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PubMed1987

Defective distal regulatory element at the 5' upstream of rat prolactin gene of steroid-nonresponsive GH-subclone.

The prolactin-nonproducing (PRL-) GH cell strains (rat pituitary tumor cells in culture). GH12C1 and F1BGH12C1, do not respond to steroid hormones estradiol or hydrocortisone (HC). However, the stimulatory effect of estradiol and the inhibitory effect of hydrocortisone on prolactin synthesis can be demonstrated in the prolactin-producing GH cell strain, GH4C1. In this investigation we have examined the 5' end flanking region of rat prolactin (rat PRL) gene of steroid-responsive, GH4C1 cells to identify the positive and negative regulatory elements and to verify the status of these elements in steroid-nonresponsive F1BGH12C1 cells. Results presented in this report demonstrate that the basel level expression of the co-transferred Neo gene (neomycin phosphoribosyl transferase) is modulated by the distal upstream regulatory elements of rat PRL gene in response to steroid hormones. The expression of adjacent Neo gene is inhibited by dexamethasone and is stimulated by estradiol in transfectants carrying distal regulatory elements (SRE) of steroid-responsive cells. These responses are not observed in transfectants with the rat PRL upstream sequences derived from steroid-nonresponsive cells. The basal level expression of the host cell alpha-2 tubulin gene is not affected by dexamethasone. We report here the identification of the distal steroid regulatory element (SRE) located between 3.8 and 7.8 kb upstream of the transcription initiation site of rat PRL gene. Both the positive and the negative effects of steroid hormones can be identified within this upstream sequence. This distal SRE appears to be nonfunctional in steroid-nonresponsive cells. Though the proximal SRE is functional, the defect in the distal SRE makes the GH substrain nonresponsive to steroid hormones. These results suggest that both the proximal and the distal SREs are essential for the mediation of action of steroid hormones in GH cells.

Animals↗

PubMed1998

Tumor necrosis factor-alpha stimulates the maturation of sterol regulatory element binding protein-1 in human hepatocytes through the action of neutral sphingomyelinase.

The mechanism by which genes involved in cholesterol biosynthesis and import are preferentially up-regulated in response to sterol depletion was elucidated with the cloning of sterol regulatory element binding protein-1 (SREBP-1). SREBP-1 is a transcription factor whose entry into the nucleus is gated by sterol-regulated proteolysis. We have investigated the role of tumor necrosis factor-alpha (TNF-alpha) as a mediator of SREBP-1 maturation in human hepatocytes. TNF-alpha is capable of inducing SREBP-1 maturation in a time- and dose-dependent manner that is consistent with the kinetics of TNF-alpha-mediated activation of neutral sphingomyelinase (N-SMase). Antibodies to N-SMase inhibit TNF-alpha-induced SREBP-1 maturation suggesting that N-SMase is a necessary component of this signal transduction pathway. Ceramide, a product of sphingomyelin hydrolysis, is also capable of inducing SREBP-1 maturation. The mature form of SREBP-1 generated by TNF-alpha, sphingomyelinase or ceramide treatment translocates to the nucleus and binds the sterol regulatory element. This promotes transcription of the gene upstream of the sterol regulatory element. A unique finding of our studies is that ceramide stimulated SREBP-1 maturation even in the presence of cholesterol and 25-hydroxycholesterol both of which are known suppressors of SREBP-1 maturation. Our findings indicate that ceramide-mediated maturation of SREBP-1 maturation is a novel sterol-independent mechanism by which cholesterol homeostasis may be regulated.

Antibodies↗

PubMed2003

A general approach for identifying distant regulatory elements applied to the Gdf6 gene.

Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distant regulatory elements into smaller intervals for detailed study. The mouse Gdf6 gene is expressed in a number of distinct embryonic locations that are involved in the patterning of skeletal and soft tissues. To identify sequences responsible for Gdf6 regulation, we first isolated a series of overlapping bacterial artificial chromosomes (BACs) that extend varying distances upstream and downstream of the gene. A LacZ reporter cassette was integrated into the Gdf6 transcription unit of each BAC using homologous recombination in bacteria. Each modified BAC was injected into fertilized mouse eggs, and founder transgenic embryos were analyzed for LacZ expression mid-gestation. The overlapping segments defined by the BAC clones revealed five separate regulatory regions that drive LacZ expression in 11 distinct anatomical locations. To further localize sequences that control expression in developing skeletal joints, we created a series of BAC constructs with precise deletions across a putative joint-control region. This approach further narrowed the critical control region to an area containing several stretches of sequence that are highly conserved between mice and humans. A distant 2.9-kilobase fragment containing the highly conserved regions is able to direct very specific expression of a minimal promoter/LacZ reporter in proximal limb joints. These results demonstrate that even distant, complex regulatory sequences can be identified using a combination of BAC scanning, BAC deletion, and comparative sequencing approaches.

Animals↗

PubMed1977

Microbial models and regulatory elements in the control of purine metabolism.

Bacterial systems have been used to identify and characterize the organization of the genetic units and the regulatory elements that control purine metabolism. An analysis of 13 genes that control the biosynthesis of AMP and GMP has revealed three multigenic operons. These show properties of gene contiguity, promoter sites, coordinate expression and polarity effects. The unit controlling the formation of IMP is one operon (pur JHD) consisting of three genes which together control the formation of phosphoribosylglycinamide synthetase (EC 6.3.4.13), an early enzyme in the biosynthetic pathway, and a terminal bifunctional complex (IMP cyclohydrolase--formyltransferase). Regulatory mutants were isolated and characterized by several methods including the use of a unique fusion of two unrelated operons. Both operator constitutive and repressor type (purR) mutations have been identified. The purR product functions in the common control of several genetically distinct enzymes that participate before the formation of IMP. Plasmid DNA enriched for the purE operon has been isolated and used in the study of the role of nucleotide effectors in the binding of repressor-like proteins. AMP but not GMP is needed for binding, and purR mutants are deficient in the binding substance. Mutants with differential blocks in the salvage and interconverting reactions have been used to characterize the regulatory elements of the formation and the activity of guanosine kinase, GMP reductase (EC 1.6.6.8), and purine nucleoside phosphorylase (EC 2.4.2.1). Two structural gene products (purF) and (purG) have been implicated as possible regulatory elements for the use of guanosine, and a role for glutamine in the induction of GMP reductase has been revealed.

Adenosine Monophosphate↗

PubMed1998

A regulatory element of the human keratin 18 gene with AP-1-dependent promoter activity.

The human keratin 18 (K18) gene is expressed in a restricted but diverse subset of differentiated epithelial tissues and carcinomas. The 10-kilobase pair K18 gene contains all of the genetic information necessary for tissue-specific, copy number-dependent and integration site-independent expression in transgenic mice. We identified a 100-base pair regulatory element that activates the K18 proximal promoter in the presence of the previously identified first intron enhancer. Deletion of the element greatly diminished K18 expression. This regulatory element also has cryptic, AP-1-dependent promoter activity in the absence of the normal promoter, which results in 10-40-fold higher levels of K18 RNA expression in transgenic mice. The high activity of this cryptic promoter is dependent upon the first intron enhancer. These experiments define interactive regulatory regions of the K18 gene that modulate expression in diverse epithelial cell types and identify an unusual regulatory element with promoter activity that may be useful for high level heterologous gene expression in transgenic animals.

Animals↗

PubMed1996

Cellular proteins that bind to the hepatitis B virus posttranscriptional regulatory element.

The hepatitis B virus posttranscriptional regulatory element (PRE), which resides in the 3' region of the viral S transcripts, is important for the high-level expression of these mRNA species. We have previously shown that the PRE acts intranuclearly in cis to allow efficient export of intronless transcripts into the cytoplasm, in a manner that is independent of viral trans-acting factors. We here present data demonstrating that there are widely dispersed subelements in the PRE that are important for its function. All of these subelements bind, albeit with different affinities, to the same or similar host nuclear factor(s) containing two proteins, approximately 30 and 45 kDa in mass. The affinity of protein binding to a subelement is positively correlated with the ability of the subelement to activate intronless gene expression. Therefore, it appears that the PRE functions by having multiple binding sites for nuclear proteins that may be directly or indirectly involved in export of unspliced mRNA species.

Base Sequence↗

PubMed1996

A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene.

In earlier studies the DNA site required for sterol regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase was shown to be distinct from the classic sterol regulatory element (SRE-1) of the low density lipoprotein receptor gene (Osborne, T. F. (1991) J. Biol. Chem 266, 13947-13951). However, oxysterol-resistant cells that continuously overproduce one of the sterol regulatory element binding proteins in the nucleus result in high unregulated expression of both genes (Yang, J., Brown, M. S., Ho, Y. K., and Goldstein, J. L. (1995) J. Biol. Chem. 270, 12152-12161) suggesting a direct role for the SREBPs in the activation of the reductase gene. In the present studies we demonstrate that SREBP-1 binds to two adjacent sites within the previously identified sterol regulatory element of the reductase gene even though there is only limited homology with the SRE-1 of the receptor. We also show that SREBP-1 specifically activates the reductase promoter in transient DNA transfection studies in HepG2 cells and that mutations which eliminate sterol regulation and SREBP-1 binding also abolish transient activation by SREBP-1. Although specific, the magnitude of the activation observed is considerably lower than for the low density lipoprotein (LDL) receptor analyzed in parallel, suggesting there is an additional protein required for activation of the reductase promoter that is limiting in the transient assay. SREBP also binds to two additional sites in the reductase promoter which probably plan an auxiliary role in expression. When the DNA sequence within the sites are aligned with each other and with the LDL receptor SRE-1, a consensus half-site is revealed 5'-PyCAPy-3'. The LDL receptor element contains two half-sites oriented as a direct repeat spaced by one nucleotide. The SREBP proteins are special members of the basic-helix-loop-helix-zipper (bHLHZip) family of DNA binding proteins since they bind the classic palindromic E-box site as well as the direct repeat SRE-1 element. The SREBP binding sites in both the reductase and those recently identified in other sterol regulated promoters appear to contain a half-site with considerable divergence in the flanking residues. Here we also show that a 22-amino acid domain located immediately adjacent to the basic domain of the bHLHZip region is required for SREBP to efficiently recognize divergent sites in the reductase and 3-hydroxy-3-methylglutaryl-CoA synthase promoters but, interestingly, this domain is not required for efficient binding to the LDL direct repeat SRE-1 or to a palindromic high-affinity E-box element.

Base Sequence↗

PubMed1993

Purification of mouse MEP-1, a nuclear protein which binds to the metal regulatory elements of genes encoding metallothionein.

Metal regulatory elements (MREs) shared by metallothionein (MT) gene promoters are essential for metal induction of MT genes. MEP-1, a nuclear protein which binds to these elements has been purified from heavy metal-resistant mouse L cells using footprinting, Southwestern and UV cross-linking techniques to assay its binding activity. The purification scheme, starting from crude nuclear extracts, involved a combination of heparin-Sepharose and MRE-DNA affinity chromatography. The purified protein preparation showed a single polypeptide band of 108 kDa on polyacrylamide gel electrophoresis, and 2D-gel analyses revealed the presence of a protein species migrating as a single population of approximately 110 kDa. MEP-1 does not appear to be glycosylated since it eluted with the flow-through on a Wheat Germ Sepharose column. It was retained by a zinc-Chelating Sepharose column suggesting that amino acid residues (i.e., cysteine, histidine) which have an affinity for zinc ions are exposed on the protein surface. Binding studies with the purified protein indicated that it binds specifically to MRE sequences and that the binding can be abolished by a point mutation in the MRE core consensus sequence or by the addition of the chelating agent 1,10-phenanthroline. Binding activity can be restored by the addition of zinc ions to the chelated protein. These results suggest that MEP-1 is one of the major proteins interacting with MRE sequences.

Animals↗

PubMed1998

Identification of glyceraldehyde-3-phosphate dehydrogenase as a cellular protein that binds to the hepatitis B virus posttranscriptional regulatory element.

The hepatitis B virus posttranscriptional regulatory element (PRE) is an RNA cis-element that is required for high-level expression of viral surface gene transcripts and appears to function by activating mRNA export to the cytoplasm. We have previously shown that multiple fragments of the PRE bind to two cellular proteins of approximately 35 and 55 kDa in molecular mass and that this binding correlates with function. By a combination of column chromatographic techniques and SDS-polyacrylamide gel electrophoresis, we have been able to purify the smaller protein. Amino-terminal sequencing of the purified protein shows identity to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an RNA-binding glycolytic enzyme that has been implicated in the export of tRNA. Immunoprecipitation analysis reveals that GAPDH is indeed present in the protein-RNA complex resulting from incubation of crude nuclear extracts with a functional region of the PRE. Furthermore, binding of the cellular 35 kDa protein to the PRE fragment is blocked by NAPDH, as would be expected for RNA binding by GAPDH. Finally, purified commercial GAPDH also binds specifically to this RNA fragment. Therefore, GAPDH is one of the cellular proteins that binds to the PRE, and may be involved in the posttranscriptional regulation of hepatitis B virus gene expression.

Amino Acid Sequence↗

PubMed2005

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple, divergent species. This approach distinguishes multispecies conserved sequences (MCS) in noncoding regions from more rapidly evolving neutral DNA. Here, we have analyzed a region of approximately 238kb containing the human alpha globin cluster that was sequenced and/or annotated across the syntenic region in 22 species spanning 500 million years of evolution. Using a variety of bioinformatic approaches and correlating the results with many aspects of chromosome structure and function in this region, we were able to identify and evaluate the importance of 24 individual MCSs. This approach sensitively and accurately identified previously characterized regulatory elements but also discovered unidentified promoters, exons, splicing, and transcriptional regulatory elements. Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs.

Animals↗

PubMed1990

cis-acting negative regulatory element of prolactin gene.

The prolactin (PRL) gene in clonal strains of rat pituitary tumor cells in culture (GH cells) exhibit several regulatory responses, similar to the ones observed in rat pituitary gland. A comparative analysis of regulation of PRL gene expression in PRL-producing (PRL+) and PRL-nonproducing (PRL-) GH cells was conducted by monitoring the PRL promoter driven transient expression of chloramphenicol acetyltransferase (CAT) gene in GH4C1 (PRL+) and GH12C1 (PRL-) cells. The PRL promoter activity was drastically inhibited only in PRL-nonproducing cells (PRL-) and not in PRL producing cells (PRL+) when a 80-base pair (bp) DNA sequence from 5'-flanking region of PRL gene (located between -330 and -250 bp) was included in the PRL-CAT fusion gene constructs. Furthermore, a DNA/protein interaction involving this 80-bp DNA sequence and a 60-kDa nuclear protein was detected only in PRL- cells but not in PRL+ GH cells. These results suggested that the strain-specific suppression of PRL gene in PRL-, GH12C1 cells was mediated via interaction of a cis-acting negative regulatory element with a negative regulatory trans-acting factor in these cells. The negative regulatory element within the AT-rich 80-bp DNA sequence was mapped immediately adjacent to the site of interaction of trans-activators of PRL gene.

Animals↗

PubMed1988

Transient expression in mammalian cells of the bacterial reporter gene encoding mercuric reductase: effects of various regulatory elements.

The effect of several transcriptional regulatory elements on gene expression in mammalian cells was investigated. As a reporter gene we have used the bacterial gene merA coding for the enzyme mercuric reductase. Several plasmids were constructed with different promoter/enhancer sequences (pSV/E, pSV/L, pMT, pRSV or pAd) at the 5' end and different splicing (small intron of the T antigen of SV40 or the second intron of the rabbit beta-globin gene) and/or polyadenylation signals (AEn, ALn or AR beta Gn) at the 3' end of the merA gene. Expression was measured in five different mammalian cell lines. In COS cells the highest level of expression is obtained with pSV/L and the lowest level with pSV/E. In HeLa, CV-1, Ltk-, and CHO cells merA expression is relatively high, under control of pRSV and pMT and relatively low under control of pSV/L and pAd. The introns studied have a negative effect on the expression of merA. The presence of a polyadenylation signal downstream from the gene is essential for its expression. The three different polyadenylation signals studied give a similar stimulatory effect on the level of expression of the merA gene.

Animals↗

PubMed1993

Tissue-specific and wound-inducible pattern of expression of the mannopine synthase promoter is determined by the interaction between positive and negative cis-regulatory elements.

In transgenic tobacco plants the regulatory region of the Agrobacterium genes involved in mannopine synthesis (pmas) directs expression in vascular tissues and is induced upon wounding. To identify cis-acting sequences required for the cell-type-specific and wound-inducible expression of this regulatory region, the expression pattern of chimeric genes in which 5' upstream deletions of the pmas 1' promoter direct the expression of the beta-glucuronidase coding sequence, was analyzed in transgenic tobacco plants. It was found that the pmas1' promoter is specifically expressed in phloem cells and that this tissue-specific pattern of expression is the result of the interaction of at least two negative regulatory elements with a positive element that directs expression in many cell types. It was also found that wound induction is mediated by two different mechanisms, one of them involving a dramatic change in tissue-specific expression.

Agrobacterium tumefaciens↗

PubMed2001

Role of polypyrimidine tract binding protein in the function of the hepatitis B virus posttranscriptional regulatory element.

The hepatitis B virus posttranscriptional regulatory element (PRE) is an RNA element that increases the expression of unspliced mRNAs, apparently by facilitating their export from the nucleus. We have identified a cellular protein that binds to the PRE as the polypyrimidine tract binding protein (PTB), which shuttles rapidly between the nucleus and the cytoplasm. Mutants of the PRE with mutations in PTB binding sites show markedly decreased activity, while cells that stably overexpress PTB show increased PRE-dependent gene expression. Export of PTB from the nucleus, like PRE function, is blocked by a mutant form of Ran binding protein 1 but not by leptomycin B. Therefore, PTB is important for PRE activity and appears to function as an export factor for PRE-containing mRNAs.

Base Sequence↗

PubMed1995

In vitro binding and functional studies comparing the human CYP1A1 negative regulatory element with the orthologous sequences from rodent genes.

In previous studies, we identified a 21 bp palindrome (-794 to -774) located within the negative regulatory element of the human CYP1A1 gene consisting of an 8 bp inverted repeat and 5 bp spacer. This element specifically binds protein(s) present in HepG2 nuclear extract preparations and is capable of down-regulating heterologous promoters and enhancers in transient expression assays. Conserved guanine/cytosine-rich regions which flank the palindrome also were implicated in this activity. In the present study, we examined similar regions from the rat (-881 to -746) and mouse (-822 to -683) CYP1A1 genes for their ability to bind nuclear protein and down-regulate heterologous promoters and enhancers. These rodent DNA fragments contain the conserved guanine/cytosine-rich sequences, as well as half-sites similar to those found in the human CYP1A1 palindrome. However, each half-site is separated by approximately 40 bp. DNase I footprint analyses revealed the presence of rat and mouse nuclear proteins which gave a similar protection pattern as that observed with nuclear proteins from the human cell line, HepG2. Electrophoretic mobility shift assays with the human negative regulatory element demonstrated the formation of specific DNA-protein complexes with rat and mouse nuclear protein(s). Interestingly, two specific DNA-protein complexes were observed with rodent extracts as compared to the single specific complex seen with human extract. Specific binding was not observed with either the orthologous rat or mouse fragments using human or rodent extracts. In transient expression assays, the rat and mouse fragments were unable to down-regulate enhancer/promoter activity. This absence of negative regulatory activity occurred whether transfections were performed in human, rat or mouse hepatoma cell lines. The human negative regulatory element, which was previously shown to down-regulate heterologous enhancers/promoters approximately 70% in human cells, did not exhibit this activity in rodent cell lines. UV cross-linking and southwestern blot analyses indicated a high degree of similarity between human and rodent NRE binding proteins, although some differences also were apparent. The possible implications of these findings with regards to species differences in the regulation of CYP1A1 expression are discussed.

Animals↗

PubMed1994

Regulatory elements and transcription factors controlling basal and cytokine-induced expression of the gene encoding intercellular adhesion molecule 1.

The gene encoding intercellular adhesion molecule 1 (ICAM-1) is transcriptionally induced in response to inflammatory and immunomodulatory cytokines. To investigate the mechanisms controlling ICAM-1 gene expression, we have identified regulatory DNA sequences responsible for maintaining basal and mediating induced transcription in response to tumor necrosis factor alpha (TNF-alpha) and interferon gamma (IFN-gamma). Regulatory elements centered 115, 60, and 40 bp upstream from the ICAM-1 transcription start site were implicated in cytokine-independent gene expression. Regulatory elements dedicated to TNF-alpha and IFN-gamma were identified 190 and 90 bp, respectively, upstream from the ICAM-1 transcription start site. A combination of mutagenesis and DNA-binding assays revealed that the TNF-alpha response element is composite, consisting of binding sites for both C/EBP and NF-kappa B. The IFN-gamma response element behaved as a simple regulatory element that selectively binds to an IFN-gamma-inducible activity composed, at least in part, of p91. These observations provide a framework for understanding how extracellular signals dynamically regulate the adhesive properties of mammalian cells.

Base Sequence↗

PubMed1999

Characterization of cleavage enzymes for sterol regulatory element binding protein in hamster liver microsomes.

Sterol regulatory element binding proteins (SREBP-1 and SREBP-2) are the key transcription factors for the regulation of the cellular cholesterol level. To identify proteolytic enzymes for SREBPs, a fluorogenic peptide substrate, MOCAc-GRSVLSFK(Dnp)rr-NH2, was synthesized according to the proposed cleavage site of human SREBP-2. In microsome fractions from hamster liver, we found a peptidase activity inhibitable by the synthetic inhibitor Ac-GRSVL-aldehyde with an IC50 of 40 nM. This peptidase separated into three peaks of approximately 400 kDa, 60 kDa, and 30 kDa (Mp400, Mp60 and Mp30 respectively) upon gel permeation chromatography. Mp30 was purified to apparent homogeneity with an Mr of 32 kDa. The partial amino acid sequence of Mp30 possessed homology to cathepsin B (EC 3.4.22.1). A 109 kDa protein band on SDS-PAGE which corresponded to Mp400 exhibited homology to neprilysin (EC 3.4.24.11) in partial amino acid sequence. These findings suggest several degradative pathways for SREBP in liver microsome membranes.

Amino Acid Sequence↗

PubMed1991

A protein with a binding specificity similar to NF-kappa B binds to a steroid-dependent regulatory element in the ovalbumin gene.

The chicken ovalbumin gene is regulated at the level of transcription by four classes of steroid hormones. A steroid-dependent regulatory element (SDRE) found from -900 to -732 is required for this steroid-mediated induction. To define more precisely sequences of the SDRE required for steroidal induction, a series of exonuclease III deletions were made in the 3' end of the SDRE. Fusion genes containing the mutant ovalbumin 5'-flanking sequences linked to the chloramphenicol acetyltransferase structural gene (CAT) were transfected into steroid-responsive primary oviduct cells. These functional studies defined a region of the SDRE from -793 to -759 that is essential for induction by steroids. Analysis of protein interactions in this 34-base pair region by copper-phenanthroline footprinting and methylation interference assays defined nucleotides required for protein binding. Footprinting showed protection of residues extending from -784 to -765, an area that included nucleotides that, when methylated, interfered with protein binding. In addition, this footprinted region contained 10 nucleotides that were identical to sequences contained in the beta-interferon gene regulatory element. An oligomer synthesized to this region of homology produced two DNA-protein complexes with oviduct nuclear proteins. Although this region of the interferon gene regulatory element binds the transcription factor NF-kappa B, an oligomer from the immunoglobulin kappa light chain gene known to bind NF-kappa B did not compete with the SDRE oligomer for binding to oviduct nuclear proteins. Surprisingly, this same NF-kappa B oligomer was able to restore steroid responsiveness to an SDRE mutant, while an oligomer from the immunoglobulin heavy chain gene inserted in the same position did not affect induction by steroids. These data suggest that a protein binding to sequences in the SDRE that are similar to an NF-kappa B-binding site participates in the steroid-mediated increase in transcription of the chicken ovalbumin gene.

Animals↗