAMP responsive promoters; the 5 to 10 residues flanking this palindrome on each side have no apparent sequence homology with known elements in other promoters. Nuclear extract from a variety of tissues and cells were examined; these included rat liver and testes and cultured cells of human and hamster origin. The DNasel footprint is strong over and around the palindromic element for each of the extracts and is equivalent in size (approximately 22 residues); footprinting over the Sp1 binding sites is seen also. Two potential tissue-specific binding sites, present in liver but not in testes, were found corresponding to residues -13 to -10 and +33 to +48, respectively. Protein binding to the palindromic element was confirmed by an electrophoretic mobility shift assay with the core promoter as probe. Binding specificity of the 22 residue palindromic element, as revealed by oligonucleotide competition, is different from that of AP-1 binding element. Controlled proteolysis with trypsin was used to study structural properties of proteins forming the mobility shift bands. Following digestion with trypsin, most of the palindrome binding activity of each extract corresponded to a sharp, faster migrating band, potentially representing a DNA binding domain of the palindrome binding protein.

Transcription switch of two phosphoglycerate kinase genes during spermatogenesis as determined with mouse testis sections in situ

In order to elucidate the mechanistic interpretations underlying differential expression of the two phosphoglycerate kinase (PGK) genes during mammalian spermatogenesis, localization of its mRNAs in mouse testis sections was determined by in situ hybridization. MRNA for nonsperm-type PGK-1 was identified in nongerminal Leydig and Sertoli cells, spermatogonia, and spermatocytes, but was not detected in spermatids. In contrast, mRNA for sperm-type PGK-2 was notable in leptotene spermatocytes, becoming most abundant in pachytene spermatocytes. It was amply present in spermatids only up to step 10, completely disappearing after step 12. It is possible to assume that a transcription switch of the two PGK genes ensued following the onset of meiosis. These findings taken together with previous observations indicate that differential expression of the two PGK genes during mammalian spermatogenesis is regulated at the transcriptional and post-transcriptional levels.

The ski oncogene induces muscle differentiation in quail embryo cells

Quail embryo cells (QECs) are primary cultures of fibroblastoid cells that become myogenic after infection with avian retroviruses expressing the ski oncogene (SKVs). ski also stimulates proliferation of QECs and induces morphological transformation and anchorage-independent growth. Paradoxically, ski-transformed clones picked from soft agar are capable of muscle differentiation. ski-induced differentiation is essentially indistinguishable from that of uninfected myoblasts in culture with regard to muscle-specific gene expression, commitment, and inhibition by growth factors or other oncogenes. However, ski-induced myoblasts have less stringent requirements for growth and differentiation. Uninfected QECs cannot differentiate and do not express an early marker for the myogenic lineage. Clonal analysis indicates that at least 40% of QECs are converted by ski to differentiating myoblasts. The data suggest that ski induces either the capacity for differentiation in an "incompetent" muscle precursor or the determination of nonmyogenic cells to the myogenic lineage.