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PubMed1998

Identification of trophoblast-specific regulatory elements in the mouse placental lactogen II gene.

Placental lactogen II, the major ligand for the PRL receptor during the second half of gestation in rodents, is synthesized specifically by placental trophoblast giant cells. A transient transgenic analysis has been used to localize the giant cell-specific regulatory region within the mouse placental lactogen II gene to sequences between -1340 and -2019 upstream of the transcriptional start site. More precise mapping of the regulatory elements has been accomplished by transfection of promoter constructs into Rcho-1 trophoblast cells, resulting in the characterization of two positive regulatory elements in the -1471 to -1340 region; two other regulatory elements have been implicated but not further characterized, a negative regulatory element between -2019 and -1778 and another positive element within the region from -1340 to -569. Both of the characterized positive regulatory elements are recognized by factors that are enriched in differentiated giant cells compared with proliferative trophoblasts, and these factors are either absent or at low levels in fibroblasts. The complexes that form on the two elements are distinct and neither element competes with the other for factor binding, thus implicating at least two different regulatory elements in late-gestational trophoblast giant cell-specific gene expression.

Animals↗

PubMed2006

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

BACKGROUND: A complete understanding of the regulatory mechanisms of gene expression is the next important issue of genomics. Many bioinformaticians have developed methods and algorithms for predicting transcriptional regulatory mechanisms from sequence, gene expression, and binding data. However, most of these studies involved the use of yeast which has much simpler regulatory networks than human and has many genome wide binding data and gene expression data under diverse conditions. Studies of genome wide transcriptional networks of human genomes currently lag behind those of yeast. RESULTS: We report herein a new method that combines gene expression data analysis with promoter analysis to infer transcriptional regulatory elements of human genes. The Z scores from the application of gene set analysis with gene sets of transcription factor binding sites (TFBSs) were successfully used to represent the activity of TFBSs in a given microarray data set. A significant correlation between the Z scores of gene sets of TFBSs and individual genes across multiple conditions permitted successful identification of many known human transcriptional regulatory elements of genes as well as the prediction of numerous putative TFBSs of many genes which will constitute a good starting point for further experiments. Using Z scores of gene sets of TFBSs produced better predictions than the use of mRNA levels of a transcription factor itself, suggesting that the Z scores of gene sets of TFBSs better represent diverse mechanisms for changing the activity of transcription factors in the cell. In addition, cis-regulatory modules, combinations of co-acting TFBSs, were readily identified by our analysis. CONCLUSION: By a strategic combination of gene set level analysis of gene expression data sets and promoter analysis, we were able to identify and predict many transcriptional regulatory elements of human genes. We conclude that this approach will aid in decoding some of the important transcriptional regulatory elements of human genes.

Algorithms↗

PubMed1997

Cell and viral regulatory elements enhance the expression and function of a human immunodeficiency virus inhibitory gene.

Regulated expression of recombinant genes in CD4+ cells is an important objective for gene therapy of AIDS, as these cells represent the principal target for viral replication of human immunodeficiency virus (HIV). We report here that specific combinations of CD4 cell-specific and viral regulatory elements can enhance expression of an antiviral gene product. Different viral regulatory elements were incorporated into a previously reported CD4 locus control region to increase the expression of reporter genes in T and monocytic cell lines. The CD4-specific regulatory elements were included to enhance expression in CD4 cells, and viral regulatory regions, including the cytomegalovirus immediate-early (CMV IE) upstream enhancer, which contains the kappa B and Ap1 regulatory elements and a Tat-responsive element of the HIV type 1 long terminal repeat, were used to increase gene expression and modulate its activity in response to viral infection. In transient transfection assays, this vector was 100- to 1,000-fold more active than the original CD4 regulatory elements alone. Expression of an inhibitory form of the Rev protein, Rev M10, was more effective than previously described vectors and protected against productive viral replication in CD4+ peripheral blood mononuclear cells. The combination of CD4 lineage-specific and viral regulatory elements will facilitate the development of more effective antiviral genetic strategies for AIDS.

CD4 Antigens↗

PubMed2003

Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins.

For evolution by gene duplication, differentiation of both regulatory elements and proteins is important. Particularly the former is thought to have large effects on morphological evolution, since differential expression of genes is essential for development. In this report, recent knowledge on regulatory elements is reviewed that is relevant to the population genetics aspects of gene duplication. Regulatory elements usually consist of multiple binding sites of two or more transcription factors. The amount of gene product is quantitatively regulated, and is thought to be subject to stabilizing selection. The intensity of stabilizing selection depends upon the level of constraint imposed by regulatory networks. Gene duplication has significant effects on stabilizing selection via perturbation of gene expression. It is pointed out that constraints coming from regulatory networks are most important for survival of duplicate genes, and that both drift and selection are at work in the process of acquisition of new gene expression and function.

Evolution, Molecular↗

PubMed1989

An internal regulatory element controls troponin I gene expression.

During skeletal myogenesis, approximately 20 contractile proteins and related gene products temporally accumulate as the cells fuse to form multinucleated muscle fibers. In most instances, the contractile protein genes are regulated transcriptionally, which suggests that a common molecular mechanism may coordinate the expression of this diverse and evolutionarily unrelated gene set. Recent studies have examined the muscle-specific cis-acting elements associated with numerous contractile protein genes. All of the identified regulatory elements are positioned in the 5'-flanking regions, usually within 1,500 base pairs of the transcription start site. Surprisingly, a DNA consensus sequence that is common to each contractile protein gene has not been identified. In contrast to the results of these earlier studies, we have found that the 5'-flanking region of the quail troponin I (TnI) gene is not sufficient to permit the normal myofiber transcriptional activation of the gene. Instead, the TnI gene utilizes a unique internal regulatory element that is responsible for the correct myofiber-specific expression pattern associated with the TnI gene. This is the first example in which a contractile protein gene has been shown to rely primarily on an internal regulatory element to elicit transcriptional activation during myogenesis. The diversity of regulatory elements associated with the contractile protein genes suggests that the temporal expression of the genes may involve individual cis-trans regulatory components specific for each gene.

Animals↗

PubMed2005

Imprinting and looping: epigenetic marks control interactions between regulatory elements.

Gene regulation involves various cis-regulatory elements that can act at a distance. They may physically interact each other or with their target genes to exert their effects. Such interactions are beginning to be uncovered in the imprinted Igf2/H19 domain.(1) The differentially methylated regions (DMRs), containing insulators, silencers and activators, were shown to have physical contacts between them. The interactions were changeable depending on their epigenetic state, presumably enabling Igf2 to move between an active and a silent chromatin domain. The study gives us a novel view on how regulatory elements influence gene expression and how epigenetic modifications modulate their long-range effects.

Alleles↗

PubMed1995

Different composite regulatory elements direct expression of the human alpha subunit gene to pituitary and placenta.

To identify elements of the human alpha subunit gene necessary for cell-specific expression, we generated an array of block mutations spanning approximately 400 base pairs (bp) of promoter proximal region and examined them using transient transfection analysis in pituitary (alpha T3) and placental (BeWo) cell lines. Comparison of promoter activity in the two cell types revealed both common and unique elements required for transcription in pituitary and placenta. Two strong elements, the cyclic AMP response element (CRE) and the upstream regulatory element (URE), regulate expression of the alpha subunit gene in BeWo cells. In contrast, promoter activity in alpha T3 cells requires an array of weaker elements. These include the CREs, the URE, as well as two previously described elements, pituitary glycoprotein hormone basal element (PGBE) and gonadotrope-specific element (GSE), and two new elements we designated as the alpha basal elements 1 and 2 (alpha BE1 and alpha BE2). These new elements reside between -316 and -302 bp (alpha BE1) and -296 and -285 bp (alpha BE2) of the human alpha subunit promoter and bind distinct proteins designated alpha BP1 and alpha BP2, respectively. Southwestern blot analysis revealed that alpha BE1 specifically binds 54- and 56-kDa proteins. Additional studies disclosed several potential interactions between proteins that bind the CRE and proteins that occupy PGBE, alpha BE1, and alpha BE2, suggesting that gonadotrope-specific expression occurs through a unique composite regulatory element that includes components of the placenta-specific enhancer.

Animals↗

PubMed2001

Sterol regulatory element binding protein-1a regulation of the steroidogenic acute regulatory protein gene.

The binding of tropic hormones to their specific receptors in steroidogenic cells stimulates the cAMP second-messenger system in the presence of steroidogenic factor-1 (SF-1) to increase expression of steroidogenic acute regulatory (StAR) protein, facilitating the transfer of cholesterol to the inner mitochondrial membrane. The increased use of cholesterol in steroidogenesis triggers activation of sterol- sensitive genes through a second regulatory pathway involving the binding of sterol regulatory element (SRE)-binding proteins (SREBP) to SREs located in the promoter regions of these genes. A search of the rat StAR promoter revealed five potential SRE sites, which demonstrated specific binding with recombinant SREBP-1a. Overexpression of SREBP-1a, -1c or -2 in HTB-9 cells cotransfected with the rat StAR promoter resulted in an increase in promoter-driven luciferase activity. In addition, SREBP-1a was able to activate the StAR promoter through an E-box but only in a promoter construct lacking SREs. SREBPs are known to be weak transcriptional activators and require the presence of additional coactivators like Sp1 and nuclear factor-Y (NF-Y) to elicit maximum activation. Electrophoretic mobility shift assays demonstrated that Sp1, SF-1, and NF-Y enhanced SREBP-1a binding to SREs in the StAR promoter. There was a 4-fold increase in StAR promoter luciferase reporter gene expression when HTB-9 cells were cotransfected with expression vectors for SREBP-1a and NF-Y. In addition, the combined action of SREBP-1a and SF-1 increased both basal (1.6-fold) and cAMP-induced (3.5-fold) activation of the rat StAR promoter. Although Sp1 enhanced SREBP-1a binding to an SRE, Sp1 was not able to increase StAR promoter activity in the presence of SREBP-1a. These results suggest that SREBP-induced regulation of the rat StAR gene is responsive to selective combinations of transcriptional cofactors that could necessitate the convergence of multiple regulatory pathways to enhance gene transcription.

Animals↗

PubMed2004

Transcription factor NF2d9 (LBP-1a) interacts with the positive regulatory element for the xenobiotic responsive element.

PREX is a positive regulatory element for xenobiotic responsive element (XRE)-mediated gene expression that is located upstream of the XRE in the CYP2A8 gene. Using gel mobility shift assays, we demonstrated that NF2d9 (LBP-1a), a transcription factor related to CP2 (LBP-1c/LSF), bound directly to PREX and also interacts indirectly with XRE. Luciferase-reporter gene assays showed that the overexpression of NF2d9 enhanced PREX and XRE-driven CYP2A8 gene transcriptional induction. These findings suggest that the interaction of NF2d9 with PREX and XRE enhances XRE-driven CYP2A8 gene transcriptional induction.

Animals↗

PubMed2004

Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.

The creation, preservation, and degeneration of cis-regulatory elements controlling developmental gene expression are fundamental genome-level evolutionary processes about which little is known. Here, we identify critical differences in cis-regulatory elements controlling the expression of the sea urchin aboral ectoderm-specific spec genes. We found multiple copies of a repetitive sequence element termed RSR in genomes of species within the Strongylocentrotidae family, but RSRs were not detected in genomes of species outside Strongylocentrotidae. spec genes in Strongylocentrotus purpuratus are invariably associated with RSRs, and the spec2a RSR functioned as a transcriptional enhancer and displayed greater activity than did spec1 or spec2c RSRs. Single-base pair differences at two cis-regulatory elements within the spec2a RSR increased the binding affinities of four transcription factors, SpCCAAT-binding factor at one element and SpOtx, SpGoosecoid, and SpGATA-E at another. The cis-regulatory elements to which these four factors bound were recent evolutionary acquisitions that acted to either activate or repress transcription, depending on the cell type. These elements were found in the spec2a RSR ortholog in Strongylocentrotus pallidus but not in RSR orthologs of Strongylocentrotus droebachiensis or Hemicentrotus pulcherrimus. Our results indicated that a dynamic pattern of cis-regulatory element evolution exists for spec genes despite their conserved aboral ectoderm expression.

Animals↗

PubMed1991

Activity and enhancer binding factors for BK virus regulatory elements in differentiating embryonal carcinoma cells.

We have studied cell type specificity of expression of the human papovavirus BK regulatory elements in undifferentiated and differentiated embryonal carcinoma (EC) cells as a model system. While the activity of the regulatory elements of this virus was marginal in undifferentiated cells, differentiation by retinoic acid and DMSO resulted in a dramatic increase in the activity. To correlate in vivo activity of the regulatory elements with interaction with cellular transcription factors, we performed DNase I footprinting experiments. A GC-rich region was protected in both undifferentiated and differentiated cells. An additional four protected sites were detected in retinoic acid-differentiated cells and at least one of these additional sites was weakly protected in DMSO-differentiated cells. The sequences of the differentiated cell type-specific protected regions showed homology to a nuclear factor 1 (NF-1) binding motif and to a muscle creatine kinase gene enhancer motif. The intensity, competition, and pattern of protection of these sites were different in the two differentiated cell types, suggesting the involvement of different transcription factors regulating the activity of BKV regulatory elements in the two cell types.

BK Virus↗

PubMed1986

Characterization of the phosphoenolpyruvate carboxykinase (GTP) promoter-regulatory region. I. Multiple hormone regulatory elements and the effects of enhancers.

Transcription of the gene for cytosolic Phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) (PEPCK) from rat liver is increased by cAMP and glucocorticoids and decreased by insulin. A PEPCK-thymidine kinase (TK) chimeric gene was transfected into FTO-2B rat hepatoma cells, which were TK-deficient. Previous studies showed that a cAMP regulatory element is located at the 5' end of the PEPCK gene. In this report, we demonstrate that the 5' end of the gene also contains a glucocorticoid regulatory element, but not one for insulin. Regions of the PEPCK gene that contain these regulatory elements were attached to the Herpes simplex virus TK structural gene containing its own promoter. The hormone regulatory elements within the 5' flanking region of the PEPCK gene conferred cAMP and glucocorticoid responsiveness on the TK gene after transfection into FTO-2B cells. Like viral enhancer elements, these regulatory elements functioned properly when placed in either orientation at various positions 5' or 3' to TK. The presence of the SV40 enhancer element upstream from the PEPCK-TK gene had little effect on the basal level of expression or hormonal regulation of the chimeric gene.

Animals↗

PubMed2005

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Here, we report our efforts in building a mammalian Transcriptional Regulatory Element Database (TRED) with associated data analysis functions. It collects cis- and trans-regulatory elements and is dedicated to easy data access and analysis for both single-gene-based and genome-scale studies. Distinguishing features of TRED include: (i) relatively complete genome-wide promoter annotation for human, mouse and rat; (ii) availability of gene transcriptional regulation information including transcription factor binding sites and experimental evidence; (iii) data accuracy is ensured by hand curation; (iv) efficient user interface for easy and flexible data retrieval; and (v) implementation of on-the-fly sequence analysis tools. TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED).

Animals↗

PubMed1994

Vascular expression of the grp1.8 promoter is controlled by three specific regulatory elements and one unspecific activating sequence.

The bean grp1.8 full-length promoter is specifically active in vascular tissue during normal development of tobacco. Deletion of a negative regulatory element resulted in ectopic activity of the promoter in cortical cells of hypocotyls, roots and stems. A 169 bp fragment (-205 to -36) of the grp1.8 promoter conferred vascular-specific expression to CaMV 35S minimal promoters whereas a 141 bp fragment (-205 to -64) strongly activated these minimal promoters both in vascular and cortical cells. These experiments defined a new regulatory element (VSE) that is essential for vascular-specific expression and is located between -64 and -36. The 141 bp grp1.8 promoter sequence had enhancer-like properties as it was active in both orientations. A 24 bp sequence (bp -119 to -96, corresponding to the SE1 regulatory element) enhanced expression from several minimal promoters strongly but unspecifically, whereas a 26 bp sequence (-98 to -73, corresponding to the RSE regulatory element) induced vascular-specific expression. Thus, the grp1.8 promoter is regulated by a combinatorial mechanism that can integrate the action of different, non-additively acting regulatory elements into vascular-specific expression.

Base Sequence↗

PubMed2005

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements.

With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.

Animals↗

PubMed1993

Hepatocyte nuclear factor-4 activates medium chain acyl-CoA dehydrogenase gene transcription by interacting with a complex regulatory element.

We have recently identified a complex transcriptional regulatory element in the medium chain acyl-CoA dehydrogenase (MCAD) gene promoter region that confers response to retinoids through interaction with receptors for all-trans-retinoic acid (RARs) and 9-cis-retinoic acid (RXRs) (Raisher, B. D., Gulick, T., Zhang, Z., Strauss, A. W., Moore, D. D., and Kelly, D. P. (1992) J. Biol. Chem. 267, 20264-20269). We examined the interaction of this element (RAREMCAD) with hepatocyte nuclear factor-4 (HNF-4), an orphan receptor with a tissue expression pattern similar to that of MCAD. Electrophoretic mobility shift assays and cotransfection experiments showed that HNF-4 binds with high affinity to RAREMCAD to activate transcription by an RXR-independent mechanism. Mutational analysis revealed that the MCAD HNF-4 response element consists of an imperfect direct repeat homologous to the consensus sequence for binding to the thyroid receptor/RAR/RXR subgroup of receptors and that distinct sequence requirements dictate HNF-4 binding and transactivation. Mobility shift assays with anti-HNF-4 antiserum demonstrated that the MCAD HNF-4 response element binds endogenous rat liver HNF-4 supporting its role in the regulation of MCAD gene expression in vivo. Thus, HNF-4 activates MCAD gene transcription via a complex regulatory element, the architecture of which carries important implications for the structure of HNF-4 response elements in general.

3T3 Cells↗

PubMed2002

Phylogenetic footprinting reveals multiple regulatory elements involved in control of the meiotic recombination gene, REC102.

REC102 is a meiosis-specific early exchange gene absolutely required for meiotic recombination in Saccharomyces cerevisiae. Sequence analysis of REC102 indicates that there are multiple potential regulatory elements in its promoter region, and a possible regulatory element in the coding region. This suggests that the regulation of REC102 may be complex and may include elements not yet reported in other meiotic genes. To identify potential cis-regulatory elements, phylogenetic footprinting analysis was used. REC102 homologues were cloned from other two Saccharomyces spp. and sequence comparison among the three species defined evolutionarily conserved elements. Deletion analysis demonstrated that the early meiotic gene regulatory element URS1 was necessary but not sufficient for proper regulation of REC102. Upstream elements, including the binding sites for Gcr1p, Yap1p, Rap1p and several novel conserved sequences, are also required for the normal regulation of REC102 as well as a Rap1p binding site located in the coding region. The data in this paper support the use of phylogenetic comparisions as a method for determining important sequences in complex promoters.

Base Sequence↗

PubMed2005

Discovery of regulatory elements in vertebrates through comparative genomics.

We have analyzed issues of reliability in studies in which comparative genomic approaches have been applied to the discovery of regulatory elements at a genome-wide level in vertebrates. We point out some potential problems with such studies, including difficulties in accurately identifying orthologous promoter regions. Many of these subtle analytical problems have become apparent only when studying the more complex vertebrate genomes. By determining motif reliability, we compared existing tools when applied to the discovery of vertebrate regulatory elements. We then used a statistical clustering method to produce a computational catalog of high quality putative regulatory elements from vertebrates, some of which are widely conserved among vertebrates and many of which are novel regulatory elements. The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques.

Algorithms↗