CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms

1993 ◽  
Vol 13 (12) ◽  
pp. 7612-7624
Author(s):  
E M Klenova ◽  
R H Nicolas ◽  
H F Paterson ◽  
A F Carne ◽  
C M Heath ◽  
...  

A novel sequence-specific DNA-binding protein, CTCF, which interacts with the chicken c-myc gene promoter, has been identified and partially characterized (V. V. Lobanenkov, R. H. Nicolas, V. V. Adler, H. Paterson, E. M. Klenova, A. V. Polotskaja, and G. H. Goodwin, Oncogene 5:1743-1753, 1990). In order to test directly whether binding of CTCF to one specific DNA region of the c-myc promoter is important for chicken c-myc transcription, we have determined which nucleotides within this GC-rich region are responsible for recognition of overlapping sites by CTCF and Sp1-like proteins. Using missing-contact analysis of all four nucleotides in both DNA strands and homogeneous CTCF protein purified by sequence-specific chromatography, we have identified three sets of nucleotides which contact either CTCF or two Sp1-like proteins binding within the same DNA region. Specific mutations of 3 of 15 purines required for CTCF binding were designed to eliminate binding of CTCF without altering the binding of other proteins. Electrophoretic mobility shift assay of nuclear extracts showed that the mutant DNA sequence did not bind CTCF but did bind two Sp1-like proteins. When introduced into a 3.3-kbp-long 5'-flanking noncoding c-myc sequence fused to a reporter CAT gene, the same mutation of the CTCF binding site resulted in 10- and 3-fold reductions, respectively, of transcription in two different (erythroid and myeloid) stably transfected chicken cell lines. Isolation and analysis of the CTCF cDNA encoding an 82-kDa form of CTCF protein shows that DNA-binding domain of CTCF is composed of 11 Zn fingers: 10 are of C2H2 class, and 1 is of C2HC class. CTCF was found to be abundant and conserved in cells of vertebrate species. We detected six major nuclear forms of CTCF protein differentially expressed in different chicken cell lines and tissues. We conclude that isoforms of 11-Zn-finger factor CTCF which are present in chicken hematopoietic HD3 and BM2 cells can act as a positive regulator of the chicken c-myc gene transcription. Possible functions of other CTCF forms are discussed.

1993 ◽  
Vol 13 (12) ◽  
pp. 7612-7624 ◽  
Author(s):  
E M Klenova ◽  
R H Nicolas ◽  
H F Paterson ◽  
A F Carne ◽  
C M Heath ◽  
...  

A novel sequence-specific DNA-binding protein, CTCF, which interacts with the chicken c-myc gene promoter, has been identified and partially characterized (V. V. Lobanenkov, R. H. Nicolas, V. V. Adler, H. Paterson, E. M. Klenova, A. V. Polotskaja, and G. H. Goodwin, Oncogene 5:1743-1753, 1990). In order to test directly whether binding of CTCF to one specific DNA region of the c-myc promoter is important for chicken c-myc transcription, we have determined which nucleotides within this GC-rich region are responsible for recognition of overlapping sites by CTCF and Sp1-like proteins. Using missing-contact analysis of all four nucleotides in both DNA strands and homogeneous CTCF protein purified by sequence-specific chromatography, we have identified three sets of nucleotides which contact either CTCF or two Sp1-like proteins binding within the same DNA region. Specific mutations of 3 of 15 purines required for CTCF binding were designed to eliminate binding of CTCF without altering the binding of other proteins. Electrophoretic mobility shift assay of nuclear extracts showed that the mutant DNA sequence did not bind CTCF but did bind two Sp1-like proteins. When introduced into a 3.3-kbp-long 5'-flanking noncoding c-myc sequence fused to a reporter CAT gene, the same mutation of the CTCF binding site resulted in 10- and 3-fold reductions, respectively, of transcription in two different (erythroid and myeloid) stably transfected chicken cell lines. Isolation and analysis of the CTCF cDNA encoding an 82-kDa form of CTCF protein shows that DNA-binding domain of CTCF is composed of 11 Zn fingers: 10 are of C2H2 class, and 1 is of C2HC class. CTCF was found to be abundant and conserved in cells of vertebrate species. We detected six major nuclear forms of CTCF protein differentially expressed in different chicken cell lines and tissues. We conclude that isoforms of 11-Zn-finger factor CTCF which are present in chicken hematopoietic HD3 and BM2 cells can act as a positive regulator of the chicken c-myc gene transcription. Possible functions of other CTCF forms are discussed.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4453-4453
Author(s):  
Tal David-Kalish ◽  
Deborah Rund ◽  
Elad Malik ◽  
Sara Bar Cohen

Abstract CYP3A4 is the most abundant cytochrome P450 enzyme in the liver and is involved in the metabolism of most clinically used drugs. An A to G substitution in the nifedipine responsive element (NFSE) in the promoter of this gene has been found to be associated with a lower incidence of pediatric therapy-related leukemia (Felix, Proc Natl Acad Sci USA95:13176, 1998) and adult therapy-related leukemia (Rund et al, Leukemia, accepted for publication). To study the effect of this polymorphism on gene expression in hematopoietic cells, we constructed reporter plasmids with the luciferase gene (in pGL3E) under control of the CYP3A4 promoter, using both the polymorphic and normal sequences. These plasmids were transfected into several cell lines of hematopoietic origin and luciferase was quantitated. We used KG1a (myeloid leukemia), K562 (CML blast crisis), and as controls, MelA1, a melanoma line and HepG2, a hepatoma line. Experiments were repeated at least three times for each cell line. The results consistently demonstrated 20–30% lower luciferase activity (in KG1a and K562 respectively) using the polymorphic sequence as compared to the normal sequence while the MelA1 and HepG2 lines showed the opposite effect, a 25% higher luciferase expression with the variant sequence. The results for HepG2 were in agreement with those reported by Rebbeck (Environmental and Molecular Mutagenesis49:299, 2003). To identify the factors binding at NFSE which may influence expression, electrophoretic mobility shift assays were performed using nuclear extracts of both cell lines (K562, KG1a, and HL60) and patient leukemia cells with a DNA probe representing the normal and polymorphic sequences. A gel shift was demonstrated, indicating binding of nuclear extracts to the region of the polymorphism. The database of transacting factors states complete homology of the polymorphic sequence of the NFSE region with the consensus binding site of HSF-1. We therefore performed a series of experiments to determine if HSF-1 is the protein binding at that site. HSF-1 is a multimeric transcription factor which binds to heat shock elements in many promoters which are rapidly transcribed following stress by increases in temperature. We found that recombinant HSF-1 did not bind to the DNA probe alone. However, nuclear extracts of cells which underwent stress by heating to 43°C for one hour (which is known to increase HSF-1 production) demonstrated increased binding to the probe representing the region of the polymorphism and Western blotting demonstrated more HSF-1 in these extracts. Using a Streptavidin-biotin system with a DNA fragment representing the NFSE region, we demonstrated that DNA binding activity to the probe was present in the elution fractions which contained HSF-1, as detected by ECL (enhanced chemoluminescence). Elution fractions which did not show DNA binding activity did not contain detectable HSF-1. We conclude that HSF-1 may be the protein which binds at the NFSE element of the CYP3A promoter but that it binds either as a multimer or as part of a complex of several proteins, which complicates its detection as a DNA binding protein.


1996 ◽  
Vol 314 (1) ◽  
pp. 293-296 ◽  
Author(s):  
Dashzeveg BAYARSAIHAN ◽  
Lewis N. LUKENS

A pyrimidine element with mirror repeats centred at position -192 bp of the chick α2(I) collagen promoter interacts with sequence-specific DNA-binding factors. These factors bind to only the pyrimidine strand of this region and have no affinity for the complementary purine strand. Binding activity is also seen with the double-stranded form of this element, but with less affinity than to the single-stranded pyrimidine species. Southwestern blot analyses have shown that proteins of 80 and 134 kDa in chick embryo fibroblast nuclear extracts bind to the pyrimidine strand, whereas only a 134 kDa DNA-binding protein was found in chondrocyte nuclear extracts. The binding mechanism of these nuclear proteins with single-stranded DNA might be based on a non-B-DNA conformation of the pyrimidine element. The position of this binding site in the promoter region, its potential for adopting an unusual secondary structure and the presence of the 80 kDa binding factor in chick embryo fibroblasts, but not in chondrocytes, suggest a possible role for this factor in the expression of the α2(I) collagen gene.


2001 ◽  
Vol 114 (15) ◽  
pp. 2747-2754
Author(s):  
David G. Swan ◽  
Rowena Stern ◽  
Sue McKellar ◽  
Kirsten Phillips ◽  
Chris A. L. Oura ◽  
...  

Infection of bovine leukocytes by the apicomplexan parasite Theileria annulata results in alteration of host cell gene expression and stimulation of host cell proliferation. At present, the parasite-derived factors involved in these processes are unknown. Recently, we described the characterisation of a parasite gene (TashAT2), whose polypeptide product bears AT hook DNA-binding motifs and may be transported from the parasite to the host nucleus. We now describe the isolation of a further two genes (TashAT1 and TashAT3) that are very closely related to TashAT2. All three TashAT genes are located together in a tight cluster, interspersed by two further small open reading frames, all facing head to tail. TashAT2 was shown to be expressed in all T. annulata cell lines examined, whereas TashAT1 and TashAT3 were expressed in the sporozoite stage of the parasite, and also in infected cell lines, where their expression was found to vary between different cell lines. Evidence for transport was provided by antisera raised against TashAT1 and TashAT3 that reacted with the host nucleus of T. annulata-infected cells. Reactivity was particularly strong against the host nuclei of the T. annulata-infected cloned cell line D7B12, which is attenuated for differentiation. A polypeptide in the size range predicted for TashAT3 was preferentially detected in host enriched D7B12 nuclear extracts. DNA-binding analysis demonstrated that fusion proteins containing the AT hook region of either TashAT1 or TashAT2 bound preferentially to AT rich DNA.


Blood ◽  
2000 ◽  
Vol 95 (8) ◽  
pp. 2715-2718 ◽  
Author(s):  
Junichi Tsukada ◽  
Yoko Toda ◽  
Masahiro Misago ◽  
Yoshiya Tanaka ◽  
Philip E. Auron ◽  
...  

Abstract The activation status of a recently identified STAT (signal transducers and activators of transcription) factor, LIL-Stat (lipopolysaccharide [LPS]/IL-1–inducible Stat) in adult T-cell leukemia (ATL) cells was investigated by electrophoretic mobility shift assays using nuclear extracts of leukemic cells from 7 patients with ATL and a GAS (gamma interferon activation site)-like element termed LILRE (LPS/IL-1–responsive element), which is found in the human prointerleukin 1β (IL1B) gene. Spontaneous DNA binding of LIL-Stat was observed in all ATL cells examined. However, in normal human peripheral lymphocytes, DNA binding of LIL-Stat was detected only after stimulation with IL-1. These results demonstrated that LIL-Stat is constitutively activated in ATL cells. Furthermore, our transient transfection studies using LILRE chloramphenicol acetyltransferase (CAT) reporters argue that LIL-Stat in ATL cells functions as a transcriptional activator through binding to the LILRE in theIL1B gene.


1998 ◽  
Vol 18 (10) ◽  
pp. 5852-5860 ◽  
Author(s):  
Frédérique Verdier ◽  
Raquel Rabionet ◽  
Fabrice Gouilleux ◽  
Christian Beisenherz-Huss ◽  
Paule Varlet ◽  
...  

ABSTRACT Two distinct genes encode the closely related signal transducer and activator of transcription proteins STAT5A and STAT5B. The molecular mechanisms of gene regulation by STAT5 and, particularly, the requirement for both STAT5 isoforms are still undetermined. Only a few STAT5 target genes, among them the CIS (cytokine-inducible SH2-containing protein) gene, have been identified. We cloned the human CIS gene and studied the human CIS gene promoter. This promoter contains four STAT binding elements organized in two pairs. By electrophoretic mobility shift assay studies using nuclear extracts of UT7 cells stimulated with erythropoietin, we showed that these four sequences bound to STAT5-containing complexes that exhibited different patterns and affinities: the three upstream STAT binding sequences bound to two distinct STAT5-containing complexes (C0 and C1) and the downstream STAT box bound only to the slower-migrating C1 band. Using nuclear extracts from COS-7 cells transfected with expression vectors for the prolactin receptor, STAT5A, and/or STAT5B, we showed that the C1 complex was composed of a STAT5 tetramer and was dependent on the presence of STAT5A. STAT5B lacked this property and bound with a stronger affinity than did STAT5A to the four STAT sequences as a homodimer (C0 complex). This distinct biochemical difference between STAT5A and STAT5B was confirmed with purified activated STAT5 recombinant proteins. Moreover, we showed that the presence on the same side of the DNA helix of a second STAT sequence increased STAT5 binding and that only half of the palindromic STAT binding sequence was sufficient for the formation of a STAT5 tetramer. Again, STAT5A was essential for this cooperative tetrameric association. This property distinguishes STAT5A from STAT5B and could be essential to explain the transcriptional regulation diversity of STAT5.


2002 ◽  
Vol 70 (4) ◽  
pp. 2238-2241 ◽  
Author(s):  
Atanas Ignatov ◽  
Elizabeth J. Keath

ABSTRACT A gel shift assay was optimized to detect several general DNA binding proteins from Histoplasma capsulatum strain G217B. The electrophoretic mobility shift assay (EMSA) technique also detected protein(s) recognizing a pyrimidine-rich motif found in several Histoplasma promoters. Establishment of EMSA conditions provides an important framework to evaluate regulation of homeostatic or phase-specific genes that may influence virulence in Histoplasma and other dimorphic fungal pathogens.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2607-2607
Author(s):  
Rahul Garhwal ◽  
Zhong-Fa Yang ◽  
Alan G. Rosmarin ◽  
Peter Gaines

Abstract Abstract 2607 Pelger-Huët anomaly (PHA) is a disorder of neutrophil nuclear lobulation, in which mature human granulocytes have a mononuclear or bilobed nucleus (so-called pince-nez cells). PHA is a congenital human disorder, but nuclear hypolobation also arises as an acquired defect in pre-leukemic myelodysplastic syndromes. Lamin B receptor (LBR) is an inner nuclear membrane protein whose expression increases during myeloid differentiation, and loss of LBR expression causes PHA. We sought to examine the regulation of LBR in order to identify molecular mechanisms that contribute to neutrophil disorders, including myelodysplastic syndromes and acute myelogenous leukemia. Many hematopoietic-specific genes are regulated by the combinatorial activity of transcription factors, including the ETS factors, PU.1 and GABP (GA binding protein). GABP and PU.1 cooperate to regulate the expression of the leukocyte adhesion molecule CD18, and recently were shown to regulate the expression of the interleukin-7 receptor in developing B cells. GABP is an obligate heterotetramer that is composed of two structurally dissimilar proteins, GABPα and GABPβ. Our analysis of the Lbr gene promoter identified classic “GAGGAA” ets consensus sequences located proximal and distal to the Lbr transcription start site. Lbr promoter constructs containing either the proximal ets site or both the proximal and distal ets sites were not activated by PU.1, alone, following transfection into COS cells. However, these constructs were activated by co-expression of GABPα plus GABPβ, and combined expression of GABPα/β plus PU.1 further activated these constructs up to two-fold. This suggests that GABP and PU.1 cooperatively activate the Lbr gene promoter. Electrophoretic mobility shift assays (EMSA) using radiolabeled probes that include the distal or proximal putative ets sites and nuclear extracts from HEK-293 cells transfected with expression vectors for GABPα, GABPβ and PU.1, identified multiple low mobility bands that were competed by 100 fold excess of cold competitor probe, but not by an irrelevant control probe. Inclusion of anti-GABPα antibodies in the binding reaction disrupted mobility shifts of the probes, indicating that GABPα directly interacts with the Lbr promoter and may participate in the formation of a multimeric protein complex that binds the promoter. Similar results were observed with nuclear extracts from EML cells, which correspond to murine hematopoietic progenitor cells that can be induced to differentiate toward promyelocytic EPRO cells and thence to mature granulocytes. We examined protein expression of GABPα in HL-60 and EML/EPRO progenitor cells, and found that GABPα is highly expressed in uninduced progenitors but downregulated during either neutrophil or monocyte differentiation. We generated mice in which loxP recombination sites flank critical exons of Gabpa; in the presence of Cre recombinase the loxP sites undergo rearrangement and Gabpa is deleted. We bred these animals to mice that are transgenic for estrogen receptor (ER)-regulated Cre recombinase, and created a novel EML cell line from their bone marrow. Upon activating Cre expression with 4-hydroxytamoxifen, most EML cells died within 24 hours, as compared to control cells. This result is consistent with previous studies demonstrating that GABP is required for cell cycle progression, and suggests that GABP plays a critical role in myeloid cell survival. Together, our data indicate that the GABP tetramer binds to specific sequences of the Lbr promoter, and that GABP cooperates with PU.1 to drive Lbr expression during neutrophil differentiation. Analysis of promoter constructs with mutated ets sites in our reporter assays and mobility shift assays will further our knowledge about the importance of GABP/PU.1 complexes in Lbr gene regulation. EML cells that can undergo conditional deletion of Gabpa provide a powerful tool for analysis of the regulation of myeloid genes such as Lbr, and for the molecular mechanisms that cause disorders of myeloid maturation, including myelodysplastic syndromes and acute myelogenous leukemia. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2000 ◽  
Vol 96 (3) ◽  
pp. 1136-1143 ◽  
Author(s):  
Patrick G. Gallagher ◽  
Marc Romana ◽  
William T. Tse ◽  
Samuel E. Lux ◽  
Bernard G. Forget

To begin to study the sequence variations identified in the 5′ flanking genomic DNA of the ankyrin gene in ankyrin-deficient hereditary spherocytosis patients and to provide additional insight into our understanding of the regulation of genes encoding erythrocyte membrane proteins, we have identified and characterized the erythroid promoter of the human ankyrin-1 gene. This compact promoter has characteristics of a housekeeping gene promoter, including very high G+C content and enzyme restriction sites characteristic of an HTF-island, no TATA, InR, or CCAAT consensus sequences, and multiple transcription initiation sites. In vitro DNAseI footprinting analyses revealed binding sites for GATA-1, CACCC-binding, and CGCCC-binding proteins. Transfection of ankyrin promoter/reporter plasmids into tissue culture cell lines yielded expression in erythroid, but not muscle, neural, or HeLa cells. Electrophoretic mobility shift assays, including competition and antibody supershift experiments, demonstrated binding of GATA-1, BKLF, and Sp1 to core ankyrin promoter sequences. In transfection assays, mutation of the Sp1 site had no effect on reporter gene expression, mutation of the CACCC site decreased expression by half, and mutation of the GATA-1 site completely abolished activity. The ankyrin gene erythroid promoter was transactivated in heterologous cells by forced expression of GATA-1 and to a lesser degree BKLF.


1991 ◽  
Vol 11 (5) ◽  
pp. 2558-2566 ◽  
Author(s):  
Q H Gong ◽  
J Stern ◽  
A Dean

The epsilon-globin gene is the first of the human beta-like globin genes to be expressed during development. We have analyzed protein-DNA interactions in the epsilon-globin promoter region by DNase I footprinting and electrophoretic mobility shift experiments using nuclear extracts from K562 human erythroid cells and from nonerythroid HeLa cells. A restricted set of ubiquitous proteins, including Sp1, bound to regions of the promoter including the CACCC and CCAAT sites. Three interactions, at positions -213, -165, and +3 relative to the transcription start site, were erythroid specific and corresponded to binding of GATA-1, a transcription factor highly restricted to the erythroid lineage. Interestingly, the GATA-1 site at -165 has been conserved in the promoters of 10 mammalian embryonic globin genes. Point mutations demonstrate that GATA-1 binding to this site is necessary for interaction with an erythroid-specific enhancer but that in the absence of an enhancer, GATA-1 does not increase transcription.


Sign in / Sign up

Export Citation Format

Share Document