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PubMed2005

Targeted deletion of the chicken beta-globin regulatory elements reveals a cooperative gene silencing activity.

The chicken beta-globin locus represents a well characterized system to study the role of both proximal and distal regulatory elements in a eukaryotic multigene domain. The function of the chicken beta(A)/epsilon-intergenic enhancer and upstream regulatory elements 5'-HS1 and 5'-HS2 were studied using a gene targeting approach in chicken DT40 cells followed by microcell-mediated chromosome transfer into human erythroleukemia cells (K562). These regulatory elements all repressed expression of the rho- and beta(H)-chicken globin genes in the chromosome transfer assay. No rho- or beta(H)-globin gene expression was detected in K562 cells containing the chicken chromosome without deletions, whereas rho- and beta(H)-mRNA was activated in K562 cells containing chicken chromosomes with deletions of the intergenic enhancers, 5'-HS1 and 5'-HS2. Transcriptional activation of the rho- and beta(H)-globin genes correlated with hyperacetylation of histones H3 and H4, loss of histone H3 lysine 9 methylation, and binding of RNA polymerase II to the gene promoters. Surprisingly, the status of CpG dinucleotide methylation at the promoters did not correlate with the transcriptional status of the genes. Our results using a chromosomal transfer assay demonstrate an identical silencing function for these regulatory elements, which suggests they function as part of a common silencing pathway or complex.

Animals↗

PubMed1997

Identification of a positive regulatory element responsible for tissue-specific expression of prostate-specific antigen.

The prostate-specific antigen (PSA) promoter (PSA-P) has been identified, characterized, and determined to be tissue specific. Compared with high expression of the genomic PSA gene in prostate cells, expression of the transgene driven by the putative PSA promoter is low. This suggests that the identified promoter may be incomplete or may function optimally with additional regulatory elements. To identify the presence of additional regulatory elements, we screened sequences upstream of the PSA promoter and identified a DNA fragment of 822 bp, which enhances PSA gene expression. Combining the newly identified PSA gene regulatory sequence (PSAR) with our previously identified PSA promoter (PCPSA-P) exhibited enhanced expressional activity in the PSA-producing LNCaP cell line. With the addition of 10 to 100 nM dihydrotestosterone, a more than 1000-fold increase in expression was observed as compared to androgen-negative controls. Furthermore, although the combined regulatory element (PSAR)-PSA promoter (PCPSA-P) sequence resulted in high transgene expression in LNCaP cell lines, the combined regulatory element-promoter sequence resulted in minimal expression in the non-PSA-producing prostate cell line PC-3, renal tumor cell line R11, and cervical adenocarcinoma cell line HeLa. The newly identified 822 bp alone could also function as a promoter. Compared with the combined promoter, however, the 822-bp fragment alone demonstrated lower activity and lower responsiveness to androgen stimulation. Our results suggest that coupling the PSA promoter with an upstream regulatory element results in a marked increase in PSA expression, suggesting that the complete PSA promoter contains two functional domains: a proximal promoter and a distal promoter, which can also function as an enhancer. The enhanced gene expression of the new construct, combined with its tissue specificity and androgen responsiveness, in turn provides a foundation for the development of tissue-specific vectors for prostate cancer gene therapy.

Base Sequence↗

PubMed1995

Interleukin-6 Gene Expression by Prostaglandins and Cyclic AMP Mediated by Multiple Regulatory Elements.

We have evaluated the potential role of prostaglandins and their second-messenger Cyclic Adenosine Monophosphate (cAMP) in the activation of interleukin-6 (IL-6) promoter regulatory elements leading to IL-6 expression in monocytic cells. We demonstrate that prostaglandins of the E series and their second-messenger cAMP induce the IL-6 promoter in the murine monocytic cell line PU5-1.8. Stimulation with both cAMP and LPS results in a marked synergistic effect. We show that the endogenous IL-6 gene is induced by cAMP as well, even though to a lesser extent than by LPS, suggesting distinctive effects of cAMP and LPS on posttranscriptional events. Mutations eliminating potential transcription factor binding sites, including the multiple-response element (MRE), AP-1, NF-IL6, and NF-kappaB binding sites, significantly reduce, but do not completely abrogate, inducibility by cAMP or prostaglandin E1, whereas alterations of four additional putative regulatory elements have no effects. In contrast, LPS-induced promoter activity is almost completely abolished by mutations in the NF-kappaB binding site, suggesting that a single regulatory element is crucial for inducibility by LPS, whereas no individual element is absolutely essential for cAMP signaling. Induction of the AP-1, NF-IL-6, and NF-kappaB elements by cAMP is correlated with the appearance of inducible factors binding to these sites, whereas factors binding to the MRE are constitutively expressed. Our results suggest that cAMP and prostaglandins act through multiple, partially redundant, regulatory elements to induce IL-6 expression in monocytic cells.

Journal Article↗

PubMed1994

Proximal regulatory elements and nuclear activities required for transcription of the human Na+/H+ exchanger (NHE-1) gene.

We herein demonstrate competence of the 5' upstream region -1374 to +16 of the human growth factor-activatable Na+/H+ exchanger (NHE-1) gene to promote transcription of the chloramphenicol acetyltransferase gene in cells of hepatic origin (HepG2), vascular-smooth-muscle origin (VSM A7r5) and fibroblasts (3T3). We also describe the mapping of the regulatory elements required for such transcription. Sequential 5' end-deletions indicated that the 5' boundary of the positive regulatory elements of NHE-1 transcription is localized downstream of nucleotide -252 in both HepG2 and VSM A7r5 cells but downstream of nucleotide -654 in 3T3 cells. Footprinting analysis of the 0.25-kb promoter fragment using rat liver nuclear extracts identified 4 protected regions as follows: A, -31 to -9; B, -108 to -65; C, -124 to -111; and D, -239 to -215. Internal deletion and nucleotide substitutions within regulatory element D revealed its essential role for transcription of the human NHE-1 gene in HepG2 and VSM A7r5 cells. DNA binding and competition assays using rat liver nuclear extracts indicated that regulatory element D is recognized by 5 nuclear activities. Four of these activities (designated as NHE-1D1-4) are competed out completely by oligonucleotides containing the binding sites of transcription factors CREB, AP3, NFY, and other CCAAT box-binding proteins (C/EBP alpha or related proteins). This competition profile might be explained by the presence of homology between regulatory element D and the consensus sequence of C/EBP as well as the other competitor oligonucleotides. The actual relationship between these nuclear activities and the C/EBP family of proteins (or other transcription factors) remains to be determined.

Base Sequence↗

PubMed2006

Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast.

Fission yeast sterol regulatory element binding protein (SREBP), called Sre1p, functions in an oxygen-sensing pathway to allow adaptation to fluctuating oxygen concentrations. The Sre1p-Scp1p complex responds to oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. To examine the role of Sre1p in anaerobic gene expression in Schizosaccharomyces pombe, we performed transcriptional profiling experiments after a shift to anaerobic conditions for 1.5 h. Of the 4,940 genes analyzed, expression levels of 521 (10.5%) and 686 (13.9%) genes were significantly increased and decreased, respectively, under anaerobic conditions. Sre1p controlled 68% of genes induced > or = 2-fold. Oxygen-requiring biosynthetic pathways for ergosterol, heme, sphingolipid, and ubiquinone were primary targets of Sre1p. Induction of glycolytic genes and repression of mitochondrial oxidative phosphorylation genes largely did not require Sre1p. Using chromatin immunoprecipitation, we demonstrated that Sre1p acts directly at target gene promoters and stimulates its own transcription under anaerobic conditions. sre1+ promoter analysis identified two DNA elements that are both necessary and sufficient for oxygen-dependent, Sre1p-dependent transcription. Interestingly, these elements are homologous to sterol regulatory elements bound by mammalian SREBP, highlighting the evolutionary conservation between Sre1p and SREBP. We conclude that Sre1p is a principal activator of anaerobic gene expression, upregulating genes required for nonrespiratory oxygen consumption.

Anaerobiosis↗

PubMed1998

Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.

BACKGROUND: The sterol regulatory element binding proteins (SREBPs) are helix-loop-helix transcriptional activators that control expression of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. Unlike helix-loop-helix proteins that recognize symmetric E-boxes (5'-CANNTG-3'), the SREBPs have a tyrosine instead of a conserved arginine in their basic regions. This difference allows recognition of an asymmetric sterol regulatory element (StRE, 5'-ATCACCCAC-3'). RESULTS: The 2.3 A resolution co-crystal structure of the DNA-binding portion of SREBP-1a bound to an StRE reveals a quasi-symmetric homodimer with an asymmetric DNA-protein interface. One monomer binds the E-box half site of the StRE (5'-ATCAC-3') using sidechain-base contacts typical of other helix-loop-helix proteins. The non-E-box half site (5'-GTGGG-3') is recognized through entirely different protein-DNA contacts. CONCLUSIONS: Although the SREBPs are structurally similar to the E-box-binding helix-loop-helix proteins, the Arg-->Tyr substitution yields dramatically different DNA-binding properties that explain how they recognize StREs and regulate expression of genes important for membrane biosynthesis.

Amino Acid Sequence↗

PubMed1997

Role of positive and negative cis-regulatory elements in the transcriptional activation of the lysozyme locus in developing macrophages of transgenic mice.

Expression of the chicken lysozyme locus in macrophages is regulated by at least six different positive and negative cis-regulatory elements. Chromatin of the chicken lysozyme locus is gradually reorganized during macrophage differentiation, indicating that each cis-regulatory element is activated at a different developmental stage. Irrespective of their differential developmental activation, individual cis-regulatory regions are capable of driving transcription of the lysozyme gene in mature macrophages of transgenic mice. In order to examine the role of different cis-regulatory regions in lysozyme locus activation, we analyzed the time course of transcriptional up-regulation of deletion mutants of the lysozyme locus in a new in vitro differentiation system based on enriched primary macrophage precursor cells from the bone marrow of transgenic mice. We show that constructs carrying cis-regulatory elements which are structurally reorganized early in development are also transcriptionally active at an early stage. A construct in which the early enhancer has been deleted shows a delay in transcriptional activation. The presence or absence of a negative regulatory element has no influence on the time course of transcriptional activation of the lysozyme locus.

Animals↗

PubMed1990

Regulatory elements controlling expression of the Drosophila homeotic gene fork head.

The region-specific homeotic gene fork head (fkh) is expressed and required in a variety of tissues of the developing Drosophila embryo. In order to identify the cis regulatory elements directing the complex spatio-temporal expression pattern of fkh, we have studied the subpatterns directed by defined fragments of fkh genomic DNA. These experiments enabled us to distinguish separate regulatory elements specific for the different expression domains of fkh. In addition, our analysis revealed several unexpected features such as the redundancy of regulatory elements and the overlap of regulatory elements with the transcribed regions of other genes. Moreover, the separation of normally contiguous elements effecting expression in the posterior terminal fkh domain appears to lead to novel expression domains which do not correspond to known developmental units in the embryo.

Alleles↗

PubMed2006

A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements.

The comprehensive identification of cis-regulatory elements on a genome scale is a challenging problem. We develop a novel, steganalysis-based approach for genome-wide motif finding, called WordSpy, by viewing regulatory regions as a stegoscript with cis-elements embedded in 'background' sequences. We apply WordSpy to the promoters of cell-cycle-related genes of Saccharomyces cerevisiae and Arabidopsis thaliana, identifying all known cell-cycle motifs with high ranking. WordSpy can discover a complete set of cis-elements and facilitate the systematic study of regulatory networks.

Algorithms↗

PubMed2000

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.

COMPEL is a database on composite regulatory elements, the basic structures of combinatorial regulation. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. The structure of the relational model of COMPEL is determined by the concept of molecular structure and regulatory role of CEs. Based on the set of a particular CE, a program has been developed for searching potential CEs in gene regulatory regions. WWW search and browse routines were developed for COMPEL release 3.0. The COMPEL database equipped with the search and browse tools is available at http://compel.bionet.nsc.ru/. The program for prediction of potential CEs of NFAT type is available at http://compel.bionet.nsc. ru/FunSite.html and http://transfac.gbf.de/dbsearch/funsitep/ s_comp.html

Database Management Systems↗

PubMed1994

Evidence for a cell-specific negative regulatory element in the first intron of the gene for bovine elastin.

A cell-specific negative regulatory element has been identified in the first intron of the gene for elastin in a region between 442 and 464 bp from the translational start site. This regulatory element functions both when it is located 5' of the promoter and 3' of the chloramphenicol acetyltransferase (CAT) gene. The inhibition is observed both with the homologous elastin promoter and the heterologous SV1 promoter in transient expression experiments using rat aortic smooth-muscle cells. No inhibition was observed with NIH 3T3, Hep G2 and little, if any, with HeLa cells. Cell specificity was further confirmed by DNA mobility shift assays and the position of the negative regulatory element was localized with the use of synthetic duplex oligomers. It is proposed that this negative element plays a significant role in the modulation of the expression of the gene for elastin in the smooth-muscle cells of the aorta during development.

3T3 Cells↗

PubMed1990

Identification of cis-acting repressive sequences within the negative regulatory element of human immunodeficiency virus type 1.

The negative regulatory element of human immunodeficiency virus type 1 is a 260-nucleotide-long sequence that decreases the rate of RNA transcription initiation specified by the long terminal repeat. This region has the potential to bind several cellular transcription factors. Here it is shown that sequences which recognize the NFAT-1 and USF cellular transcription factors contribute to this negative regulatory effect. The sequences within the negative regulatory element which resemble the AP-1 site and the URS do not negatively regulate human immunodeficiency virus long terminal repeat transcription initiation.

Base Sequence↗

PubMed2026

Genetic Deletion of Cis-Regulatory Elements to Dissect the Function of the Non-coding Genome in human Preimplantation Models.

Cis-regulatory elements coordinate gene expression in a spatially and temporally controlled manner and contribute to the establishment of distinct cellular states during development. A substantial proportion of transcriptionally active cis-regulatory elements in primate embryos originated from ancient retroviral integrations into the germline. These endogenous retroviruses, also known as long terminal repeat retrotransposons, retain intrinsic regulatory activity and are often species-specific, making them strong candidates for regulating species-divergent aspects of embryonic development. Ethical and legal restrictions on human embryo research have historically limited direct investigation of gene regulation during human embryogenesis. Human naive pluripotent stem cells and three-dimensional stem cell-based blastocyst models provide alternative systems for studying early developmental processes. This protocol describes the CRISPR-Cas9-mediated deletion of endogenous retrovirus-derived cis-regulatory elements in human naive pluripotent stem cells. Preassembled Cas9 and single-guide RNA ribonucleoprotein complexes are delivered by nucleofection, followed by single-cell cloning, PCR-based genotyping, Sanger sequencing, expansion, cryopreservation, and genomic stability assessment of the edited lines. The resulting wild-type, heterozygous, and homozygous or hemizygous deletion clones provide a platform for investigating the contribution of individual endogenous retrovirus-derived elements to gene regulation in human preimplantation models. This method enables direct functional interrogation of species-specific non-coding regulatory sequences and supports the study of transcriptional mechanisms involved in early human development.

Humans↗

PubMed2005

Heterogeneous DNA methylation status of the regulatory element of the mouse Oct4 gene in adult somatic cell population.

The transcription factor Oct4 is specifically expressed in the germ line and pluripotent stem cells, and is indispensable for normal mouse development. To understand the epigenetic control of Oct4 expression, we examined the DNA methylation pattern of the Oct4 regulatory element in various types of cells. Bisulfite analysis showed that the regulatory element was unmethylated in P19 embryonal carcinoma cells, which robustly express Oct4. By contrast, the regulatory element was distinctly methylated in somatic cells, including cell lines, such as NIH3T3 embryonic fibroblast and Hepa1-6 hepatoma, as well as tissues from the adult body, such as liver, spleen, and cumulus cells. However, we found that the extent of methylation was considerably heterogeneous among the alleles in the adult somatic cells. Using a luciferase reporter construct, we demonstrated that the extent of methylation directly affects the efficiency of gene expression driven by the Oct4 regulatory element in P19 cells. These results raise the possibility that the epigenetic status of Oct4 is heterogeneous among a population of somatic cells, which may affect the efficiency of Oct4 reactivation after somatic cell nuclear transfer.

Alleles↗

PubMed1995

Binding of cellular repressor protein or the IE2 protein to a cis-acting negative regulatory element upstream of a human cytomegalovirus early promoter.

We have previously shown that the human cytomegalovirus early UL4 promoter has upstream negative and positive cis-acting regulatory elements. In the absence of the upstream negative regulatory region, the positive element confers strong transcriptional activity. The positive element contains a CCAAT box dyad symmetry and binds the cellular transcription factor NF-Y. The effect of the negative regulatory element is negated by the viral IE2 protein (L. Huang, C.L. Malone, and M.F. Stinski, J. Virol. 68:2108, 1994). We investigated the binding of cellular or viral IE2 protein to the negative regulatory region. The major cis-acting negative regulatory element was located between -168 and -134 bp relative to the transcription start site. This element could be transferred to a heterologous promoter, and it functioned in either orientation. Mutational analysis demonstrated that a core DNA sequence in the cis-acting negative regulatory element, 5'-GTTTGGAATCGTT-3', was required for the binding of either a cellular repressor protein(s) or the viral IE2 protein. The cellular DNA binding activity was present in both nonpermissive HeLa and permissive human fibroblast cells but more abundant in HeLa cells. Binding of the cellular repressor protein to the upstream cis-acting negative regulatory element correlates with repression of transcription from the early UL4 promoter. Binding of the viral IE2 protein correlates with negation of the repressive effect.

Base Sequence↗

PubMedDate not supplied

[Mechanism of action of sterol regulatory element binding proteins (SREBPs) in cholesterol and fatty-acid biosynthesis].

Cholesterol is an important lipid in higher organisms, and its concentration must be maintained in narrow limits depending of the cell needs. An excess of dietary cholesterol can lead to serious health problems, however, if consumption of this lipid is restricted in the diet, cells have the capacity to synthesize it. For the synthesis of cholesterol, the cell uses a family of proteins named sterol regulatory element binding proteins (SREBP's), that are transcriptional factors involved in the control of expression of genes of cholesterol and fatty acids synthesis. SREBP's regulate gene transcription by binding to cis-acting elements denominated sterol regulatory elements (SRE-1). SREBP's are localized in the endoplasmic reticulum, but in the event that the cell needs to synthesize cholesterol, the NH2-terminal portion of these proteins is cleaved by two specific proteases, and then travels into the nucleus to function as transcriptional factor. The present review shows the details of the mechanism that the cell uses to regulate cholesterol biosynthesis by the SREBP's, and its potential metabolic implications.

Animals↗

PubMed2006

Mutational analysis of the Myxococcus xanthus Omega4406 promoter region reveals an upstream negative regulatory element that mediates C-signal dependence.

C signaling plays a key role in coordinating cell movement and differentiation during the multicellular developmental process of Myxococcus xanthus. C signaling regulates expression of genes induced after about 6 h into development, when cells are forming mounds. One gene whose expression depends absolutely on C signaling was identified by insertion of a transposable element at site Omega4406 which generated a transcriptional fusion between lacZ and an upstream promoter. We have investigated regulation of the Omega4406 promoter. A 5' deletion revealed a negative regulatory element located between bp -533 and -100 relative to the transcriptional start site. In the absence of this element, the promoter was still developmentally regulated but about fourfold more active. Also, the truncated promoter region retained normal dependence on two developmental regulators, FruA and DevS, but lost its dependence on the C-signaling protein CsgA. We infer that C signaling partially overcomes the negative effect of the upstream element on activity of the Omega4406 promoter. Deletion of downstream DNA between bp 50 and 140 caused a threefold loss in expression, suggesting that a positive regulatory element lies in this region. Additional positive and negative regulatory elements are present in the region from bp -69 to -49, based on the effects of multiple-base-pair mutations. Within this region, a 5-bp element and a C-box-like sequence resemble sequences found in other developmentally regulated M. xanthus promoter regions, but the effects of single-base-pair changes in these sequences suggest that each functions uniquely. We conclude that regulation of the Omega4406 promoter involves multiple positive and negative regulatory elements located upstream and downstream of the region typically bound by RNA polymerase.

Bacterial Proteins↗

PubMed1989

Rat ornithine decarboxylase gene. Nucleotide sequence, potential regulatory elements, and comparison to the mouse gene.

Expression of ornithine decarboxylase is regulated by a variety of hormonal and other stimuli in rat cells and tissues. To study this phenomenon at the molecular level, we isolated and sequenced a cDNA-encoding rat ornithine decarboxylase and deduced its amino acid sequence. The cDNA clone was used to isolate a clone from a rat genomic library which contained the sequence of the entire rat ornithine decarboxylase gene. The gene comprised 12 exons and 11 introns and spanned 7.7 kilobases. Two polyadenylation signals (AATAAA) were located 310 and 697 base pairs 3' to the translational termination codon and were responsible for the occurrence of two hybridizing mRNA species in Northern blots of rat cells and tissues. S1 nuclease mapping suggested that there were multiple transcriptional start sites; the major one appeared to be located 2269 base pairs of genomic sequence 5' to the ATG translational initiation site, representing 274 bases of mRNA. Several potential regulatory elements were identified in the 5'-promoter regions or in the first intron: a TATA box, GC boxes, AP-1 and AP-2 binding sites, a cAMP-responsive element, a glucocorticoid regulatory element, and RNA polymerase III promoter sequences. The 5'-noncoding region of the mRNA was extremely rich in G + C; secondary structure predictions suggested that almost this entire region could form stable secondary structures, with an overall free energy of formation (delta G) of -114 kcal/mol. The potential regulatory elements identified in both the promoter region of the gene and the 5'-untranslated region of the mRNA may be involved in the complex regulation of rat ornithine decarboxylase expression.

Amino Acid Sequence↗