Enhancer sequences and the regulation of gene transcription

Enhancer Function in the 3D Genome

In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A model of an activator chromatin compartment is substantiated, which provides the possibility of transferring activating factors from an enhancer to a promoter without establishing direct contact between these elements. The mechanisms of selective activation of individual promoters or promoter classes by enhancers are also discussed.

Transcription factor engineering in CHO cells for recombinant protein production

The continuous increase of approved biopharmaceutical products drives the development of more efficient recombinant protein expression systems. Chinese hamster ovary (CHO) cells are the mainstay for this purpose but have some drawbacks, such as low levels of expression. Several strategies have been applied to increase the productivity of CHO cells with different outcomes. Transcription factor (TF) engineering has emerged as an interesting and successful approach, as these proteins can act as master regulators; the expression and function of a TF can be controlled by small molecules, and it is possible to design tailored TFs and promoters with desired features. To date, the majority of studies have focused on the use of TFs with growth, metabolic, cell cycle or endoplasmic reticulum functions, although there is a trend to develop new, synthetic TFs. Moreover, new synthetic biological approaches are showing promising advances for the development of specific TFs, even with tailored ligand sensitivity. In this article, we summarize the strategies to increase recombinant protein expression by modulating and designing TFs and with advancements in synthetic biology. We also illustrate how this class of proteins can be used to develop more robust expression systems.

mRNA Transcriptomics of Galectins Unveils Heterogeneous Organization in Mouse and Human Brain

Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies.

Results: In order to fill this crucial gap in our understanding of brain galectins, we analyzed the in situ hybridization and microarray data of adult mouse and human brain respectively, from the Allen Brain Atlas, to resolve each galectin-subtype’s spatial distribution across brain distinct cytoarchitecture. Next, transcription factors (TFs) that may regulate galectins were identified using TRANSFAC software and the list obtained was further curated to sort TFs on their confirmed transcript expression in the adult brain. Galectin-TF cluster analysis, gene-ontology annotations and co-expression networks were then extrapolated to predict distinct functional relevance of each galectin in the neuronal processes. Data shows that galectins have highly heterogeneous expression within and across brain sub-structures and are predicted to be the crucial targets of brain enriched TFs. Lgals9 had maximal spatial distribution across mouse brain with inferred predominant roles in neurogenesis while LGALS1 was ubiquitously expressed in human. Limbic region associated with learning, memory and emotions and substantia nigra associated with motor movements showed strikingly high expression of LGALS1 and LGALS8 in human vs. mouse brain. The overall expression profile of galectin-8 was most preserved across both these species, however, galectin-9 showed maximal preservation only in the cerebral cortex.

Conclusion: It is for the first time that a comprehensive description of galectins’ mRNA expression profile in brain is presented. Results suggests that spatial transcriptome changes in galectins may contribute to differential brain functions and evolution across species that highlights galectins as novel signatures of brain heterogeneity and functions, which if disturbed, can promote several brain disorders.

Architectural and Functional Commonalities between Enhancers and Promoters

With the explosion of genome-wide studies of regulated transcription, it has become clear that traditional definitions of enhancers and promoters need to be revisited. These control elements can now be characterized in terms of their local and regional architecture, their regulatory components, including histone modifications and associated binding factors, and their functional contribution to transcription. This Review discusses unifying themes between promoters and enhancers in transcriptional regulatory mechanisms.

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.

High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics

Completion of the human and mouse genomes has inspired new initiatives to obtain a global understanding of the functional regulatory networks governing gene expression. Enhancers are primary regulatory DNA elements determining precise spatio- and temporal gene expression patterns, but the observation that they can function at any distance from the gene(s) they regulate has made their genome-wide characterization challenging. Since traditional, single reporter approaches would be unable to accomplish this enormous task, high throughput technologies for mapping chromatin features associated with enhancers have emerged as an effective surrogate for enhancer discovery. However, the last few years have witnessed the development of several new innovative approaches that can effectively screen for and discover enhancers based on their functional activation of transcription using massively parallel reporter systems. In addition to their application for genome annotation, these new high throughput functional approaches open new and exciting avenues for modeling gene regulatory networks.

Recruitment of transcription complexes to enhancers and the role of enhancer transcription

Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we provide an overview of enhancer function and discuss how transcription of enhancers or enhancer-generated transcripts could contribute to the regulation of gene expression during development and differentiation.

Development: lights, camera, action--the Drosophila embryo goes live!

Live imaging of developmental gene expression in Drosophila embryos opens up exciting new prospects for understanding gene regulation during development.

Enhancer dysfunction: how the main regulators of gene expression contribute to cancer

A genome-wide epigenetic analysis of enhancer elements in colon cancer has implicated distal gene regulatory DNA sequences in the establishment of an oncogenic transcriptional program.

Controlling the elongation phase of transcription with P-TEFb

The positive transcription elongation factor b (P-TEFb) is a cyclin-dependent kinase that controls the elongation phase of transcription by RNA polymerase II (RNAPII). This process is made possible by the reversal of effects of negative elongation factors that include NELF and DSIF. In complex organisms, elongation control is critical for the regulated expression of most genes. In those organisms, the function of P-TEFb is influenced negatively by HEXIM proteins and 7SK snRNA and positively by a variety of recruiting factors. Phylogenetic analyses of the components of the human elongation control machinery indicate that the number of mechanisms utilized to regulate P-TEFb function increased as organisms developed more complex developmental patterns.

Investigation of transcription factor AP-2 beta genotype in women with premenstrual dysphoric disorder

It has repeatedly been shown that the serotonergic system is involved in the symptomatology of premenstrual dysphoric disorder (PMDD). Women with PMDD are reported to differ from symptom-free controls with regard to serotonin-related biological markers. Evidence from family and twin studies suggests a genetic contribution to the aetiology of PMDD. The expression of human transcription factor AP-2beta in neural crest cell lineages and neuroectodermal cells suggests that this protein may be of importance for functional characteristics of neurons by regulating the expression of target genes. Within the monoaminergic systems, several genes have binding sites for AP-2beta in regulatory regions, suggesting an involvement of AP-2beta in these systems. The gene encoding AP-2beta is located on chromosome 6p12-p21.1 and includes a polymorphic region consisting of a variable number of [CAAA] repeats located in the second intron. We have earlier shown that AP-2beta genotype is associated with serotonergic phenotypes and that brainstem levels of AP-2beta correlate positively to serotonin metabolism in rat frontal cortex. The aim of this study was to investigate the relationship between PMDD and transcription factor AP-2beta genotype. The participants included 176 women with PMDD and 91 healthy controls. Genotyping was performed by polymerase chain reactions. We did not observe any differences in AP-2beta genotype frequencies between PMDD subjects and controls. Our results suggest that AP-2beta genotype is not a risk factor for PMDD. To our knowledge, this is the first study investigating transcription factor AP-2beta genotype in women with PMDD. Hence, these results should be considered preliminary until replicated.

Transcription initiation of the yeast IMD2 gene is abolished in response to nutrient limitation through a sequence in its coding region

The yeast IMD2 to IMD4 and GUA1 genes, involved in GMP synthesis, are highly expressed in exponentially growing cells but are shut off when cells cease to grow upon nutrient limitation. We show for the IMD2 gene that this effect is not specific to certain carbon sources or to growth rate. Strikingly, the cis elements responsible for this nutritional response are contained within a 23-nucleotide sequence in the coding region of the IMD2 gene. Despite its very unusual location, this regulatory sequence mediates the repression of transcription initiation. From our data, we conclude that GMP synthesis is downregulated upon nutrient limitation through an active mechanism. We show that this transcriptional shutoff abolishes any possibility of the induction of IMD2, even under drastic conditions of guanylic nucleotide limitation. Taken together, these results indicate that low levels of guanylic nucleotides could be required for proper entry into stationary phase.

Interaction between P-TEFb and the C-terminal domain of RNA polymerase II activates transcriptional elongation from sites upstream or downstream of target genes

Transcriptional elongation by RNA polymerase II (RNAPII) is regulated by the positive transcription elongation factor b (P-TEFb). P-TEFb is composed of Cdk9 and C-type cyclin T1 (CycT1), CycT2a, CycT2b, or CycK. The role of the C-terminal region of CycT1 and CycT2 remains unknown. In this report, we demonstrate that these sequences are essential for the activation of transcription by P-TEFb via DNA, i.e., when CycT1 is tethered upstream or downstream of promoters and coding sequences. A histidine-rich stretch, which is conserved between CycT1 and CycT2 in this region, bound the C-terminal domain of RNAPII. This binding was required for the subsequent expression of full-length transcripts from target genes. Thus, P-TEFb could mediate effects of enhancers on the elongation of transcription.

Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation

Analysis of physiological mechanisms that control transcription often requires extrapolation of in vitro measurements into in vivo mechanisms. This extrapolation is complex, as mammalian genes are commonly organized into broad chromosomal domains, and such domains cannot be readily reconstituted in vitro. Thus, the nucleoprotein structure of chromosomes constitutes a considerable impediment to elucidating transcriptional mechanisms. The development of assays to measure protein-DNA interactions and chromatin structure in living cells has greatly facilitated progress in understanding physiological transcriptional mechanisms. Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells, thereby providing a snapshot of the native chromatin structure and factors bound to genes in different functional states. ChIP involves treating cells or tissue briefly with formaldehyde to crosslink proteins to DNA. An antibody against a protein suspected of binding a given cis-element is then used to immunoprecipitate chromatin fragments. Polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element reveals whether a specific DNA sequence is recovered in an immune-specific manner and therefore whether the protein contacted the site in living cells. The central focus of this review is the use of ChIP to study transcriptional activation over long distances on chromosomes.

Use of Saccharomyces cerevisiae in the identification of novel transcription factor DNA binding specificities

Members of the steroid/hormone nuclear receptor superfamily regulate target gene transcription via recognition and association with specific cis-acting sequences of DNA, called hormone response elements (HREs). The identification of novel HREs is fundamental to understanding the physiological function of nuclear receptor-mediated signalling pathways. A number of these receptors are transcriptionally active, or can be induced to an active state, when expressed in the yeast strain Saccharomyces cerevisiae. This aspect of nuclear receptor activity was used to screen random rat genomic DNA fragments for their ability to function as a HRE for the farnesoid X-activated receptor (FXR). An isolated genomic fragment mediated FXR transcriptional activation without the co-expression of the retinoid-X receptor (RXR), a receptor previously thought to be an obligate heterodimer partner for FXR function. This genomic sequence of DNA contained a pair of highly conserved HRE half-sites arranged in an everted orientation and separated by 3 bp (ER3). Furthermore, it was located 240 bp from a highly conserved TATA box motif. A minimal ER3 sequence of DNA was further demonstrated to function as a FXR HRE and was bound in vitro by FXR-expressing yeast extracts. Using RT-PCR, an expressed mRNA fragment was identified within an 8 kb region downstream of the putative TATA box motif. This sequence of DNA was observed to bear homology to a cDNA found in mouse blastocyst. These findings define a novel FXR DNA binding specificity but, more importantly, these data suggest that this strategy might be universally applied to any transcription system that can be reconstituted in yeast.

[Genetics and molecular medicine in cardiology]

The discoveries on molecular aspects of cellular function are changing the concepts of health and disease. All medical fields, including cardiology, have been enriched with several diagnostic test to determine predisposition and to detect molecular dysfunctions. This review on the genetic and molecular aspects of cardiovascular diseases is written at the Centenary of the rediscovery of Mendel's principles on heredity and at the time of the announcement of the end of the human genome sequencing task. The review starts with considerations on the pluricellular constitution of the human body, and the principles of genetics with their molecular bases; including a short description of the methods for gene mapping. The following sections give a historic synopsis on the concepts of medical genetics, molecular medicine, and the Human Genome Project. The review ends with a brief description of the spectrum of genetic diseases, using examples of cardiovascular diseases.

A distal Schwann cell-specific enhancer mediates axonal regulation of the Oct-6 transcription factor during peripheral nerve development and regeneration

The POU domain transcription factor Oct-6 is a major regulator of Schwann cell differentiation and myelination. During nerve development and regeneration, expression of Oct-6 is under the control of axonal signals. Identification of the cis-acting elements necessary for Oct-6 gene regulation is an important step in deciphering the complex signalling between Schwann cells and axons governing myelination. Here we show that a fragment distal to the Oct-6 gene, containing two DNase I-hypersensitive sites, acts as the Oct-6 Schwann cell-specific enhancer (SCE). The SCE is sufficient to drive spatially and temporally correct expression, during both normal peripheral nerve development and regeneration. We further demonstrate that a tagged version of Oct-6, driven by the SCE, rescues the peripheral nerve phenotype of Oct-6-deficient mice. Thus, our isolation and characterization of the Oct-6 SCE provides the first description of a cis-acting genetic element that responds to converging signalling pathways to drive myelination in the peripheral nervous system.

Transcriptional regulation of the POU gene Oct-6 in Schwann cells

Genetic evidence suggests that the POU transcription factor Oct-6 plays a pivotal role as an intracellular regulator of Schwann cell differentiation. In the absence of Oct-6 function Schwann cells are generated in appropriate numbers and these cells differentiate normally up to the promyelin stage at which they transiently arrest. During peripheral nerve development Oct-6 expression is initiated in Schwann cell precursors and is strongly upregulated in promyelin cells. Oct-6 expression is subsequently extinguished in terminally differentiating Schwann cells. Thus, identification and characterisation of the DNA elements involved in this stage specific regulation may lead us to the signaling cascade and the axon-derived signals that drive Schwann cell differentiation and initiate myelination. Here we present experiments that aim at identifying such regulatory sequences.

Regulated expression of human angiotensinogen gene by hepatocyte nuclear factor 4 and chicken ovalbumin upstream promoter-transcription factor

We previously identified various upstream and downstream regulatory elements and factors important for hepatic expression of the human angiotensinogen (ANG) gene, the precursor of vasoactive octapeptide angiotensin II. In the present study, to further investigate the molecular mechanism of human ANG transcriptional regulation, we generated transgenic mice carrying the fusion gene composed of the 1. 3-kilobase promoter of the human ANG gene, its downstream enhancer, and the chloramphenicol acetyltransferase reporter gene. Because expression of the chloramphenicol acetyltransferase gene was observed strongly in the liver and weakly in the kidney, we suspected that hepatocyte nuclear factor (HNF) 4 with a tissue expression pattern similar to that of the reporter gene would regulate ANG transcription. In vitro assays indicated that HNF4 bound to the promoter elements and strongly activated the ANG transcription, but that chicken ovalbumin upstream promoter transcription factor (COUP-TF), a transcriptional repressor, dramatically repressed human ANG transcription through the promoter elements and the downstream enhancer core elements. Furthermore, COUP-TF dramatically decreased the human ANG transcription in the mouse liver by the Helios Gene Gun system in vivo. These results suggest that an interplay between HNF4 and COUP-TF could be important in hepatic human ANG transcription.

An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis

The rocG gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by SigL (sigma(54))-containing RNA polymerase and requires for its expression RocR, a member of the NtrC/NifA family of proteins that bind to enhancer-like elements, called upstream activating sequences (UAS). Unlike the case for other sigma(54)-dependent genes, rocG has no UAS; instead, its expression depends on a sequence located 1.5 kilobases downstream of the rocG promoter, beyond the end of the rocG coding region. The same sequence also serves as the UAS for the downstream rocABC operon and can activate rocG if moved upstream of its promoter. Furthermore, the activating sequence can be moved as far as 15 kilobases downstream of the rocG promoter and still retain partial activity.

The yeast Cryptococcus neoformans uses 'mammalian' enhancer sites in the regulation of the virulence gene, CNLAC1

Transcriptional regulation in mammalian and plant cells is distinguished from fungi by the presence of blocks of multiple interacting DNA binding sites distributed over a relatively large upstream region of genes and the ability to use glutamine-rich enhancers such as Sp1. We offer evidence that the haploid yeast Cryptococcus neoformans contains a virulence gene, CNLAC1, having regulatory properties more similar to mammalian systems than to that of yeast. We used a novel promoter plasmid, pVEW, and electromobility shift assay techniques adapted for the fungus for the first systematic structural and functional study of a 5'-enhancer region of a basidiomycete fungus using the upstream region of CNLAC1. Two groups of interactive enhancer regions, located over a range of 1.5kb from the mRNA start site are involved in CNLAC1 regulation (region 2: -1721 to -1615 and region 7) in addition to a TATA promoter at position -539. Region 2 contains a consensus Sp1 site and region 7 contains a consensus E2F site, each of which shows significant binding to nuclear proteins under derepressed conditions; cooperative binding was also suggested between DNA-binding protein of these sites and those binding nearby CCAAT sequences in each region. Two regions of repression were also evident under derepressed conditions (region 5: -1351 to -1207 and region 8: -991 to -971). Identification of functional Sp1 binding sites and the presence of multiple interactive enhancer sites over a fairly large upstream range suggests that cryptococcal transcriptional regulation contains features often associated with higher eukaryotic regulation. C. neoformans thus may provide a unique system for the study of certain aspects of higher eukaryotic transcription, using yeast genetic approaches. In addition, properties of basidiomycete yeast such as Cryptococcus exemplified in the present study suggest an evolutionary progression in gene regulation within fungi toward properties exhibited in the kingdoms Animalia and Plantae.

An enhancer region within the copia untranslated leader contains binding sites for Drosophila regulatory proteins

The untranslated leader region (ULR) of the Drosophila LTR retrotransposon copia is known to be critical to the element's expression in a variety of species. Two copia ULR size variants are prevalent in natural populations. The more transcriptionally active full length variants contain within their ULRs two tandemly repeated copies of a 28-bp region of dyad symmetry with a sequence similarity to the core sequence of the SV40 enhancer. The region of dyad symmetry contains two inverted repeats of a 8-bp motif (TTGTGAAA) that occurs at three additional locations within the ULR. The less active ULR gap variants differ from full length variants in that they contain only one copy of the 28-bp sequence. We show that the full length copia ULR in either orientation but not the gap ULR can significantly enhance expression of a minimal hsp 70 promoter. We demonstrate by EMSA that the full length ULR, the gap ULR and the 28-bp sequence are each capable of binding the Drosophila CCAAT/enhancer binding protein (DmC/EBP) and another previously uncharacterized factor, copia binding factor-1 (CBF-1). Another Drosophila protein previously implicated in fat body specific expression of the alcohol dehydrogenase gene (Adh), the Box-B-binding factor-2 (BBF-2), is also shown to bind to the copia ULR.

Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation

Significant differences in levels of copia [Drosophila long terminal repeat (LTR) retrotransposon] expression exist among six species representing the Drosophila melanogaster species complex (D. melanogaster, Drosophila mauritiana, Drosophila simulans, Drosophila sechellia, Drosophila yakuba, and Drosophila erecta) and a more distantly related species (Drosophila willistoni). These differences in expression are correlated with major size variation mapping to putative regulatory regions of the copia 5' LTR and adjacent untranslated leader region (ULR). Sequence analysis indicates that these size variants were derived from a series of regional duplication events. The ability of the copia LTR-ULR size variants to drive expression of a bacterial chloramphenicol acetyltransferase reporter gene was tested in each of the seven species. The results indicate that both element-encoded (cis) and host-genome-encoded (trans) genetic differences are responsible for the variability in copia expression within and between Drosophila species. This finding indicates that models purporting to explain the dynamics and distribution of retrotransposons in natural populations must consider the potential impact of both element-encoded and host-genome-encoded regulatory variation to be valid. We propose that interelement selection among retrotransposons may provide a molecular drive mechanism for the evolution of eukaryotic enhancers which can be subsequently distributed throughout the genome by retrotransposition.

Neuron-specific gene expression of synapsin I. Major role of a negative regulatory mechanism

The synapsins are a family of neuron-specific phosphoproteins that selectively bind to small synaptic vesicles in the presynaptic nerve terminal. The human synapsin I gene was functionally analyzed to identify control elements directing the neuron-specific expression of synapsin I. By directly measuring the mRNA transcripts of a reporter gene, we demonstrate that the proximal region of the synapsin I promoter is sufficient for directing neuron-specific gene expression. This proximal region is highly conserved between mouse and human. Deletion of a putative binding site for the zinc finger protein, neuron-restrictive silencer factor/RE-1 silencing transcription factor (NRSF/REST), abolished neuron-specific expression of the reporter gene almost entirely, allowing constitutively acting elements of the promoter to direct expression in a non-tissue-specific manner. These constitutive transcriptional elements are present as a bipartite enhancer, consisting of the region upstream (nucleotides -422 to -235) and downstream (nucleotides -199 to -143) of the putative NRSF/REST-binding site. The latter contains a motif identical to the cAMP response element. Both regions are not active or are only weakly active in promoting transcription on their own and show no tissue-specific preference. From these data we conclude that neuron-specific expression of synapsin I is accomplished by a negative regulatory mechanism via the NRSF/REST binding motif.

Interactions between the regulatory regions of two Adh alleles

A region (NS1) that acts like an enhancer is located approximately 300 bp upstream of the larval cap site in the Adh gene of D. melanogaster. When this sequence is deleted (delta NS1), the gene fails to express ADH protein. Gene expression can be restored by placing a second Adh gene with an intact enhancer elsewhere on the same plasmid. In these circumstances, both genes are expressed equally regardless of their orientation on the plasmid. In this report we further characterize the interactions that occur when a single enhancer activates expression from a proximal and distant promoter. We have made the following observations: (1) While the two genes are expressed equivalently, their expression relative to a plasmid carrying two intact genes is reduced by a factor of 2 to 6 depending on the orientation of the two genes. (2) The single enhancer drives expression of both genes on any given plasmid molecule. (3) The enhancer does not interact with the Adh gene from which the NS7 region (which spans the larval TATA box) is removed. (4) Expression of the delta NS1 gene can be restored by an intact gene when both are inserted together into the Drosophila genome via P element-mediated transformation. (5) Increasing the separation between the two genes on a plasmid by up to 15 kbp does not prevent the restoration of expression of the delta NS1 gene. We propose a model that explains how a single enhancer can stimulate equal expression from two genes.

[Leu5]enkephalin-encoding sequences are targets for a specific DNA-binding factor

A DNA-binding factor with high affinity and specificity for the [Leu5]enkephalin-encoding sequences in the prodynorphin and proenkephalin genes has been characterized. The factor has the highest affinity for the [Leu5]-enkephalin-encoding sequence in the dynorphin B-encoding region of the prodynorphin gene, has relatively high affinity for other [Leu5]enkephalin-encoding sequences in the prodynorphin and proenkephalin genes, but has no apparent affinity for similar DNA sequences coding for [Met5]-enkephalin in the prodynorphin or proopiomelanocortin genes. The factor has been named [Leu5]enkephalin-encoding sequence DNA-binding factor (LEF). LEF has a nuclear localization and is composed of three subunits of about 60, 70, and 95 kDa, respectively. The highest levels were observed in rat testis, cerebellum, and spleen and were generally higher in late embryonal compared to newborn or adult animals. LEF activity was also recorded in human clonal tumor cell lines. LEF inhibited the transcription of reporter genes in artificial gene constructs where a [Leu5]enkephalin-encoding DNA fragment had been inserted between the transcription initiation site and the coding region of the reporter genes. These observations suggest that the [Leu5]enkephalin-encoding sequences in the prodynorphin and proenkephalin genes also have regulatory functions realized through interaction with a specific DNA-binding factor.

Binding of the transcription activator NRI (NTRC) to a supercoiled DNA segment imitates association with the natural enhancer: an electron microscopic investigation

Electron microscopic visualization indicates that the transcription activator NRI (NTRC) binds with exceptional selectivity and efficiency to a sequence-induced superhelical (spiral) segment inserted upstream of the glnA promoter, accounting for its observed ability to substitute for the natural glnA enhancer. The cooperative binding of NRI to the spiral insert leads to protein oligomerization which, at higher concentration, promotes selective coating of the entire superhelical segment with protein. Localization of NRI at apical loops is observed with negatively supercoiled plasmid DNA. With a linear plasmid, bending of DNA is observed. We confirm that NRI is a DNA-bending protein, consistent with its high affinity for spiral DNA. These results prove that spiral DNA without any homology to the NRI-binding sequence site can substitute for the glnA enhancer by promoting cooperative activator binding to DNA and facilitating protein oligomerization. Similar mechanisms might apply to other prokaryotic and eukaryotic activator proteins that share the ability to bend DNA and act efficiently as multimers.

Modulator factor-binding sequence of the sea urchin early histone H2A promoter acts as an enhancer element

The sea urchin early H2A histone gene, like the other four members of the repeating units, is transiently expressed during very early development. To investigate the mechanisms underlying the faithful expression of the early H2A gene, we focused our attention on the modulator element. We showed by DNase I cleavage protection patterns that the modulator includes the upstream sequence element 1 (USE1) and mapped at nucleotides -137 to -108 in the early H2A gene promoter. Functional tests conducted by microinjection into sea urchin embryos then showed that the modulator element binds the transcriptional factor called modulator-binding factor 1 (MBF-1). We found in fact that coinjection of an excess of the MBF-1-binding site, either as the modulator or as the USE1, efficiently impaired the activity of the H2A promoter. An unexpected finding was the expression of the reporter gene from the early H2A promoter at the gastrula stage of embryonic development, when the early histone genes are transcriptionally silent. In addition, we also found that the modulator element was active at the gastrula stage. The potential enhancer activity of the modulator was tested by microinjecting several constructs containing single or multiple copies of the modulator element placed 5' or 3' to a thymidine kinase gene (tk) promoter in both sea urchin embryos and Xenopus laevis oocytes and determining the expression of a reporter chloramphenicol acetyltransferase gene under the control of the linked tk promoter. We found that an oligonucleotide bearing the MBF-1-binding site activates the expression of the reporter gene independently of the position and orientation. We conclude that the modulator binds the MBF-1 activator and that it is a transcriptional enhancer of the early H2A histone gene.

Complex functional interactions at the early enhancer of the PQ strain of BK virus

BK virus is a human papovavirus that latently infects a majority of the world's population. There are more than 30 strains of the virus, most of which differ in the structure of the early enhancer region. The enhancer of the progenitor strain, WW, from which the other strains can be derived, consists of four conserved DNA domains, P, Q, R, and S. Rearrangement of the enhancer occurs upon passage in tissue culture and is thought to occur during virus replication. The strain under study, PQ, was selected upon passage of the Gardner strain (PPPQS) in the permissive cell line, Vero. Mutational analysis of the entire enhancer region demonstrates the importance of five cis-acting sequences: DNA sites B, C, and F, which have homology to the NF-1 protein binding sequence; one purine-rich motif designated A; and site D, which is similar to an SP-1 protein binding site. Two sites, B and C, appear to have a negative influence on gene activity. To study the functional interactions in more detail, promoter-enhancer constructions that contain different combinations of the five DNA sites linked to the chloramphenicol acetyltransferase gene were tested for early gene activity. The results reveal that the proteins binding to the enhancer functionally cooperate with each other. The effects of making mutations at the DNA sites are very similar to the effects of using excess enhancer DNA sequences to titrate the proteins that bind to the cis-acting DNA sites (in vivo competition). Moreover, the effects of changing the spacing between the DNA sites also demonstrate that there are cooperative interactions among the proteins that bind to the PQ strain enhancer. DNA sites B, C, and F are clearly protected from DNase I digestion by Vero cell nuclear proteins. In addition, mutation of each DNA site alters its sensitivity to DNase I in the presence of Vero cell proteins. Interestingly, mutation of site B affects protein binding to site B as well as to sites A, C, D, and F. These results suggest that cooperative functional and physical interactions occur at the early enhancer of the PQ strain.

Liver-specific DNase I-hypersensitive sites and DNA methylation pattern in the promoter region of a 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene

The mRNA for the liver isozyme of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase is transcribed from the L promoter of gene A. We show here that L-promoter activity is tissue specific. To identify on the gene in situ potential cis-acting sequences, we have examined 15 kb of its 5' region for DNase I-hypersensitive sites detectable on chromatin. We have also evaluated the DNA methylation status of the 3.7-kb encompassing the L promoter. Five DNase I-hypersensitive sites were detected on liver chromatin, three upstream (M1 at position -4500, L2 at position -1000, L1 at position -200) and two downstream (I1 at position +3000, I2 at position +3500) from the L-type mRNA transcription initiation site. Their presence correlated with transcriptional activity as they were not observed on chromatin from kidney, a tissue where gene A is not expressed. Sites M1 and L1 corresponded to the M and L promoters, respectively, providing in vivo evidence for a promoter localization obtained earlier with cloned DNA only. Site I2 coincided with a glucocorticoid-responsive unit described by others, but its presence did not depend on glucocorticoids. Thus, sites L2 and I1 could correspond to novel control elements. While DNA was methylated around position -2000 both in liver and kidney, downstream from that position it was fully demethylated in liver but not in kidney. This pattern changed during development of fetal liver. The data suggest mechanisms for the lack of activity of the L promoter in kidney and for its activation in developing and adult liver.

An upstream promoter element of the Acanthamoeba castellanii TBP gene binds a DNA sequence specific transcription activating protein, TPBF

We have characterized a positive-acting element in the upstream portion of the Acanthamoeba TBP gene promoter. The 27 bp element (TPE), located within the promoter between -97 and -70, stimulates transcription in an orientation independent fashion and tolerates modest changes in its distance from the TATA box. The TPE does not, however, function synergistically nor when positioned 3000 bp 5' or 260 base pairs 3' of the transcription start site. The TPE binds a DNA sequence-dependent factor, TPBF, which we have partly purified. TPBF was characterized using in vitro transcription, DNase I footprinting, methylation interference and electrophoretic mobility shift assays. TPBF does not have a counterpart in HeLa cells, but nonetheless strongly stimulates transcription of the Acanthamoeba TBP gene in mammalian extracts. Our results also suggest that there are additional positively and negatively acting elements within the TBP gene promoter, for which a model is presented.

Enhancer-like activity of A1gR1-binding site in alginate gene activation: positional, orientational, and sequence specificity

Significant activation of promoters of alginate genes such as algD or algC occurs in mucoid Pseudomonas aeruginosa during its proliferation in the lungs of cystic fibrosis patients. These promoters have been shown to be responsive to environmental signals such as high osmolarity. The signaling is mediated by a so-called two-component signal transduction system, in which a soluble protein, AlgR2, undergoes autophosphorylation and transfers the phosphate to a DNA-binding response regulator protein, AlgR1. The phosphorylated form of AlgR1 has a high affinity for binding at upstream sequences of both the algC and algD promoters. Two AlgR1-binding sites (ABS) have been reported upstream of the algC gene. One of the two ABSs (algC-ABS1, located at -94 to -81) is critical for the algC activation process, while the second ABS (algC-ABS2, located at +161 to +174) is only weakly active. We now report the presence of a third ABS within the structural gene of algC, and this ABS (algC-ABS3) is also important for algC promoter activation. algC-ABS1 can be replaced functionally by algC-ABS2, algD-ABS1, or algD-ABS2 and somewhat weakly by algD-ABS3. Introduction of a half-integral turn in the DNA helix between the algC site of transcription initiation and algC-ABS1 allowed only slight reduction of promoter activity, suggesting that the binding site could be appreciably functional even when present in the opposite face of the helix. Activation of the algC promoter is independent of the relative location (upstream or downstream of the mRNA start site), the number of copies, or the orientation of algC-ABS1, suggesting that it behaves like a eukaryotic enhancer element in promoting transcription from the algC promoter.

Comparison of IL-1 alpha effectiveness in activating murine pre-B and T cell lines

Interleukin-1 (IL-1) is a potent agent that induces a wide range of biological effects. The action of IL-1 is mediated by surface IL-1 receptors (IL-1R). Two types of IL-1 receptors have been identified in lymphocytes. In this study we examined activity of IL-1 alpha in two murine lymphocyte lines that express different types of IL-1 receptors. The T lymphoid cell line EL-4 6.1 C10 expresses type I IL-1R that mediates IL-1 alpha-induced IL-2 gene expression and secretion of IL-2. The pre-B lymphoid cell line 70Z/3 was previously shown to express type II IL-1R and responds to IL-1 alpha by expressing immunoglobulin kappa light chain mRNA and increased levels of surface IgM. We found that IL-1 alpha was as potent in inducing IgM expression in 70Z/3 cells as it was in inducing IL-2 secretion in EL-4 6.1 C10 cells. Likewise, the IL-1 alpha concentration sufficient to trigger kappa light chain gene expression in 70Z/3 cells was similar to the concentration of IL-1 alpha sufficient to trigger IL-2 gene expression in EL-4 6.1 C10. In both cell lines, IL-1 alpha activated NF-kappa B-like DNA-binding activity but in EL-4 6.1 C10 cells the IL-1 alpha concentration sufficient to induce NF-kappa B response was 1000-fold lower than in 70Z/3 cells. Monoclonal antibody, mAb M15, to the type I IL-1R blocked IL-1-induced responses in EL-4 6.1 C10 cells. Surprisingly mAb M15 also blocked IL-1 action in 70Z/3 cells, even though these cells predominantly express type II IL-1R. 15% of the total IL-1 binding sites in 70Z/3 cells were recognized by mAb M15. Human IL-1 receptor antagonist (IL-1ra), which binds to the natural murine type I but not the type II IL-1R, blocked IL-1 alpha responses in EL-4 6.1 C10 and 70Z/3 cells. Although at low levels, Northern blot analysis confirmed that 70Z/3 cells express low levels of type I IL-1R mRNA. Taken together, these results suggest that type I IL-1R are expressed and transduce IL-1 signals in both 70Z/3 and El-4 6.1 C10 cells.

Partial characterization of a novel 'GGA' factor which binds to the osteonectin promoter in bovine bone cells

Osteonectin (On)/SPARC (secreted protein, acidic and rich in cysteine) is a highly conserved extracellular matrix protein found in bone and other tissues throughout vertebrate evolution. In previous studies, approximately 500 bp of DNA 5' to the transcription start point (tsp) and a part of exon 1, including homopurine (Rn)/homopyrimidine (Yn)-rich sequences (the 'GGA box' and its complements), was demonstrated to be important in upregulation of On gene expression in a cell-specific manner. The purpose of this study was to decipher the transcriptional regulation of On through its cis- and trans-acting elements. DNase I footprinting analysis indicated protein binding which may be related to the transcriptional factors, AP2, SP1 and a novel 'GGA' factor which binds to the 3' end of the promoter (-286 to +43 to the tsp). Comparisons of footprinting between nuclear extracts of bone (On-expressing) cells and Madin and Darby bovine kidney (MDBK) (nonexpressing) cells indicate that 'GGA' factor binding to a purine GGGGA/GGA-rich sequence is cell-type specific and therefore may be involved in the cell-specific expression of this gene. From ultraviolet (UV)-crosslinking experiments, this 'GGA' factor was demonstrated to be a single 40-kDa protein.

A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila

We have characterized an element near the 5' boundary of the chicken beta-globin domain that insulates a reporter gene from the activating effects of a nearby beta-globin locus control region (5'HS2) when assayed in the human erythroid cell line K562. We show that the insulation mechanism is directional, that it operates at the level of transcription, and that it involves the alteration of chromatin structure over the promoter of the gene. The insulator has no significant stimulatory or inhibitory effects of its own. In transgenic Drosophila, the insulator protects the white minigene from position effects. The action of the insulator thus is not restricted to erythroid or mammalian cells, suggesting that such elements may serve an important and widely distributed function in the organization of chromatin structure.

Regulatory elements of the human proopiomelanocortin gene promoter

Proopiomelanocortin (POMC) is expressed predominantly in the corticotrophic cells of the pituitary. Regulatory sequences required for the expression of the human (h) POMC gene were investigated using transient expression of hPOMC-CAT fusion genes in pituitary and nonpituitary cells in combination with DNase I footprint and gel retardation assays. Gene transfer experiments revealed that the hPOMC promoter is more efficiently transcribed in AtT-20 pituitary cells than in HeLa cells. Using deletion analysis, negative regulatory elements between nucleotides -676 and -414 and positive regulatory elements between nucleotides -414 and -93 could be identified. When placed in front of the heterologous thymidine kinase (tk) promoter, nucleotides -414/-223 enhance transcription in AtT-20 cells and in primary cultures of human pituitary tumor cells, but not in various nonpituitary cell lines. In contrast, a -112/-93 element enhances transcription of the tk promoter in all cells tested. DNase I footprint analysis revealed five sites protected by nuclear extracts obtained from AtT-20 cells within nucleotides -414 and -83 of the hPOMC promoter region. In contrast, only one of these sites (between nucleotides -115 and -83) was protected by nuclear extracts from HeLa cells. Gel mobility-shift experiments revealed that an oligonucleotide comprising nucleotides -112/-93 binds a novel nuclear protein. This protein may contribute to the non-cell type-specific expression of the hPOMC gene outside the pituitary, whereas at least five transcription factors seem to be required for high basal transcription of the gene in corticotrophic cells.

Identification of the initiation region of DNA replication in the murine immunoglobulin heavy chain gene and possible function of the octamer motif as a putative DNA replication origin in mammalian cells

An origin region of DNA replication in the murine immunoglobulin heavy chain (IgH) gene was identified by BrdU pulse labeling and PCR amplification methods. The origin region spans about 1000 base pairs and contains the region of transcriptional enhancer in which the octamer sequence is present. The octamer sequence, TNATTTGCAT, is a well-conserved promoter/enhancer element responsible for B cell-specific transcription and is also found in the regulatory sequences for histone genes and others. Its activity as an autonomously replicating sequence was further examined. The murine IgH enhancer region containing the octamer motif was cloned in pUC18 and transfected to HeLa cells. After 60-65 h, the low molecular weight DNA was extracted and the degree to which the plasmid DNA had been replicated in the cells was measured by back-transformation of competent bacteria. Five to ten copies of the plasmid were detected per cell. The replicated plasmid-form DNA could be detected by this assay for at least 7 days after transfection. Synthetic oligonucleotides corresponding to the octamer and the Ephrussi box in the IgH enhancer were also cloned into pUC18 and examined for replicating activity. These plasmids replicated provided that the octamer sequence remained intact, irrespective of the Ephrussi box sequence and of the sites of insertion. These results suggest that the octamer transcriptional element may also serve as a putative origin for cellular DNA replication.

Structural analysis of the regulatory elements of the type-II procollagen gene. Conservation of promoter and first intron sequences between human and mouse

Transcription of the type-II procollagen gene (COL2A1) is very specifically restricted to a limited number of tissues, particularly cartilages. In order to identify transcription-control motifs we have sequenced the promoter region and the first intron of the human and mouse COL2A1 genes. With the assumption that these motifs should be well conserved during evolution, we have searched for potential elements important for the tissue-specific transcription of the COL2A1 gene by aligning the two sequences with each other and with the available rat type-II procollagen sequence for the promoter. With this approach we could identify specific evolutionarily well-conserved motifs in the promoter area. On the other hand, several suggested regulatory elements in the promoter region did not show evolutionary conservation. In the middle of the first intron we found a cluster of well-conserved transcription-control elements and we conclude that these conserved motifs most probably possess a significant function in the control of the tissue-specific transcription of the COL2A1 gene. We also describe locations of additional, highly conserved nucleotide stretches, which are good candidate regions in the search for binding sites of yet-uncharacterized cartilage-specific transcription regulators of the COL2A1 gene.

The -6.1-kilobase chicken lysozyme enhancer is a multifactorial complex containing several cell-type-specific elements

In the chromatin domain of the chicken lysozyme gene of myeloid and oviduct cells, which both have the potential to activate the gene, a developmentally stable DNase I-hypersensitive site is formed around 6.1 kb upstream of the gene. This implies that this DNA region, which has previously been demonstrated to function as a transcriptional enhancer element in myeloid cells, is intimately involved in the cell-type-specific activation of the lysozyme gene locus. Deletion analysis identifies a 157-bp minimal fragment that confers the same promacrophage-specific enhancer activity as the originally described 562-bp -6.1-kb enhancer fragment. By introducing specific point mutations, we demonstrate in transient gene transfer experiments that the minimal fragment consists of at least six adjacent elements, each substantially contributing to enhancer function. The compact multifactorial enhancer complex includes a nuclear factor I (NF-I)/TGGCA binding site, homologies to AP1, and octanucleotide or enhancer core consensus motifs. Point mutation of the NF-I binding site results in the loss of NF-I binding in vitro and enhancer activity in vivo after gene transfer. Surprisingly, four overlapping oligonucleotides, each consisting of at least two elements of the -6.1-kb enhancer, confer myeloid-cell-specific enhancer activity. We found several myeloid-cell-specific DNA-binding proteins interacting with the -6.1-kb enhancer, a result consistent with that described above. Therefore, we suggest that more than a single trans-acting factor mediates the cell type specificity of the -6.1-kb enhancer.