Localization and functional analysis of DNase-I-hypersensitive sites in the human c-sis/PDGF-B gene transcription unit and its flanking regions

Sarcomas: genetics, signalling, and cellular origins. Part 2: TET-independent fusion proteins and receptor tyrosine kinase mutations

Although the mechanisms that underlie sarcoma development are still poorly understood, the identification of non-random chromosomal translocations and receptor tyrosine kinase mutations associated with defined sarcoma types has provided new insight into the pathogenesis of these tumours. In Part 1 of the review (J Pathol 2007;213:4-20), we addressed sarcomas that express fusion genes containing TET gene family products. Part 2 of the review summarizes our current understanding of the implications of fusion genes that do not contain TET family members in sarcoma development, as well as that of specific mutations in genes encoding receptor tyrosine kinases (RTKs). The final section will serve as a summary of both reviews and will attempt to provide a synthesis of some of the emerging principles of sarcomagenesis.

PKC inhibition is involved in trichosanthin-induced apoptosis in human chronic myeloid leukemia cell line K562

Trichosanthin (TCS), a type I ribosome-inactivating protein, induces cell death in various cell types including several tumor cell lines. However, the mechanism remains largely uncharacterized. In this study, we investigated the possible mechanism underlying its cytotoxicity by using human chronic myeloid leukemia cell line K562. We found that TCS induced apoptosis in K562 cells in a time- and concentration-dependent manner and can be blocked by caspase-3 inhibitors. Interestingly, TCS treatment induced a transient elevation in intracellular calcium concentration and a slow increase in reactive oxygen species production, while calcium chelators and antioxidants had no obvious effect on TCS-induced apoptosis, suggesting that calcium changes and reactive oxygen species may not be involved in TCS-mediated apoptosis in K562 cells. Instead we found that TCS partly inhibited PKC activity. Indeed, the PKC activator, PMA, inhibited while the PKC inhibitor, calphostin c, enhanced TCS-induced apoptosis. These PKC modulators had similar effects on TCS-induced cleavage of caspase-3, and caspase-3 inhibitors prevented calphostin c-enhanced apoptosis induced by TCS. In summary, we conclude that TCS induces apoptosis in K562 cells partly via PKC inhibition and caspase-3 activation.

Promoter analysis of the human translation termination factor 1 gene

The human translation termination factor 1 (ETF1) gene encodes a class-1 release factor, eRF1, which catalyses termination of protein synthesis at all three stop codons. In this report, we describe the functional organization of the 5'-region of the gene. Primer extension and ribonuclease protection mapping revealed three transcription start sites clustered within approximately 10 bp. DNase I-hypersensitive site analysis identified five hypersensitive sites, one of which was located downstream of the initiation start sites. We used transient expression assays to define the 5'-regulating regions and in vivo and in vitro footprinting analysis to identify potential cis-acting regulatory elements. A basal promoter, spanning nucleotides -210/+117, contained no TATA box but a putative initiator element (Inr) and multiple potential Sp1/Sp3 binding sites, and thus displayed some of the features of a housekeeping gene. An additional upstream promoter containing positive and negative regulatory elements also regulated ETF1 gene expression. Real-time quantitative RT-PCR analysis showed tissue-specific expression of ETF1 transcripts in mouse tissues. Our results are suggestive of a constitutive expression of the human ETF1 gene but with possible cell- and tissue-specific regulation.

DNase I hypersensitivity analysis of non-pituitary human prolactin gene expression

The expression of non-pituitary human PRL is initiated at a unique 5' untranslated exon located approximately 5.7 kb upstream of the pituitary-specific transcriptional start site. Unlike pituitary PRL expression, transcriptional regulation from the upstream promoter does not rely on the POU-homeodomain protein Pit-1. We have used DNase I mapping of chromatin from PRL-producing and non-producing human lymphoblastoid cell lines to identify hypersensitive sites unique to the PRL expressing phenotype. Analysis of 22 kb of 5' flanking DNA revealed DNase I hypersensitive sites in intron A-1 separating the pituitary from non-pituitary specific transcription start site which were only detected in the PRL-producing cell line. Transient transfection showed strong transcriptional activity directed by this region only in the antisense orientation and in a non cell-type specific manner. Transfection experiments with deletion mutants of 5259 bp of the non-pituitary PRL promoter region also revealed promoter activity not restricted to the PRL expressing phenotype. These data suggest that non-pituitary PRL gene expression may be regulated by elements located in intron A-1 and that recapitulation of cell-specific expression requires a unique cellular context and chromatin assembly.

A novel type of regulatory element is required for promoter-specific activity of the PDGF-B intronic enhancer region

We have previously described a non-classical, promoter-specific enhancer for the human Platelet-Derived Growth Factor B (PDGF-B) gene. In JEG-3 choriocarcinoma cells the activity of the enhancer depends upon co-operation with a sequence (the Enhancer-Dependent cis Co-activator "EDC" element) within the promoter. The PDGF-B enhancer fails to activate heterologous promoters, indicating that promoter-specificity depends on an element within the enhancer that can recognise a target sequence within the promoter. Here we identify a sequence within the enhancer of the PDGF-B gene which directs activation of the PDGF-B promoter by distal cis-acting elements. This specifies the wild-type PDGF-B promoter as the target for the enhancer and has been designated the EDC specificity element (EDCse). The cell-type specific nature of this interaction is extended by the observation that the EDCse is also dispensable for enhancer activity in breast-cancer cells (ZR-75). Concomitant to this observation, JEG-3 and ZR-75 cells differ in the binding of nuclear factors to the EDCse. We discuss the relevance of the EDC/EDCse system in regulation of gene expression.

Chicken vigilin gene: a distinctive pattern of hypersensitive sites is characteristic for its transcriptional activity

Vigilin, a multidomain hn-ribonucleo-K-homologous protein, is part of a ribonucleoprotein complex with cognate tRNA and is found in both the nucleus and the cytoplasm. In an approach to identify genomic regions involved in regulation of the chicken vigilin gene, we carried out transfection studies with a reporter gene in suitable chicken cells. After including a distantly positioned 5'-sequence in the construct, we observed a 10.5-fold increase in luciferase (EC 1. 13.12.7) expression compared with basal promoter activity. Accordingly, chromatin analysis of freshly isolated embryonic tendon fibroblasts with high levels of vigilin mRNA expression shows a DNase-I-hypersensitive site (DHS1) localized 2.2 kb upstream of the transcriptional start site. Similarly, phytohaemagglutinin-stimulated lymphocytes with a 4-fold elevated expression of vigilin mRNA compared with resting lymphocytes also exhibited this unique DHS, having switched from that found at 3.3 kb (DHS2) in resting lymphocytes. Furthermore, using gel-retardation experiments with DNA representing either DHS1 or DHS2, a specific interaction with chicken nuclear extracts was seen.

Oxidative damage and fibrogenesis

Various chronic disease processes are characterized by progressive accumulation of connective tissue under-going fibrotic degeneration. Evidence of oxidative reactions is often associated with fibrogenesis occurring in liver, lung, arteries, and nervous system. Moreover, an increasing bulk of experimental and clinical data supports a contributory role of oxidative stress in the pathogenesis of this kind of disease. Indeed, many etiological agents of fibrogenesis stimulate free radical reactions either directly or through inflammatory stimuli. Free radicals, as well as products of their reaction with biomolecules, appear to modulate the activity of the two cellular types mainly involved in the process, namely phagocytes and extracellular matrix-producing cells. Lipid peroxidation and certain lipid peroxidation products induce genetic overexpression of fibrogenic cytokines, the key molecules in the pathomechanisms of fibrosis, as well as increased transcription and synthesis of collagen. Both these events can be downregulated, at least in experimental models, by the use of antioxidants. The effect of oxidative stress on cytokine gene expression appears to be an important mechanism by which it promotes connective tissue deposition.

Identification of regulatory sequences in the promoter of the PDGF B-chain gene in malignant mesothelioma cell lines

Platelet-derived growth factor (PDGF) B-chain mRNA is readily detectable in malignant mesothelioma (MM) cell lines, but not in normal mesothelial (NM) cell lines. The high affinity receptor for PDGF B-chain dimers, the PDGF beta-receptor, is expressed in MM cell lines. NM cell lines predominantly express the PDGF alpha-receptor. Coexpression of the PDGF beta-receptor and its ligand may lead to an autocrine growth stimulating loop in the malignant cell type. In nuclear run off experiments, PDGF B-chain mRNA was detectable in MM cells only, indicating an increased level of transcription in this cell type. The proximal promoter of the PDGF B-chain gene contains DNaseI hypersensitive (DH) sites and mediates reporter gene activation in both normal and malignant cells. Nuclear proteins, extracted from both cell types, interact with DNA sequences within the proximal promoter around bp-64 to -61 relative to the transcription start site. Electrophoretic mobility shift assays (EMSAs) indicate that these factors are more abundantly present in the malignant than in the normal cell type. A DH site around -9.9 kb was found in both cell types. When tested in CAT assays, this region exerted a stimulatory effect on transcription in malignant cells. The elevated level of transcription of the PDGF B-chain gene in malignant cells may well be the result of interaction of regulatory sites in the proximal promoter and an enhancing element located at -9.9 kb from the transcription start site.

Cell-type-specific modulation of PDGF-B regulatory elements via viral enhancer competition: a caveat for the use of reference plasmids in transient transfection assays

The human platelet-derived growth factor-B (PDGF-B) gene has been shown to display a wide range of levels of mRNA transcription in a variety of cell types. Functional analyses of PDGF-B gene expression have begun to reveal intricate, cell-type-specific regulatory mechanisms involving multiple control elements. We have previously isolated and characterised several elements involved in the control of human PDGF-B gene expression in the JEG-3 choriocarcinoma cell line and in the breast cancer-derived cell line, ZR-75. Assessment of the positive or negative regulatory contributions of these elements was carried out using transient transfection assays. Such studies routinely require the inclusion of a reference plasmid in order to determine transfection efficiency. Here we show that competition for regulatory factors occurs in transfected cells between viral enhancers and elements regulating PDGF-B gene transcription. A frequently used reference plasmid which utilises the SV40 promoter and enhancer region to drive expression of a beta-galactosidase reporter gene was found to severely repress the activity of a co-transfected reporter construct containing the PDGF-B promoter and its intronic enhancer in JEG-3 cells. This competition was localised to the enhancer region of the SV40 regulatory sequences and surprisingly, the effect was reversed in ZR-75 cells; where increasing the amount of reference plasmid strongly stimulated the activity of the PDGF-B construct. These results imply that the same intronic region which functions equally well as an enhancer in two distinct cell-types, may operate in response to different transcription factor complements. Furthermore, this data demonstrates that the choice of reference plasmid and its quantitative use can be a crucial factor when examining putative regulatory elements by transient transfection methods.

Differential appearance of DNase I-hypersensitive sites correlates with differential transcription of Pgk genes during spermatogenesis in the mouse

Two functional genes encoding phosphoglycerate kinase are differentially expressed during spermatogenesis in the mouse. Expression of the X-linked Pgk-1 gene is repressed coincident with X chromosome inactivation during prophase of meiosis I. At this same stage, expression of the autosomal Pgk-2 gene is initiated by tissue-specific mechanisms. To investigate the role of chromatin structure in these processes, we have examined the appearance and disappearance of DNase I-hypersensitive (DH) sites in each gene, and correlated this with transcriptional activity as measured by nuclear run-off analysis at specific stages of spermatogenesis. Our results demonstrate that the occurrence of DH sites is related to periods of active transcription. Results with the Pgk-1 gene indicate that transcriptional inactivation of the X chromosome in spermatogenic cells may not be as complete as that in somatic cells, and that maximum repression may be limited to a very transient period during the pachytene stage of first meiotic prophase. Results with the Pgk-2 gene indicate that DH sites appear coincident with, or just prior to, transcriptional activation of this gene. The implications of these results are discussed with respect to the role of X chromosome inactivation in spermatogenic cells and the developmental order of molecular events that regulate differential gene expression during spermatogenesis.

Identification of a thrombin response element in the human platelet-derived growth factor B-chain (c-sis) promoter

Thrombin is a coagulation system protease that also serves as a potent stimulator of gene expression in several cell types, including endothelial cells (EC). We and others have previously demonstrated that the transcription of platelet-derived growth factor (PDGF) B-chain (c-sis) by EC is stimulated severalfold by thrombin. Here we examine the molecular mechanism of this regulatory process using bovine aortic EC transiently transfected with a vector containing the chloramphenicol acetyltransferase (CAT) gene under the control of a 400-base pair fragment of the human PDGF B-chain promoter. Thrombin treatment of these cells caused a severalfold increase in CAT expression. Deletion analysis and site-directed mutagenesis revealed that the region spanning nucleotides -61 to -53 from the transcription initiation site (referred to as the thrombin response, or ThR, region) was critical for the transcriptional response to thrombin. Electrophoretic mobility shift assays with an oligonucleotide corresponding to the region -64 to -44, which contained the ThR region, led to the identification of a thrombin-inducible nuclear factor (TINF) in extracts from thrombin-treated, but not control, EC. TINF was formed as early as 40 min post-thrombin treatment, persisted for at least 7 h, but was no longer present after 24 h. TINF appeared in the absence of de novo protein synthesis. The ThR region consists of a repeat of a CCACCC element in an ABBA configuration, which, based on mutation analysis and transfection assays, appears to be critical in mediating thrombin stimulation of the PDGF B-chain gene. The conservation of the ThR region in the promoter of the PDGF B-chain among three species (human, feline, and murine) further supports the importance of this region as a cis-acting regulatory element.

Signals controlling the expression of PDGF

PDGF is an important polypeptide growth factor that plays an essential role during early vertebrate development and is associated with tissue repair and wound healing in the adult vertebrate. Moreover, PDGF is thought to play a role in a variety of pathological phenomena, such as cancer, fibrosis and atherosclerosis. PDGF is expressed as a dimer of A and/or B chains, the precursors of which are encoded by two single copy genes. Although the PDGF genes are expressed coordinately in a number of cell types, they are independently expressed in a majority of cell types. The expression of either PDGF gene can be affected by very diverse extracellular stimuli and the type of response is dependent on the cell type that is exposed to the stimulus. Expression of the PDGF chains can be modulated at every imaginable level: by regulating accessibility of the transcription start site, by varying the transcription initiation rate, by using alternative transcription start sites, by alternative splicing, by using alternative polyadenylation signals, by varying mRNA decay rates, by regulating efficiency of translation, by protein modification, and by regulating secretion. Even upon secretion, the activity of PDGF can be modulated by non-specific or specific PDGF-binding proteins. This review provides an overview of the cell types in which the PDGF genes are expressed, of the factors that are known to affect the expression of PDGF, and of the various levels at which the expression of PDGF genes can be regulated.

A novel human c-sis mRNA species is transcribed from a promoter in c-sis intron 1 and contains the code for an alternative PDGF B-like protein

The human platelet-derived growth factor (PDGF) B chain precursor is usually translated from a 3.5 kb c-sis/PDGF B gene transcript. The first exon of the c-sis/gene contains the code for the signal peptide of the PDGF B chain precursor, preceded by a 1 kb long untranslated sequence with potent translation inhibitory activity. In this paper we show that a novel 2.6 kb c-sis mRNA present in the human choriocarcinoma cell line JEG-3 initiates at an alternative exon 1, which we refer to as exon 1a. The 90 bp long exon 1a is located in the center of the first intron of the gene. It coincides with a very pronounced DNase-I-hypersensitive site and is preceded by a functional promoter. Of the three ATG codons present in exon 1a, the third one perfectly matches the criteria of a consensus start codon. It initiates an open reading frame that is continuous with the code for the PDGF B chain precursor but lacks the code for a signal peptide. We conclude that this novel 2.6 kb c-sis mRNA species lacks the strong translation inhibitory potential of the regular exon 1 and contains the code for a PDGF B-like protein that may be targeted to the cell nucleus.

In vivo footprinting and functional analysis of the human c-sis/PDGF B gene promoter provides evidence for two binding sites for transcriptional activators

By in vivo DMS footprint and reporter gene analyses we identified two transcription factor binding sites in the human c-sis/PDGF B gene promoter. The low basal activity of the PDGF B promoter in HeLa and undifferentiated K562 cells, which express low PDGF B mRNA levels, and in PC3 cells, which express a high PDGF B mRNA level, results from binding of a weak transcriptional activator between positions -64 and -61 relative to the transcription start site. Cytotrophoblast-like JEG-3 cells, which do not express the 3.5 kb PDGF B mRNA, contain a transcriptional activator directed at the -64/-61 sequence, but DNA methylation may render the endogenous promoter inaccessible to this activator. A CCACCCAC element at position -61/-54 was identified as the in vivo binding site for a strong transcriptional activator in phorbol ester-treated megakaryocytic K562 cells, which express a high PDGF B mRNA level. Primary human fibroblasts, which do not transcribe the PDGF B gene, contain a transcriptional activator that recognizes an element between positions -60 and -45 but does not bind to the endogenous unmethylated promoter. Our results show that the complex expression pattern of the human PDGF B gene involves the cell type-specific expression of weak and strong transcriptional activators and regulation of promoter accessibility to these factors.

DNase-I-hypersensitive sites located far upstream of the human c-sis/PDGF-B gene comap with transcriptional enhancers and a silencer and are preceded by (part of) a new transcription unit

The human c-sis gene encodes the B chain of platelet-derived growth factor (PDGF), a potent mitogen for cultured cells of mesenchymal origin. PDGF is stored in the alpha-granules of blood platelets, which are derived from bone marrow megakaryocytes and lack transcriptional machinery. Human myeloid leukemia cell line K562 can be used as a model for megakaryocytes. Phorbol-ester-mediated megakaryocytic differentiation of K562 cells is accompanied by more than 200-fold increase in the c-sis mRNA level. We have now localized transcriptional enhancers at -8.6 kb and -9.9 kb relative to the human c-sis gene transcription start site. The enhancer at -8.6 kb increases activity of the c-sis promoter by 40-60-fold specifically in K562 cells and comaps with a DNase-I-hypersensitivity (DH) site. The enhancer at -9.9 kb increases c-sis promoter activity by 5-10-fold in K562 cells and DH at that site accompanies phorbol-ester-induced megakaryocytic differentiation. In phorbol-ester-treated K562 cells the two enhancers may be negatively influenced by a silencer that comaps with DH at -10.7/-11.0 kb. Reporter gene analysis predicted that combined activity of the upstream enhancers and the c-sis promoter may result in 100-1000-fold higher promoter activity in phorbol-ester-treated K562 cells compared with untreated cells, which can fully explain the more than 200-fold increase in c-sis mRNA level. DH at -8.6 kb and -9.9 kb was also detected in human fibroblasts and in the carcinoma cell lines HeLa and PC3, which express, respectively, undetectable, low and high levels of c-sis mRNA. Although the individual DH sites displayed 4-10-fold enhancer activity in all these cells, they lost most of their biological activity when combined in a larger fragment. In addition we localized (part of) a new transcription unit at approximately 13 kb upstream of the c-sis transcription start site. The corresponding 0.45-kb sis upstream region (sur) transcript is constitutively expressed in all cell lines examined. The expression of the sur transcript is independent of the expression of c-sis mRNA and of the pattern of DH sites far upstream of the c-sis gene. Thus, at present, there is no indication that the upstream DH sites are involved in regulation of expression of the sur gene.