DNA loops induced by cooperative binding of transcriptional activator proteins and preinitiation complexes

Modulation of EGFR Gene Transcription by a Polymorphic Repetitive Sequence – a Link between Genetics and Epigenetics

The epidermal growth factor receptor (EGFR) plays a crucial role in growth, differentiation and motility of normal as well as tumor cells. The transduction of extracellular signals to the cytoplasm via the receptor not only depends on ligand binding, but is also determined by the receptor density on the cell surface. Therefore, with regard to cancer diagnosis and therapeutic approaches targeting EGFR it is important to know how the expression level of EGFR is controlled. We found that transcription activity declines with increasing numbers of CA dinucleotides of a highly polymorphic CA repeat in the first intron of the epidermal growth factor receptor gene. In vivo data from cultured cell lines support these findings, although other regulation mechanisms can compensate this effect. In addition, we showed that RNA elongation terminates at a site closely downstream of the simple sequence repeat (SSR) and that there are two separate major transcription start sites. Model calculations for the helical DNA conformation revealed a high bendability in the EGFR polymorphic region, especially if the CA stretch is extended. These data suggest that the CA-SSR can act like a joint, bringing the promoter in proximity to a putative repressor protein bound downstream of the CA-SSR. The data indicate that this polymorphism may be a marker for cancer, linking genetic and epigenetic risk factors. Furthermore, in breast cancer, heterozygous tumors with short CA-SSR showed an elevated EGFR-expression in contrast to tumours with longer CA-SSR. Tumours with loss of heterozygosity in intron 1 of egfr revealed an increased EGFR expression if the longer allele was lost. Moreover, decreased EGFR gene levels were significantly correlated with poor prognosis in breast cancer.

Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein

BACKGROUND

The tumour suppressor p53 is a central player in transcription regulation and cell fate determination. By interacting with p53 and altering its sequence-specific binding to the response elements, the hepatitis B virus X protein (HBx) was reported to re-direct p53 regulation of some genes.

RESULTS

Coupling massively parallel deep sequencing with p53 chromatin immunoprecipitation, we demonstrate that HBx modulates global p53 site selection and that this was strongly influenced by altered interaction with transcription co-factors/co-regulators as well as post-translational modifications. Specifically, HBx attenuated p53-TBP-RB1 transcription complex recruitment and interaction and this was associated with hyper-phosphorylation of p53 at serine 315 by HBx. Concurrently, HBx enhanced p53 DNA occupancy to other response elements either alone by displacing specific transcription factors such as CEBPB and NFkB1, or in complex with distinct interacting co-factors Sp1, JUN and E2F1. Importantly, re-wiring of p53 transcription regulation by HBx was linked to the deregulation of genes involved in cell proliferation and death, suggesting a role of HBx in errant cell fate determination mediated by altered p53 site selection of target genes.

CONCLUSIONS

Our study thus presents first evidence of global modes of p53 transcription alteration by HBx and provides new insights to understand and potentially curtail the viral oncoprotein.

Expression of matrix metalloproteinase (MMP)-2, MMP-9, and tissue inhibitor of MMP (TIMP)-1 in conjunctival melanomas and clinical implications

PURPOSE

To investigate the expression of matrix metalloproteinase (MMP)-2, MMP-9, and tissue inhibitor of matrix metalloproteinase (TIMP)-1 in conjunctival melanomas and their correlations with clinicopathologic parameters and prognosis.

METHODS

Fourteen conjunctival melanoma tissue samples and nine conjunctival nevus tissue samples were stained immunohistochemically for MMP-2, MMP-9, and TIMP-1. Association of MMP-2, MMP-9, and TIMP-1 expression in melanoma tissues with clinical progression in terms of metastasis, recurrence, mitotic index, thickness, base diameter, and invasion depth was analyzed.

RESULTS

In the melanoma group, 78.6% of samples showed a positive reaction for MMP-2, 85.7% for MMP-9, and 100% for TIMP-1. In the nevus group, 11.1% showed a positive reaction for MMP-2, 66.7% for MMP-9, and 100% for TIMP-1. MMP-2 expression was significantly more induced in conjunctival melanoma than in benign nevi (P = 0.002). In conjunctival melanoma, MMP-9 expression was higher in tumors >1.5 mm thick (P = 0.026) and TIMP-1 expression was higher in recurrent cases (P = 0.03). There was no significant correlation between the expression and metastasis during the follow-up period (mean, 5 years).

CONCLUSION

MMP-2, MMP-9, and TIMP-1 were expressed in the majority of conjunctival melanomas, and MMP-2 might play a role in the development and clinical behavior of conjunctival melanoma.

Bone morphogenetic proteins induce expression of metalloproteinases in melanoma cells and fibroblasts

Bone morphogenetic proteins are secreted growth factors which belong to the TGFbeta super family. In recent studies, we showed that the expression of BMP-4 and -7 is induced in melanoma cells in comparison to normal melanocytes. Functional analyses revealed that BMPs are inevitable factors for migration and invasion processes of melanoma cells; however, the role of BMPs in degradation and remodelling of the extracellular matrix remained unknown. We discovered that melanoma cell clones with reduced BMP activity, generated by stable transfection with an antisense BMP-4 construct or with the BMP inhibitor chordin, showed reduced expression of MMP-1, -2, -3 and -9. Moreover, BMPs displayed paracrine effects on stromal fibroblasts. Treatment of fibroblasts with BMP-2 or -4 led to increased MMP-1, -2, -3 and -13 expression. These data show that BMPs play an important role in dissemination of tumour cells from the primary tumour, either by enhancing the matrix degrading capacity of melanoma cells themselves or by stimulating tumour surrounding fibroblasts to induce expression of matrix metalloproteinases.

Loops in DNA: an overview of experimental and theoretical approaches

DNA loop formation plays a central role in many cellular processes. The aim of this paper is to present the state of the art and open problems regarding the experimental and theoretical approaches to DNA looping. A particular attention is devoted to the effects of the protein bridge size and of protein induced sharp DNA bending on DNA loop formation enhancement.

The transcription factors AP-1 and Ets are regulators of C3a receptor expression

The anaphylatoxin C3a is a proinflammatory mediator generated during complement activation. The tight control of C3a receptor (C3aR) expression is crucial for the regulation of anaphylatoxin-mediated effects. Key factors regulating constitutive expression of the C3aR in the mast cell line HMC-1 and receptor induction by dibutyryl-cAMP in monomyeloblastic U937 cells were determined by functional characterization of the C3aR promoter. Nucleotides -18 to -285 upstream of the translational start site proved to be critical for promoter activity in HMC-1 cells. Binding sites for the transcription factors AP-1 and Ets could be located. Overexpressed c-Jun/c-Fos (AP-1) and Ets-1 led synergistically to increased promoter activity that was substantially reduced by site-directed mutagenesis of the corresponding elements within the C3aR promoter. In HMC-1 cells, Ets interacted directly with the predicted binding motif of the C3aR promoter as determined by electromobility shift assays. AP-1 binding to the C3aR promoter was augmented during C3aR induction in U937 cells. A retroviral gene transfer system was used to express a dominant negative mutant of Ets-1 in these cells. The resulting cells failed to up-regulate the C3aR after stimulation with dibutyryl-cAMP and showed decreased AP-1 binding, suggesting that Ets acts here indirectly. Thus, it was established that Ets and the AP-1 element mediates dibutyryl-cAMP induction of C3aR promoter activity, hence providing a mechanistic explanation of dibutyryl-cAMP-dependent up-regulation of C3aR expression. In conclusion, this study demonstrates an important role of AP-1 and a member of the Ets family in the transcriptional regulation of C3aR expression, a prerequisite for the ability of C3a to participate in immunomodulation and inflammation.

Role of matrix metalloproteinases in melanoma cell invasion

Cutaneous melanomas are notorious for their tendency to metastasize. Essential steps in this process are the degradation of basement membranes and remodeling of the extracellular matrix (ECM) by proteolytic enzymes such as matrix metalloproteinases (MMPs), which are regulated by their tissue inhibitors (TIMPs). An MMP expression is not restricted to tumor cells but is also found in stromal cells, indicating that stroma-derived proteases may contribute to melanoma progression. The MMPs have been shown to interact with a broad range of non-matrix proteins including adhesion molecules, growth factors and mediators of angiogenesis and apoptosis. In this review, we evaluate new insights into the interplay of MMPs and their molecular partners in melanoma progression.

Characterization of promoter 3 of the human thromboxane A receptor gene. A functional AP-1 and octamer motif are required for basal promoter activity

The TPalpha and TPbeta isoforms of the human thromboxane A(2) receptor (TP) arise by differential splicing but are under the transcriptional control of two distinct promoters, termed Prm1 and Prm3, respectively (Coyle et al. 2002 Eur J Biochem269, 4058-4073). The aim of the current study was to determine the key factors regulating TPbeta expression by functionally characterizing Prm3, identifying the core promoter and the cis-acting elements regulating basal Prm3 activity. Hence, the ability of Prm3 and a series of Prm3 deleted/mutated subfragments to direct reporter gene expression in human erythroleukemia 92.1.7 and human embryonic kidney 293 cells was investigated. It was established that nucleotides -118 to +1 are critical for core Prm3 activity in both cell types. Furthermore, three distinct regulatory regions comprising of an upstream repressor sequence, located between -404 to -320, and two positive regulatory regions required for efficient basal gene expression, located between -154 to -106 and -50 to +1, were identified within the core Prm3. Deletion and site-directed mutagenesis of consensus Oct-1/2 and AP-1 elements within the latter -154 to -106 and -50 to +1 regions, respectively, substantially reduced Prm3 activity while mutation of both elements abolished Prm3 activity. Electromobility shift and supershift assays confirmed the specificity of nuclear factor binding to the latter Oct-1/2 and AP-1 elements. Moreover, herein it was established that the core AP-1 element mediates phorbol myristic acid-induction of Prm3 activity hence providing a mechanistic explanation of phorbol ester up-regulation of TPbeta mRNA expression.

Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar

It is characteristic of eukaryotic transcription that a unique combination of multiple transcriptional regulatory proteins bound to promoter DNA specifically activate or repress downstream target genes; this is referred to as combinatorial gene regulation. Recently determined structures have revealed different modes of protein-protein interaction on the promoter DNA from near (e.g. the Runx1-CBFbeta-DNA, NFAT-Fos-Jun-DNA, GABPalpha-GABPbeta-DNA, Ets-1-Pax-5-DNA and PU.1-IRF-4-DNA complexes) and afar with DNA looping (e.g. the c-Myb-C/EBPbeta-DNA complex), and their regulatory mechanisms.

Atomic force microscopy identification of transcription factor NFkappaB bound to streptavidin-pin-holding DNA probe

A novel method for identifying DNA-binding proteins from image analysis using AFM was developed. Here, transcription factor NFkappaB, which a well-studied example of transcription activator proteins, was used as a target protein. 5'-biotinlynated double-stranded DNA probe was labeled site specifically through high affinity with streptavidin. When the biotinylated DNA fragments were incubated with the streptavidin at a 1:2 molar ratio of DNA:streptavidin, the overall efficiency of labeling was over 90%. The double-stranded DNA probes were immobilized on a mica surface by the adsorption of streptavidin that attached to the 5'-end of DNA and applied for selection of the target protein NFkappaB in solution and then AFM was used to image the DNA probe-NFkappaB complexes. The length of the distance between 5'-labeled streptavidin and NFkappaB bound on DNA probes from AFM images is 0.64, the normalized position of the NFkappaB binding site, and this result is in close agreement with the expected 299 and 167bp values.

A relocated technique of atomic force microscopy (AFM) samples and its application in molecular biology

A kind of simple atomic force microscopy (AFM) relocated technique, which takes advantage of homemade sample locator system, is used for investigating repeatedly imaging of some specific species on the whole substrate (over 1 x 1 cm2) with resolution about 400 nm. As applications of this sample locator system, single extended DNA molecules and plasmid DNA network are shown in different AFM operational modes: tapping mode and contact mode with different tips after the substrates have been moved.

Direct atomic force microscopy visualization of integration host factor-induced DNA bending structure of the promoter regulatory region on the Pseudomonas TOL plasmid

Atomic force microscopy (AFM) was used to analyze DNA bending induced by integration host factor (IHF). The direct AFM visualization of IHF-DNA complexes on the OP1 promoter regulatory regions on the Pseudomonas TOL plasmid showed that there was no intrinsic DNA bend in the OP1 promoter region, but a sharp DNA bend was induced by binding of IHF to the region between the upstream regulatory sequence and the promoter sequence. The DNA bending angles were distributed with a mean bend angle of 123 degrees. The IHF-DNA complexes were shown to bend at the IHF binding site giving rise to an asymmetric structure. These results provide direct evidence that IHF is required functionally for activation of OP1 transcription and support the DNA-loop model that the sharp DNA bend induced by binding of IHF facilitates the contact between RNA polymerase bound by the promoter sequence and XylR protein attached to the upstream sequence in the OP1 promoter.

Surface biology of DNA by atomic force microscopy

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

Long-range electrostatic interactions influence the orientation of Fos-Jun binding at AP-1 sites

Heterodimeric transcription regulatory proteins that bind palindromic DNA sequences can potentially bind their recognition sites in two opposite orientations. The orientation of transcription factor binding can control transcriptional activity by altering interactions with proteins that bind to adjacent regulatory elements. Fos-Jun heterodimers bind to AP-1 sites with different flanking sequences in opposite orientations. A gel-based fluorescence resonance energy transfer assay, gelFRET, was used to define the mechanism whereby amino acid residues and nucleotide base-pairs outside the Fos-Jun-AP-1 contact interface determine the orientation of heterodimer binding. Exchange of three amino acid residues adjacent to the basic DNA contact regions between Fos and Jun reversed the binding orientation. The effects of these amino acid residues on the orientation of heterodimer binding depended on base-pairs flanking the core AP-1 recognition sequence. Single amino acid and base-pair substitutions had parallel effects on DNA bending by Fos-Jun-AP-1 complexes and on heterodimer orientation. The binding orientation exhibited a close correspondence with both the difference in bending propensities of opposite sides of the AP-1 site as well as the difference in bending potentials of the Fos and Jun subunits of the heterodimer. The influence of flanking DNA sequences on heterodimer orientation was attenuated in the presence of high concentrations of multivalent cations. Base substitutions up to one helical turn from the center of the AP-1 site affected the binding orientation. Modification of flanking base-pairs with positively or negatively charged functional groups had opposite effects on the orientation of heterodimer binding. These changes in DNA charge had converse effects on the orientation preferences of heterodimers in which charged amino acid residues adjacent to the basic regions were exchanged between Fos and Jun. These results indicate that the orientation of heterodimer binding is determined primarily by minimization of the electrostatic free energy of the Fos-Jun-AP-1 complex. Consequently, long-range electrostatic interactions influence the architecture of nucleoprotein complexes.

The smooth muscle gamma-actin gene promoter is a molecular target for the mouse bagpipe homologue, mNkx3-1, and serum response factor

An evolutionarily conserved vertebrate homologue of the Drosophila NK-3 homeodomain gene bagpipe, Nkx3-1, is expressed in vascular and visceral mesoderm-derived muscle tissues and may influence smooth muscle cell differentiation. Nkx3-1 was evaluated for mediating smooth muscle gamma-actin (SMGA) gene activity, a specific marker of smooth muscle differentiation. Expression of mNkx3-1 in heterologous CV-1 fibroblasts was unable to elicit SMGA promoter activity but required the coexpression of serum response factor (SRF) to activate robust SMGA transcription. A novel complex element containing a juxtaposed Nkx-binding site (NKE) and an SRF-binding element (SRE) in the proximal promoter region was found to be necessary for the Nkx3-1/SRF coactivation of SMGA transcription. Furthermore, Nkx3-1 and SRF associate through protein-protein interactions and the homeodomain region of Nkx3-1 facilitated SRF binding to the complex NKE.SRE. Mutagenesis of Nkx3-1 revealed an inhibitory domain within its C-terminal segment. In addition, mNkx3-1/SRF cooperative activity required an intact Nkx3-1 homeodomain along with the MADS box of SRF, which contains DNA binding and dimerization structural domains, and the contiguous C-terminal SRF activation domain. Thus, SMGA is a novel target for Nkx3-1, and the activity of Nkx3-1 on the SMGA promoter is dependent upon SRF.

Cloning and characterization of the human beta4-integrin gene promoter and enhancers

The cell-surface adhesion molecule alpha6beta4-integrin is a receptor for laminins and a component of hemidesmosomes. beta4-Integrin expression is restricted to proliferating basal keratinocytes in the epidermis and is suppressed when differentiation commences. Altered beta4-integrin expression levels correlate significantly with the aggressive behavior of cancers. In order to clarify the mechanisms that regulate transcription of the beta4-integrin gene, we cloned its 5'-flanking region. This 5'-flanking region was found to have a high G + C content and not to contain either TATA or CAAT boxes. Nested delimitation and reporter analyses mapped a basal promoter to nucleotides -106 to +105, surrounding the most proximal transcription initiation site. Gel retardation and mutational analyses revealed that cooperation between AP1 and Ets, interacting with other factors, mediated the promoter activity. In addition to the promoter element, enhancer activity was found in the first intron (+1905/+3933) and in a sequence upstream of the promoter region (-414/-107). These findings should facilitate our understanding of the regulation of beta4-integrin gene expression in processes such as cell growth and differentiation, apoptosis, and cancer development and metastasis.

Mapping a protein-binding site on straightened DNA by atomic force microscopy

We have developed an Atomic Force Microscopy (AFM)-based method for mapping protein-binding sites on individual, long DNA molecules (> 5 kb) at nanometer resolution. The protein is clearly detected at the apex of the bent DNA molecules. Randomly coiled DNA molecules or protein:DNA complexes were extended by a motor-controlled moving meniscus on an atomically flat surface. The immobilized molecules were detected by AFM. The straightened DNA displayed a sharp bend at the site of bound protein with the two DNA segments linearly extending from the protein-binding site. Using GAL4, a yeast transcription factor, we demonstrate good agreement of the position of the observed binding site on straightened DNA templates to the predicted binding site. The technique is expected to have significant implications in elucidating DNA and protein interactions in general, and specifically, for the measurement of promoter occupancy with unlabeled regulatory proteins at the single-molecule level.

Transcription initiation from a poly(dA) tract

The mammalian ME1 gene encodes a non-tissue-specific, helix-loop-helix transcription factor that is enriched in morphogenetically active regions during development. Regulation of mouse ME1 gene expression is controlled by a novel initiator (ME1 Inr) that promotes transcription from the center of a 13 bp poly(dA) tract. We show here that the ME1 Inr autonomously directs initiation from the poly(dA) tract both in vitro and in vivo. This transcription was dependent upon two protein complexes; MBPalpha, which associated directly with the poly(dA) tract, and MBPbeta, which introduced an approximately 60 degrees bend immediately downstream of the poly(dA) tract. The MBPalpha and MBPbeta binding sites were strikingly conserved in homologous DNA from several mammalian species and the frog Xenopus laevis. These results suggest that the ME1 Inr constitutes a robust nucleation site that promotes transcription initiation in the absence of conventional promoter elements.

The transcription activation domains of Fos and Jun induce DNA bending through electrostatic interactions

Transcription factor-induced DNA bending is essential for the assembly of active transcription complexes at many promoters. However, most eukaryotic transcription regulatory proteins have modular DNA-binding and activation domains, which appeared to exclude DNA bending as a mechanism of transcription activation by these proteins. We show that the transcription activation domains of Fos and Jun induce DNA bending. In chimeric proteins, the transcription activation domains induce DNA bending independent of the DNA-binding domains. DNA bending by the chimeric proteins is directed diametrically away from the transcription activation domains. Therefore, the opposite directions of DNA bending by Fos and Jun are caused, in part, by the opposite locations of the transcription activation domains relative to the DNA-binding domains in these proteins. DNA bending is reduced in the presence of multivalent cations, indicating that electrostatic interactions contribute to DNA bending by Fos and Jun. Consequently, regions outside the minimal DNA-binding domain can influence DNA structure, and may thereby contribute to the architectural reorganization of the promoter region required for gene activation.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos-Jun-AP-1 complex may contribute to its functional versatility at different promoters.

Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending

The effect of Fos and Jun binding on the structure of the AP-1 recognition site is controversial. Results from phasing analysis and phase-sensitive detection studies of DNA bending by Fos and Jun have led to opposite conclusions. The differences between these assays, the length of the spacer between two bends and the length of the sequences flanking the bends, are investigated here using intrinsic DNA bend standards. Both an increase in the spacer length as well as a decrease in the length of flanking sequences resulted in a reduction in the phase-dependent variation in electrophoretic mobilities. Probes with a wide separation between the bends and short flanking sequences, such as those used in the phase-sensitive detection studies, displayed no phase-dependent mobility variation. This shape-dependent variation in electrophoretic mobilities was reproduced by complexes formed by truncated Fos and Jun. Results from ligase-catalyzed cyclization experiments have been interpreted to indicate the absence of DNA bending in the Fos-Jun-AP-1 complex. However, truncated Fos and Jun can alter the relative rates of inter- and intramolecular ligation through mechanisms unrelated to DNA bending, confounding the interpretation of cyclization data. The analogous phase- and shape-dependence of the electrophoretic mobilities of the Fos-Jun-AP-1 complex and an intrinsic DNA bend confirm that Fos and Jun bend DNA, which may contribute to their functions in transcription regulation.