Specific binding of the glucocorticoid-receptor complex to the mouse mammary tumor proviral promoter region

Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets

BACKGROUND

The sentence of "Danshen (Salvia Miltiorrhizae Radix et Rhizoma) and Siwu decoction are similar in function" was first recorded in an ancient Chinese medical book "Fu Ren Ming Li Lun". This theory has far-reaching influence on the clinical practice of Chinese medicine and is highly respected by Chinese medical doctors. However, the theory has limitations and controversial part for there is no in-depth and system comparative study.

METHODS

We collected the molecular structures of 129 compounds of Danshen and 81 compounds of Siwu decoction from the literatures. MACCS fingerprints and Tanimoto similarity were calculated based on the molecular structures for comparing the structural feature. Molecular descriptors which represent physical and chemical properties were calculated by Discovery Studio. Principal component analysis (PCA) of was performed based on the descriptors. The ADMET properties were predicted by FAF-Drugs4. The effect targets for the compounds with good ADMET properties were confirmed from experimental data and predicted using the algorithm comprising Bernoulli Naive Bayes profiling.

RESULTS

Based on the molecular structures, the presented study compared the structural feature, physical and chemical properties, ADMET properties, and effect targets of compounds of Danshen and Siwu decoction. It is found that Danshen and Siwu decoction do not have the same main active components. Moreover, the 2D structure of compounds from Danshen and Siwu decoction is not similar. Some of the compounds of Danshen and Siwu decoction are similar in 3D structure. The compounds with good ADMET properties of Danshen and Siwu decoction have same predicted targets, but some have different targets.

CONCLUSIONS

It can be inferred from the result that Danshen and Siwu decoction have some similarities, but also present differences from each other in the structure of the compounds and predicted targets. This may be the material basis of the similar and different traditional efficacy of Danshen and Siwu decoction. The setence of " Danshen and Siwu decoction are similar in function. " which is used in clinical has its material basis and target connotation to some extent. However, the traditional effects of Danshen and Siwu decoction are not exactly the same.

Higher-Order Structural Determinants for Expression of the Ovalbumin Gene Family

The ovalbumin gene and the ovalbumin-related X and Y genes are expressed in the chicken oviduct in response to steroid hormones. These three genes are linked within a 100 kb domain of DNA which is preferentially sensitive to DNase I digestion in oviduct cell nuclei. No such preferential sensitivity to DNase is observed in nuclei isolated from other chicken tissues in which these genes are not transcribed. Thus, the DNase I sensitivity observed is correlated with the capacity for these genes to be expressed in oviduct. We have asked the question: are there specific signals in the DNA which are responsible for defining this domain or for conferring upon it the active, DNase I-sensitive, conformation? We have located DNA sequences belonging to a single repetitive DNA family, termed CR1, which are preferentially located in or near the boundary regions of the 100 kb domain. Therefore, these CR1 sequences are possible candidates for such a function. We have also searched for, but have not observed, any tissue-specific rearrangements of the DNA in the boundary regions of the domain. It is therefore unlikely that DNA rearrangements are involved in establishing the DNase I-sensitive domain in oviduct cells. However, we do note that a region at the far 3' end of the domain exhibits a cytidine methylation pattern which is highly variable among different chicken tissues. In particular, this region, which is approximately 30 kb downstream from the ovalbumin gene, is undermethylated in oviduct as compared to other hen tissues, and thus could be a control region involved in domain activation.

A robust characterization of retinoic acid response elements based on a comparison of sites in three species

The availability of high-throughput genomic sequencing has allowed us to construct a more robust characterization of retinoic acid response elements than was possible in the past. We located human, mouse, and rat homologs for each of 51 well-documented, conserved retinoic acid response elements. Mathematical and statistical analyses of these 153 sites, 78 of which are new, shows that 92% of response elements have direct-repeat symmetry, but that only 76% exhibit canonical spacing attributes. While the familiar '(a/g)g(g/t)tca' hexamer motif is upheld, the more relaxed sequence, '(a/g)g(g/t)(g/t)(g/c)a', represents a 10% consensus. Sites are as likely to be on the coding strand as on the non-coding strand, and 86% of them are in upstream locations. From a statistical point of view, DR1 elements are fundamentally different from DR2 and DR5 elements, but this is only evident in the 5' hexamer. While there is considerable variation in core positions, and while no nucleotide can be considered forbidden at any position, variation among species at a fixed locus appears surprisingly constrained once a functional site has been attained.

The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction

We examined in detail the DNA interaction of the nuclear receptors NGFI-B and steroidogenic factor 1 (SF-1) by using a series of gain-of-function domain swaps. NGFI-B bound with high affinity as a monomer to a nearly linear DNA molecule. The prototypic zinc modules interacted with a half-site of the estrogen receptor class, and a distinct protein motif carboxy terminal to the zinc modules (the A box) interacted with two A/T base pairs 5' to the half-site. SF-1 bound in the same manner as NGFI-B, with an overlapping but distinct sequence requirement 5' to the half-site. The key features that distinguished the NGFI-B and SF-1 interactions were an amino group in the minor groove of the SF-1 binding sequence and an asparagine in the SF-1 A box. These results define a common mechanism of NGFI-B and SF-1 DNA binding, which may underlie a competitive mechanism of gene regulation in steroidogenic tissues that express these proteins. This monomer-DNA interaction represents a third paradigm of DNA binding by nuclear receptors in addition to direct and inverted dimerization.

The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction

We examined in detail the DNA interaction of the nuclear receptors NGFI-B and steroidogenic factor 1 (SF-1) by using a series of gain-of-function domain swaps. NGFI-B bound with high affinity as a monomer to a nearly linear DNA molecule. The prototypic zinc modules interacted with a half-site of the estrogen receptor class, and a distinct protein motif carboxy terminal to the zinc modules (the A box) interacted with two A/T base pairs 5' to the half-site. SF-1 bound in the same manner as NGFI-B, with an overlapping but distinct sequence requirement 5' to the half-site. The key features that distinguished the NGFI-B and SF-1 interactions were an amino group in the minor groove of the SF-1 binding sequence and an asparagine in the SF-1 A box. These results define a common mechanism of NGFI-B and SF-1 DNA binding, which may underlie a competitive mechanism of gene regulation in steroidogenic tissues that express these proteins. This monomer-DNA interaction represents a third paradigm of DNA binding by nuclear receptors in addition to direct and inverted dimerization.

Effect of glucocorticoids on TPA-induced inhibition of gap-junctional communication and morphological transformation in Syrian hamster embryo cells

The effect of glucocorticoids on 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inhibition of gap-junctional intercellular communication (GJIC) and morphological transformation in Syrian hamster embryo (SHE) cells was examined. Fluocinolone acetonide (FA) and dexamethasone (DEX) almost completely suppressed the effect of TPA on induction of transformed morphology. On the other hand, up to 1000 times higher FA and DEX concentrations did not influence the inhibitory effect of TPA on GJIC. Neither treatment with these glucocorticoids for 4, 24 or 48 h before TPA exposure nor 24 h co-exposure with TPA altered the effect of TPA on GJIC. Thus the potent effect of glucocorticoids as inhibitors of the promotional effect of TPA on morphological transformation in SHE cells does not result in alterations of TPA-induced inhibition of GJIC.

Downregulation of JE and KC genes by glucocorticoids does not prevent the G0----G1 transition in BALB/3T3 cells

The effects of glucocorticoid hormones on the expression of the growth factor-inducible genes JE, KC, and c-myc were analyzed in parental BALB/3T3 and polyomavirus middle-T antigen-transfected cell lines. Northern (RNA) blot hybridization and run-on transcription analysis showed that (i) glucocorticoid hormones selectively inhibit JE and KC expression at the transcriptional level and (ii) the downregulatory effect of glucocorticoids on JE and KC expression is partial for serum-stimulated and middle T antigen-transformed cells and total for quiescent and exponentially growing cells. Gel mobility assays using AP-1 oligonucleotides showed a positive correlation between glucocorticoid downregulating effect and presence of the AP-1 complex. JE and KC downregulation by means of the AP-1 complex may play a role in the actions of glucocorticoids as anti-inflammatory and antitumor agents. The ability of glucocorticoids to downregulate JE and KC was used to investigate the relevance of these genes to the mitogenic response to serum growth factors. Hydrocortisone did not alter the basal DNA synthesis level displayed by quiescent 3T3 cells, but it potentiated both the mitogenic effect of platelet-derived growth factor and c-myc induction by serum growth factors. Upon serum restimulation, untreated and dexamethasone-treated quiescent 3T3 cultures entered the S phase after an identical time lag (G1). These results suggest that (i) JE and KC are not necessary for the G0----G1----S transition and (ii) c-myc overexpression is likely to be the basis for the potentiating effect of glucocorticoids on serum growth factors.

Downregulation of JE and KC genes by glucocorticoids does not prevent the G0----G1 transition in BALB/3T3 cells

The effects of glucocorticoid hormones on the expression of the growth factor-inducible genes JE, KC, and c-myc were analyzed in parental BALB/3T3 and polyomavirus middle-T antigen-transfected cell lines. Northern (RNA) blot hybridization and run-on transcription analysis showed that (i) glucocorticoid hormones selectively inhibit JE and KC expression at the transcriptional level and (ii) the downregulatory effect of glucocorticoids on JE and KC expression is partial for serum-stimulated and middle T antigen-transformed cells and total for quiescent and exponentially growing cells. Gel mobility assays using AP-1 oligonucleotides showed a positive correlation between glucocorticoid downregulating effect and presence of the AP-1 complex. JE and KC downregulation by means of the AP-1 complex may play a role in the actions of glucocorticoids as anti-inflammatory and antitumor agents. The ability of glucocorticoids to downregulate JE and KC was used to investigate the relevance of these genes to the mitogenic response to serum growth factors. Hydrocortisone did not alter the basal DNA synthesis level displayed by quiescent 3T3 cells, but it potentiated both the mitogenic effect of platelet-derived growth factor and c-myc induction by serum growth factors. Upon serum restimulation, untreated and dexamethasone-treated quiescent 3T3 cultures entered the S phase after an identical time lag (G1). These results suggest that (i) JE and KC are not necessary for the G0----G1----S transition and (ii) c-myc overexpression is likely to be the basis for the potentiating effect of glucocorticoids on serum growth factors.

Studies on protein-DNA interactions using the resonant recognition model. Application to repressors and transforming proteins

The structural features of protein-DNA interactions have been evaluated using a new information theory algorithm for the analysis of protein structure/function dependence: the so-called resonant recognition model. The physicochemical basis of this analysis was firstly validated with the trp-repressor-operator interaction as a well-defined example. The amino acid and structural features predicted by these procedures to be crucial for repressor-operator interaction were found to be clustered around the known three-dimensional structure of the active site of the trp repressor. Similar methods of analysis have been extended to the less-well-defined example of the Ha-ras p21 protein family. The results of this analysis have indicated two distinct interactive regions in p21, one associated with the guanine-nucleotide-binding site, whilst the second is proposed to be associated with a binding site for an activator protein. These studies indicate that the p21 protein, besides the ability to function as a plasma-membrane-associated guanine-nucleotide-binding regulatory protein and bind free guanine nucleotides in the cytoplasm, has the structural ability to bind guanine incorporated in DNA. Thus, p21-related proteins may have the potential to function as an DNA-binding and regulating protein with the mode of upstream DNA binding closely related to their oncogenic function.

Co-operative binding of the glucocorticoid receptor DNA binding domain is one of at least two mechanisms for synergism

Steroid induction of responsive genes functions through the synergistic activity of steroid receptor binding sequences with adjacent binding sites either for other transcription factors or for further steroid receptors. Analysis of the human glucocorticoid receptor revealed that the DNA-binding domain of the receptor is sufficient to mediate co-operative binding to adjacent receptor binding sites. This is a novel feature of the domain in addition to its DNA-binding, trans-activating and trans-repressing properties. Chimaeric proteins containing the N- or C-terminal receptor halves fused to the GAL4 DNA-binding domain do not co-operate in DNA-binding, however they do functionally synergize. Thus, at least two mechanisms contribute to the synergism of the human glucocorticoid receptor bound to two adjacent receptor binding sites.

Identification of ecdysone response elements by analysis of the Drosophila Eip28/29 gene

We have identified ecdysone-response elements (EcREs) by studying regulation of the steroid-responsive Drosophila Eip28/29 gene. First, functional assays of deletion mutants identified large sequence regions required for the response; then a blotting method using the specifically labeled steroid receptor as probe identified receptor-binding regions. Three short receptor-binding regions near Eip28/29 have been identified: Prox and Dist [521 and 2295 nucleotides, respectively, downstream of the poly(A) site] are probably required for the Eip28/29 response in cell lines; Upstream (-440) is unnecessary for that response. We have also demonstrated that an EcRE-containing region from hsp27 contains a receptor-binding site. Each of these four receptor-binding regions functions as an EcRE when placed upstream of an ecdysone nonresponsive promoter and each contains an imperfect palindrome, suggesting the consensus 5'-RG(GT)TCANTGA(CA)CY-3'. Furthermore, a synthetic 15-bp fragment containing an imperfect palindrome similar to the consensus is a fully functional EcRE. The presence of any of the EcREs leads, in the absence of hormone, to depressed gene expression. When hormone is added, it relieves this repression and causes additional activation. The similarity of the EcRE sequence to response elements for estrogen, thyroid hormone, and retinoic acid receptors suggests that the steroid receptors and their signal transduction mechanisms have been strongly and broadly conserved.

Antitumor promotion and antiinflammation: down-modulation of AP-1 (Fos/Jun) activity by glucocorticoid hormone

Glucocorticoid hormones counteract inflammation and phorbol ester tumor promotion and drastically decrease the expression of several extracellular proteases, including collagenase I. Glucocorticoid hormone inhibits basal and induced transcription of collagenase by interfering with AP-1, the major enhancer factor of the collagenase promoter. The mechanism of interference is novel in that it does not require protein synthesis, it depends on the hormone receptor but not its binding to DNA, it occurs at hormone doses one order of magnitude below those required for gene activation, and it involves down-modulation of the trans-activating function of preexisting unbound and DNA-bound AP-1. Coprecipitation experiments suggest direct AP-1-hormone receptor interaction, which also possibly explains the reverse experiment: overexpression of Fos or Jun inhibits the expression of hormone-dependent genes.

Localization of an estrogen receptor binding site near the promoter of the uteroglobin gene

By means of a DNA-cellulose competitive binding assay, we have studied the interaction of the estrogen receptor with genomic fragments of the estrogen responsive rabbit uteroglobin gene. The fragments spanned from 3255 bp upstream to 1754 bp downstream of the initiation site. Only a fragment (-396/+8) showed strong affinity for the receptor. Within this fragment a unique palindromic sequence (GGTCAccaTGCCC) was found which is very similar to the canonical consensus sequence for the estrogen receptor. A synthetic oligonucleotide of that structure specifically competed for the binding of the receptor to DNA-cellulose.

The influence of vitamin B6 on the structure and function of the glucocorticoid receptor

Pyridoxal phosphate influences several properties of steroid hormone receptors in vitro, but its role in vivo has not been clearly established. In an effort to address this issue, we have investigated the in vivo effects of vitamin B6 on the physical properties and biological function of the human glucocorticoid receptor. We demonstrate that vitamin B6 treatment of whole cells in culture produces an alteration in the isoelectric point of the receptor, as well as changes in the steroid and DNA binding capacities. Furthermore, glucocorticoid dependent transcriptional activation properties of the receptor are also altered by modulation of the vitamin B6 status. High concentrations of vitamin B6 suppress activation of transcription, while vitamin deficiency enhances responsiveness to steroid hormone. Together, these studies imply a physiological role for vitamin B6 in glucocorticoid hormone action.

Thyroid hormone receptors from IM-9 cells but not HeLa cells bind to promoters of triiodothyronine-responsive genes

We have used thyroid hormone receptors from two different human cell lines to investigate receptor binding to the promoters of thyroid hormone-responsive genes. Receptors extracted from IM-9 cells or HeLa cells displayed virtually identical affinity and specificity for [125I]triiodothyronine binding. The cells expressed a c-erbA alpha gene in the same relative proportions as the receptor concentrations. Both receptors were bound to DNA-cellulose and could be displaced with increasing concentrations of calf thymus DNA or pBR322 DNA. Relative to pBR322 DNA (designated as 1), binding to the hGH gene promoter was 8.1 +/- 1.1 using the IM-9 cell receptor. With the HeLa cell receptor relative binding was only 1.1 +/- 0.2. Similar relative differences were obtained with the mouse glandular kallikrein gene, mGK-6. In heat stability studies the IM-9 cell receptor was more resistant to heat inactivation than the HeLa receptor. Triiodothyronine receptors with identical hormone binding patterns may require the presence of an unidentified factor(s) which allows correct recognition of regulation sequences within responsive genes.

Binding of androgen-receptor complexes to alpha 2u-globulin genes and to the long terminal repeat of mouse mammary tumor virus

The binding of androgen-receptor complexes to fragments derived from two alpha 2u-globulin genes (RAP 01 and RAO 01) was studied using a DNA-cellulose competition assay. Rat prostate cytosol labelled with [3H]mibolerone was used as a source of the androgen receptor. Two controls were included in these studies: the long terminal repeat (LTR) of mouse mammary tumor virus which has previously been shown to act as an androgen response element and a fragment of the C3 gene of prostatic binding protein which has been demonstrated to bind androgen-receptor complexes. Our experiments indicate that androgen-receptor complexes bind specifically and with comparable affinity to the C3 gene fragment, the LTR and a fragment of RAP 01 located in the 5'-upstream region (bp -642 up to -584). No specific interaction was observed with fragments derived from RAO 01. The region of RAP 01 which binds androgen-receptor complexes has previously been shown to interact with glucocorticoid receptors and contains a 17 bp sequence homologous with the consensus sequence for glucocorticoid-receptor binding. A mutation in this sequence in RAO 01 may be responsible for the loss of glucocorticoid and androgen-receptor binding. It is concluded that at least one member of the alpha 2u-globulin gene family interacts directly with androgen-receptor complexes with an affinity comparable to that observed for other androgen-dependent genes. The binding is observed in a region displaying also affinity for the glucocorticoid receptor.

DNA regulatory elements for steroid hormones

Gene regulation by steroid hormones is mediated through an interaction of the hormone receptors with DNA regulatory sequences called hormone regulatory or responsive elements (HRE). An analysis of the HRE's in the DNA of mouse mammary tumour provirus, human metallothionein IIA gene, chicken lysozyme gene, chicken and Xenopus vitellogenin genes, growth hormones genes, Moloney murine sarcoma provirus, rabbit uteroglobin gene, rat tyrosine aminotransferase gene, rat tryptophan oxygenase gene and rat acidic glycoprotein gene, yields the following consensus for positively modulated glucocorticoid responsive elements (GRE): 5'-GGTACAnnnTGTTCT-3'. This element can also mediate induction by progesterone and probably by androgens, but not by estrogens. Detailed analysis of the DNA protection pattern suggests that a dimer of the hormone receptor interacts with this palindromic 15-mer. In genes that are negatively regulated by glucocorticoids an imperfect copy of the GRE is found, and repression is probably due to competition between hormone receptor and other transcription factors or enhancer binding proteins for binding to overlapping DNA sequences. The receptors without bound hormone are able to interact specifically with DNA in vitro, but binding of hormone is needed for transcriptional activation in vivo. This could be due, at least in part, to changes in the rate parameters of the receptor-DNA interaction induced by binding of the hormone to the receptor. The possible role of precise chromatin organization in glucocorticoid induction is discussed on the basis of the nucleosome phasing found in the LTR region of mouse mammary tumour virus.

Synergism of closely adjacent estrogen-responsive elements increases their regulatory potential

Recent gene transfer experiments have shown that an estrogen-responsive DNA element (ERE) GGTCANNNTGACC mediates the estrogen inducibility of the Xenopus laevis vitellogenin A1 and A2 genes as well as the chicken vitellogenin II gene. We report here on experiments that explain the estrogen regulation of the Xenopus vitellogenin B1 and B2 genes. In these genes, two ERE homologues, which have only low, if any, regulatory capacity on their own, act synergistically to achieve high estrogen inducibility. Furthermore we show that synergism of EREs is most efficient, when the two elements are closely adjacent and that it is lost when the synergistic elements are separated by 125 basepairs. In-vitro estrogen receptor binding experiments indicate that co-operative binding of estrogen receptors to closely adjacent EREs is not essential for synergism of ERE homologues that have no intrinsic regulatory capacity. Functional synergism of EREs is observed in the human estrogen-responsive MCF-7 cell line as well as in mouse fibroblasts (Ltk-) cotransfected with estrogen receptor expression vectors. Even expression of a truncated receptor protein lacking 178 amino acid residues of the amino-terminal end allows synergism, suggesting that the amino-terminal end preceding the DNA-binding domain of the estrogen receptor is not required.

A twenty-two-fold increase in the relative affinity of estrogen receptor to poly (dA-dC).poly (dG-dT) in the presence of polyamines

We studied the relative efficacy of polyamines to facilitate the binding of estrogen receptor to poly(dA-dC).poly(dG-dT). In the absence of polyamines, 1,400 micrograms/ml of this polynucleotide eluted 50% of bound estrogen receptor from DNA-cellulose. In contrast, 50% estrogen receptor was eluted by 65 micrograms/ml of poly(dA-dC).poly(dG-dT) complexed with 150 microM spermidine. Putrescine and spermine also enhanced the ability of poly(dA-dC).poly(dG-dT) to elute estrogen receptor, but the magnitude of the effect was not as high as that of spermidine. Control experiments with calf thymus DNA and poly(dA-dT).poly(dA-dT) showed 6- and 3-fold increase, respectively in their affinity for estrogen receptor in the presence of spermidine. The dramatic increase in the affinity of poly(dA-dC).poly(dG-dT) for estrogen receptor in the presence of polyamines might be a result of the conversion of the polynucleotide to the left-handed Z-DNA form. These results show that polyamines are capable of participating in estrogenic regulation of gene expression by altering the affinity of the receptor for specific DNA sequences.

The steroid and thyroid hormone receptor superfamily

Analyses of steroid receptors are important for understanding molecular details of transcriptional control, as well as providing insight as to how an individual transacting factor contributes to cell identity and function. These studies have led to the identification of a superfamily of regulatory proteins that include receptors for thyroid hormone and the vertebrate morphogen retinoic acid. Although animals employ complex and often distinct ways to control their physiology and development, the discovery of receptor-related molecules in a wide range of species suggests that mechanisms underlying morphogenesis and homeostasis may be more ubiquitous than previously expected.

A 13 bp palindrome is a functional estrogen responsive element and interacts specifically with estrogen receptor

Sequences located upstream of the transcription initiation site of the Xenopus vitellogenin A2 (vit A2) gene contain a hormone dependent enhancer that confers estrogen control to the heterologous thymidine kinase (tk) promoter. As a minimal functional estrogen responsive element (ERE), we have defined the 13 bp palindrome GGTCACAGTGACC. This ERE binds estrogen receptor preferentially in vitro. Although the ERE shares some structural features with the glucocorticoid responsive element (GRE) it is distinct from this element since it neither binds glucocorticoid receptor in vitro nor does it confer glucocorticoid inducibility to a fusion gene. Point mutations within the ERE decrease its affinity for the estrogen receptor and result in a complete loss of estrogen inducibility.

Glucocorticoid receptor binding to defined regions of alpha 2u-globulin genes

A DNA-cellulose competition assay was used to study binding of glucocorticoid receptor complexes to two alpha 2u-globulin genes, RAP 01 and RAO 01. Two binding regions were found in RAP 01, one localized between bp -642 and -452, the other between -252 and -118 from the transcriptional initiation site. Only the second region was found in RAO 01. The binding affinity was comparable to that observed using a long terminal repeat fragment of mouse mammary tumor virus. Both regions contain sequences homologous to a 17-bp consensus proposed for the glucocorticoid receptor binding. Therefore, despite evidence that glucocorticoid induction of alpha 2u-globulin may be indirect, a direct action of the receptor in the 5'-upstream region of the genes cannot be excluded.

Androgen receptor-binding regions of an androgen-responsive gene

The interaction of 5 alpha-dihydrotestosterone-receptor complexes with purified DNA fragments representing upstream, coding and intervening sequences of the prostate binding protein C3(1) gene was investigated using a DNA-cellulose competition binding assay. The partially purified androgen-receptor complexes which were used in the assay had proven DNA-binding capabilities. Two fragments were identified with relatively high affinity for androgen-receptor complexes. A 300 bp fragment extending from -220 to +80 and a 500 bp fragment derived entirely from the first intron consistently competed most effectively in the system. The presence of a high affinity site or sites in or near the promoter region of the gene is consistent with current models of transcriptional activation of hormone-responsive genes by steroid receptors. High affinity sites for steroid receptors within introns may indicate a role for receptors in regulation of transcription at other stages, or in post-transcriptional modification.

pBR322 contains glucocorticoid regulatory element DNA consensus sequences

A computer search of the pBR322 DNA sequence identified five sites matching reported glucocorticoid regulatory element (GRE) DNA consensus sequences and three related sites. A pBR322 DNA fragment containing one GRE site was shown to bind immobilized HeLa S3 cell glucocorticoid receptor and to compete for receptor binding in a competitive binding assay. Conversely, a pBR322 DNA fragment devoid of GRE sites showed barely detectable interaction with glucocorticoid receptor in either of these assays. These results demonstrate the importance of GRE consensus sequences in glucocorticoid receptor interactions with DNA, and further identify a cause for high background binding observed when pBR322 DNA is used as a negative control in studies of glucocorticoid receptor-DNA interactions.

Application of a protein-blotting procedure to the study of human glucocorticoid receptor interactions with DNA

To exert their effects, glucocorticoid receptor complexes interact selectively with DNA sequences known as glucocorticoid regulatory elements. We have studied the interaction between human glucocorticoid receptors and mouse mammary tumor virus (MMTV) DNA by means of a procedure that permits analysis after immobilization of the receptor on nitrocellulose. Proteins from crude cytosolic or nuclear extracts were electrophoresed on NaDodSO4/PAGE gels, soaked in a urea buffer to remove NaDodSO4, transferred to nitrocellulose, and probed with nick-translated MMTV [32P]DNA in a 5% nonfat dry milk buffer, which minimizes nonselective DNA-protein interactions. We present evidence that MMTV [32P]DNA interacts selectively with the glucocorticoid receptor. These data include comigration of [3H]dexamethasone mesylate-labeled band and bound MMTV [32P]DNA on gel electrophoresis systems; localization of DNA-binding activity in the cytosol of cells incubated with steroid at 0 degrees C and in the nucleus and cytosol of cells incubated at 37 degrees C; binding of the MMTV DNA to highly purified receptor; and absence of MMTV DNA binding activity in extracts from cells whose receptor has been down-regulated. Furthermore, glucocorticoid receptors analyzed under these conditions exhibit selective binding to DNA fragments that contain glucocorticoid regulatory elements.

Expression of mink cell focus-forming murine leukemia virus-related transcripts in AKR mice

We used a synthetic 16-base-pair mink cell focus-forming (MCF) env-specific oligomer as radiolabeled probe to study MCF murine leukemia virus (MuLV)-related transcripts in brain, kidney, liver, spleen, and thymus tissues of AKR mice ranging from 5 weeks to 6 months (mo) of age. Tissue-specific expression of poly (A) + RNAs was seen: 6.0-kilobase (kb) transcripts were detected in the liver and kidney; 7.2- and 1.8-kb RNA species were present in the thymus. In addition, all the tissues tested contained 3.0-kb messages. The transcription of these MCF-related mRNAs was independent of the presence of ecotropic and xenotropic MuLVs. In general, expression of the MCF env-related transcripts appeared to peak at 2 mo of age; these messages were barely detectable in brain, kidney, liver, and spleen tissues after 2 mo and in thymus tissue after 4 mo of age. All of the subgenomic MCF env-related mRNAs (6.0, 7.2, 1.8, and 3.0 kb) appeared to contain the 190-base-pair cellular DNA insert, characteristic of the long terminal repeats associated with endogenous MCF env-related proviruses (A. S. Khan and M. A. Martin, Proc. Natl. Acad. Sci. USA 80:2699-2703, 1983). No genomic-size (8.4-kb) transcripts corresponding to endogenous MCF-related proviruses were detected. An 8.4-kb MCF env-related mRNA was first seen at 3 mo of age, exclusively in thymus tissue. This species most likely represents the first appearance of a recombinant MCF-related MuLV genome. The transcripts which were detected in thymus tissue might be involved in the generation of leukemogenic MCF viruses.

Steroid-dependent interaction of transcription factors with the inducible promoter of mouse mammary tumor virus in vivo

We have used exonuclease protection in vivo as an assay to detect interaction of nuclear factors with the steroid-inducible promoter of mouse mammary tumor virus. Binding of two factors is detected uniquely at the steroid-activated promoter, and results in protection of sequences between -82 and approximately +12 One factor is identified as the murine homolog of nuclear factor 1. The second (designated factor i) binds downstream of nuclear factor 1 and protects sequences extending over the cap site. Binding activities associated with both factors can be detected in crude nuclear extracts; their apparent concentrations are unaffected by hormone treatment of the cells. These results demonstrate that glucocorticoid induction of transcription results from receptor-mediated establishment of a transcription factor complex at the promoter rather than activation of a preexisting complex.

A distinct glucocorticoid hormone response regulates phosphoprotein maturation in rat hepatoma cells

Glucocorticoid hormone-dependent maturation of the mouse mammary tumor virus (MMTV) phosphorylated polyprotein (Pr74) allows experimental access to certain posttranslational regulatory circuits under steroid control in M1.54 cells, an MMTV-infected rat hepatoma cell line. Pulse-chase experiments revealed that [35S]methionine-labeled Pr74 synthesized in uninduced cells could be converted posttranslationally into p24, a stable phosphorylated maturation product, only after 4 h of exposure to 1 microM dexamethasone, a synthetic glucocorticoid. This regulated processing could be prevented by prior exposure, during the chase period, to inhibitors of RNA (actinomycin D) or protein (cycloheximide or puromycin) synthesis. Moreover, half-maximal production of p24 occurred at 10 nM dexamethasone, a concentration that approximated half-maximal receptor binding and stimulation of MMTV transcript synthesis. Kinetic, hormonal, and genetic evidence suggest that p24 expression did not require or result from the overall glucocorticoid-dependent increase in polyprotein concentration. First, 20 h after dexamethasone withdrawal, Pr74 maturation was completely deinduced, whereas the absolute level of this MMTV precursor remained 10-fold over its basal level. Second, progesterone, which competes with dexamethasone for receptor binding, facilitated the regulated production of p24 but prevented the steroid-mediated accumulation of functional MMTV mRNA. Lastly, certain glucocorticoid-responsive variants, derived from M1.54 cells by resistance to complement cytolysis, expressed p24 in the presence or absence of glucocorticoid-induced levels of Pr74. Taken together, our results suggest that the glucocorticoid-regulated maturation of MMTV phosphopolyproteins resulted from an independent hormone response that required normal receptor function and de novo RNA and protein synthesis.

Two different cis-active elements transfer the transcriptional effects of both EGF and phorbol esters

Short cis-active sequences of the rat prolactin or Moloney murine leukemia virus genes transfer transcriptional regulation by both epidermal growth factor and phorbol esters to fusion genes. These sequences act in a position- and orientation-independent manner. Competitive binding analyses with nuclear extracts from stimulated and unstimulated cells suggest that different trans-acting factors associate with the regulatory sequence of each gene. A model is proposed suggesting that both epidermal growth factor and phorbol esters stimulate the transcription of responsive genes via discrete classes of hormone-dependent, enhancer-like elements that bind different trans-acting factors, even in the absence of hormone stimulation.

Enhancer binding proteins predicted by informational spectrum method

Enhancer sequences analysed using the informational spectrum method (ISM) show a characteristic frequency at .0488. It has been shown that the characteristic frequency for some DNA binding proteins overlaps the characteristic frequency of their target DNA sequences. We suggest here that two types of proteins, homeoproteins and the glucocorticoid receptors, might bind to enhancer sequences.

Sequence-specific DNA binding of the progesterone receptor to the uteroglobin gene: effects of hormone, antihormone and receptor phosphorylation

The effects of ligand binding and receptor phosphorylation on the interaction of progesterone receptor with specific DNA sequences in the uteroglobin gene were studied by nitro-cellulose filter binding and DNase I footprinting. High affinity sites were mapped upstream from the transcription start and in the first intron. They contained a common TGTTCACT sequence. These sites were occupied with similar affinity by the receptor, either in its free state, or complexed with the hormone or an antagonist (RU486); and also by receptor which had been phosphorylated in vivo in a hormone-dependent manner. In all cases identical footprints were observed. These experiments led to the following conclusions. The hormone-dependency of receptor binding to DNA or chromatin is observed in intact cells and in crude cellular extracts but not with purified receptor. Thus in situ, the unliganded receptor probably interacts with some nuclear component(s) which stabilizes it in a 'non-activated' form (non-chromatin and non-DNA binding form). When isolated, the receptor may undergo activation, even in the absence of the hormone. Binding by receptor of an antihormone (and possibly receptor phosphorylation) exerts an effect on gene transcription through a mechanism which is different from (and probably follows) receptor interaction with the gene.

Thyroid hormone receptors bind to defined regions of the growth hormone and placental lactogen genes

The intracellular receptor for thyroid hormone is a protein found in chromatin. Since thyroid hormone stimulates transcription of the growth hormone gene through an unknown mechanism, the hypothesis that the thyroid hormone-receptor complex interacts with defined regions of this gene has been investigated in a cell-free system. Nuclear extracts from human lymphoblastoid IM-9 cells containing thyroid hormone receptors were incubated with L-3,5,3'-tri[125I]iodothyronine and calf thymus DNA-cellulose. Restriction fragments of the human growth hormone gene were added to determine their ability to inhibit labeled receptor binding to DNA-cellulose. These fragments encompassed nucleotide sequences from about three kilobase pairs upstream to about four kilobase pairs downstream from the transcription initiation site. The thyroid hormone-receptor complex bound preferentially to the 5'-flanking sequences of the growth hormone gene in a region between nucleotide coordinates -290 and -129. The receptor also bound to an analogous promoter region in the human placental lactogen gene, which has 92% nucleotide sequence homology with the growth hormone gene. These binding regions appear to be distinct from those that are recognized by the receptor for glucocorticoids, which stimulate growth hormone gene expression synergistically with thyroid hormone. The presence of thyroid hormone was required for binding of its receptor to the growth hormone gene promoter, suggesting that thyroid hormone renders the receptor capable of recognizing specific gene regions.

Receptor-mediated pharmacodynamics of prednisolone in the rat

A pharmacokinetic/pharmacodynamic model describing receptor-mediated effects of prednisolone is presented. The basis of the model is the generally accepted mechanism of action of steroid hormones in which corticosteroids bind to cytosolic receptors forming steroid-receptor complexes, which are activated and translocated into the nucleus. There the complexes associate with specific DNA sequences and modulate the rate of transcription of DNA into specific RNAs that code for the synthesis of proteins that elicit biological responses. Prednisolone, 5 or 50 mg/kg, was administered intravenously to adrenalectomized rats. Total plasma, free plasma, CBG-free plasma, and liver prednisolone concentrations were measured simultaneously with free hepatic cytosolic glucocorticoid receptor concentrations and tyrosine aminotransferase (TAT) activity of the liver as a function of time. The association/dissociation kinetics of prednisolone binding to the glucocorticoid receptor were measured separately in vitro at 37 degrees C. Total plasma, free plasma, and CBG-free plasma prednisolone concentrations could be used equally well in the model to account for the time course of receptor concentrations and TAT activity. However, use of liver steroid concentrations resulted in an overestimation of receptor depletion. Steroid concentrations in plasma increased 20 to 30-fold with a tenfold increase in dose, but receptor occupancy and TAT activity over time increased about threefold. While prednisolone pharmacokinetics were dose-dependent, parameters describing receptor kinetics and TAT activity were constant at each prednisolone dose. The major determinants of receptor-mediated glucocorticoid activity are confirmed to be the availability of the receptor, drug-receptor dissociation rate, and corticosteroid persistence in the biophase.

Glucocorticoid agonists as well as antagonists are effective inducers of mouse mammary tumor virus RNA in mouse mammary tumor cells treated with inhibitors of ADP-ribosylation

Glucocorticoids increase expression of specific genes by a mechanism involving binding to and "activation" of a specific receptor protein. Other steroids, such as RU 486, bind to the glucocorticoid receptor but the resultant steroid-receptor complex is unable to activate glucocorticoid sensitive genes. In the present study we have observed that steroid regulation of the glucocorticoid-regulated mouse mammary tumor virus (MMTV) genome in cultured mouse mammary tumor cells is altered by treatment of the cells with inhibitors of (ADP-ribose)n synthetase. The ability of glucocorticoid agonists to increase MMTV is about 2-fold increased by the inhibitor treatment. Interestingly, RU 486 and other steroids that are normally inactive in control cells are very good inducers of MMTV in the treated cells. This alteration in MMTV expression is associated with a 37% increase in nuclear binding of the glucocorticoid, triamcinolone acetonide, and also RU 486 in the inhibitor-treated cells. Steroids that do not bind to the glucocorticoid receptor are not inducers in control or in treated cells. The results point to a role for ADP-ribosylation of proteins as a negative regulator of MMTV expression and suggest a mechanism for activation of steroid-sensitive genomes.

Glucocorticoid mechanism of action: monoclonal antibodies as experimental tools

In order to provide a further insight into glucocorticoid receptor (GR)-mediated action of glucocorticoid hormones, we produced ten monoclonal antibodies against rat GR. In studies combining physicochemical separation methods with antibody methodology, we established that the molybdate-stabilised GR contains one steroid-binding monomer. Using a monoclonal anti-GR antibody-based immunoaffinity chromatographic procedure, we purified two non-ligand-binding proteins, with molecular weights of 80,000 and 90,000, present in the molybdate-stabilised GR complex. These proteins are not recognised by monoclonal antibodies directed against GR. The possible relation of these two proteins to heat shock proteins remains to be established. Immunohistochemical studies of GR in the central nervous system of the rat provided new information on the distribution of GR, particularly in the hypothalamus. Studies of intracellular receptor localisation in rat brain after endocrine manipulations gave results in support of the classical concept of translocation of GR from cytoplasm to cell nucleus. Studies with a cell culture system also supported the existence of GR in the cytoplasm as well as in the cell nucleus.

Distinct sequence elements involved in the glucocorticoid regulation of the mouse mammary tumor virus promoter identified by linker scanning mutagenesis

In the proviral DNA of mouse mammary tumor virus (MMTV), sequences up to approximately equal to 200 base-pairs from the RNA start site are required for stimulation of transcription by glucocorticoid hormones in cultured cells. A total of 26 mutant plasmids with clustered point mutations or small deletions in the hormone control region of the MMTV long terminal repeat were constructed, linked to the coding portion of the Herpes simplex virus thymidine kinase gene, and introduced by transfection into LTK- cells. Transcription from mutant DNA in the presence or absence of hormone was quantified by S1 nuclease protection assays. Our analysis revealed the presence of at least three control elements that affect the extent of transcription stimulation by glucocorticoid hormones: (1) a distal element, between -181 and -172 base-pairs from the RNA initiation site. Linker scanning mutants in this segment have a reduction of up to 20-fold in the hormone response with respect to wild type. (2) An element around position -120, defined by a mutation of 4 base-pairs between -121 and -117, which causes a fivefold reduction. (3) An element from approximately equal to -78 to -70, defined by a mutant with also a roughly fivefold lower stimulation. The first two are included in areas that have been shown by others to interact in vitro with hormone-receptor complexes; the last one overlaps the in vitro binding site of a nuclear protein factor. A mutant lacking all three elements (-193 to -70) is completely non-inducible by glucocorticoids. Together with earlier results obtained with 5' deletion mutants, the data show that the largest contribution to the stimulatory response is made by the distal element, which however does require the presence of both more-proximal ones for the response to be maximal. In the absence of the distal one, the two proximal elements together produce a residual stimulation in the order of 5 to 10% of wild type, while the -70 element alone is ineffective. In addition, we show that a functional TATA homology is required for maximum stimulation. It appears that transcriptional regulation of MMTV by glucocorticoid hormones is achieved by the concerted action of multiple sequence modules, not all of which correspond to receptor binding sites in vitro.

Affinity labelling of steroid hormone receptors

Affinity labelling techniques have proved indispensable for the study of reversible biological recognition systems, since they conserve ligand-receptor interaction by covalent linkage. Using photo- and electrophilic labelling, it has become possible to unequivocally identify steroid hormone receptors and their proteolytic degradation products and it is simple to establish receptor peptide maps even in crude receptor preparations. The isolation of receptor proteins has been greatly simplified, as their integrity can be analyzed at any step of a purification protocol by SDS-PAGE analysis after crosslinking. Moreover, affinity-labelled receptors can be purified under denaturing conditions, e.g., in high-resolving preparative SDS-PAGE, and the material obtained can be efficiently used to generate anti-receptor antibodies. Peptide mapping after crosslinking of related receptors has been used to assess the degree of structural homology between different forms of steroid hormone receptors and receptors of different species. Peptide sequence analysis of purified crosslinked receptor protein and anti-receptor antibodies have provided the basis for cloning corresponding genes. Techniques have been established to demonstrate--via crosslinking--that the cloned DNA sequences correspond to the receptor gene binding the correct ligand. The analytical and preparative crosslinking methods developed for steroid receptors are potentially important for the study of any system in which signal transduction proceeds via the reversible interaction between biological macromolecules.

The estrogen-receptor complex is bound at unusual chromatin regions

The estrogen receptor of MCF-7 cells labeled with high specific activity estradiol was used to mark the chromatin binding sites for this regulatory molecule. Many of these sites are especially sensitive to nuclease, and produce on digestion a series of uniquely sedimenting products. Several of these have been examined in some detail in this paper. These include a form of receptor that sediments in trace digests at 9S but in more extensive digests at 7S, fast mononucleosomes of about 12.5S, and a species at 15S. Two components of digests, fast mononucleosomes and dinucleosomes were isolated and subjected to further digestion. Much of the hormone on these isolated particles was found to be sensitive to additional hydrolysis, although some was nuclease resistant. It appears that a major fraction of the hormone receptor complexes bound to MCF-7 cell chromatin occurs at nucleosome-free regions which can be detected as transient hydrolysis intermediates.