A novel SATB1 binding site in the BCL2 promoter region possesses transcriptional regulatory function

ABSTRACT Serratia marcescens cells swarm at 30°C but not at 37°C, and the underlying mechanism is not characterized. Our previous studies had shown that a temperature upshift from 30 to 37°C reduced the expression levels of flhDCSm and hagSm in S. marcescens CH-1. Mutation in rssA or rssB, cognate genes that comprise a two-component system, also resulted in precocious swarming phenotypes at 37°C. To further characterize the underlying mechanism, in the present study, we report that expression of flhDCSm and synthesis of flagella are significantly increased in the rssA mutant strain at 37°C. Primer extension analysis for determination of the transcriptional start site(s) of flhDCSm revealed two transcriptional start sites, P1 and P2, in S. marcescens CH-1. Characterization of the phosphorylated RssB (RssB∼P) binding site by an electrophoretic mobility shift assay showed direct interaction of RssB∼P, but not unphosphorylated RssB [RssB(D51E)], with the P2 promoter region. A DNase I footprinting assay using a capillary electrophoresis approach further determined that the RssB∼P binding site is located between base pair positions −341 and −364 from the translation start codon ATG in the flhDCSm promoter region. The binding site overlaps with the P2 “−35” promoter region. A modified chromatin immunoprecipitation assay was subsequently performed to confirm that RssB∼P binds to the flhDCSm promoter region in vivo. In conclusion, our results indicated that activated RssA-RssB signaling directly inhibits flhDCSm promoter activity at 37°C. This inhibitory effect was comparatively alleviated at 30°C. This finding might explain, at least in part, the phenomenon of inhibition of S. marcescens swarming at 37°C.

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Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)38778-2 ◽

1990 ◽

Vol 265 (17) ◽

pp. 10055-10060

Author(s):

J W Winkelman ◽

G W Hatfield

Keyword(s):

Escherichia Coli ◽

Binding Site ◽

Promoter Region ◽

Integration Host Factor ◽

Host Factor ◽

Factor Binding Site ◽

Factor Binding

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Induction of the Cellular E2F-1 Promoter by the Adenovirus E4-6/7 Protein

Journal of Virology ◽

10.1128/jvi.74.5.2084-2093.2000 ◽

2000 ◽

Vol 74 (5) ◽

pp. 2084-2093 ◽

Cited By ~ 23

Author(s):

Joel Schaley ◽

Robert J. O'Connor ◽

Laura J. Taylor ◽

Dafna Bar-Sagi ◽

Patrick Hearing

Keyword(s):

Dna Binding ◽

Binding Site ◽

Transient Expression ◽

Binding Sites ◽

Promoter Region ◽

Fluorescent Protein ◽

Protein Accumulation ◽

Promoter Regions ◽

Single Binding Site

ABSTRACT The adenovirus type 5 (Ad5) E4-6/7 protein interacts directly with different members of the E2F family and mediates the cooperative and stable binding of E2F to a unique pair of binding sites in the Ad5 E2a promoter region. This induction of E2F DNA binding activity strongly correlates with increased E2a transcription when analyzed using virus infection and transient expression assays. Here we show that while different adenovirus isolates express an E4-6/7 protein that is capable of induction of E2F dimerization and stable DNA binding to the Ad5 E2a promoter region, not all of these viruses carry the inverted E2F binding site targets in their E2a promoter regions. The Ad12 and Ad40 E2a promoter regions bind E2F via a single binding site. However, these promoters bind adenovirus-induced (dimerized) E2F very weakly. The Ad3 E2a promoter region binds E2F very poorly, even via a single binding site. A possible explanation of these results is that the Ad E4-6/7 protein evolved to induce cellular gene expression. Consistent with this notion, we show that infection with different adenovirus isolates induces the binding of E2F to an inverted configuration of binding sites present in the cellular E2F-1 promoter. Transient expression of the E4-6/7 protein alone in uninfected cells is sufficient to induce transactivation of the E2F-1 promoter linked to chloramphenicol acetyltransferase or green fluorescent protein reporter genes. Further, expression of the E4-6/7 protein in the context of adenovirus infection induces E2F-1 protein accumulation. Thus, the induction of E2F binding to the E2F-1 promoter by the E4-6/7 protein observed in vitro correlates with transactivation of E2F-1 promoter activity in vivo. These results suggest that adenovirus has evolved two distinct mechanisms to induce the expression of the E2F-1 gene. The E1A proteins displace repressors of E2F activity (the Rb family members) and thus relieve E2F-1 promoter repression; the E4-6/7 protein complements this function by stably recruiting active E2F to the E2F-1 promoter to transactivate expression.

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RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.11.12.6317-6327.1991 ◽

1991 ◽

Vol 11 (12) ◽

pp. 6317-6327 ◽

Cited By ~ 1

Author(s):

M Vidal ◽

R F Gaber

Keyword(s):

Saccharomyces Cerevisiae ◽

Target Genes ◽

Current Data ◽

Regulatory Function ◽

Fourfold Increase ◽

Recessive Mutations ◽

Activation Of Transcription ◽

Transcriptional Regulatory ◽

Low Levels ◽

Full Activation

In Saccharomyces cerevisiae, TRK1 and TRK2 encode the high- and low-affinity K+ transporters, respectively. In cells containing a deletion of TRK1, transcription levels of TRK2 are extremely low and are limiting for growth in media containing low levels of K+ (Trk- phenotype). Recessive mutations in RPD1 and RPD3 suppress the TRK2, conferring an approximately fourfold increase in transcription. rpd3 mutations confer pleiotropic phenotypes, including (i) mating defects, (ii) hypersensitivity to cycloheximide, (iii) inability to sporulate as homozygous diploids, and (iv) constitutive derepression of acid phosphatase. RPD3 was cloned and is predicted to encode a 48-kDa protein with no extensive similarity to proteins contained in current data bases. Deletion of RPD3 is not lethal but confers phenotypes identical to those caused by spontaneous mutations. RPD3 is required for both full repression and full activation of transcription of target genes including PHO5, STE6, and TY2. RPD3 is the second gene required for this function, since RPD1 is also required. The effects of mutations in RPD1 and RPD3 are not additive, suggesting that these genes are involved in the same transcriptional regulatory function or pathway.

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C/EBPβ and GATA-1 Synergistically Regulate Activity of the Eosinophil Granule Major Basic Protein Promoter: Implication for C/EBPβ Activity in Eosinophil Gene Expression

Blood ◽

10.1182/blood.v94.4.1429 ◽

1999 ◽

Vol 94 (4) ◽

pp. 1429-1439 ◽

Cited By ~ 47

Author(s):

Yuji Yamaguchi ◽

Hitoshi Nishio ◽

Kenji Kishi ◽

Steven J. Ackerman ◽

Toshio Suda

Keyword(s):

Binding Site ◽

Cell Line ◽

Binding Sites ◽

Basic Protein ◽

Regulatory Role ◽

Expression Vectors ◽

Regulatory Function ◽

Dependent Manner ◽

Major Basic Protein ◽

Eosinophil Granule

Abstract Eosinophil granule major basic protein (MBP) is expressed exclusively in eosinophils and basophils in hematopoietic cells. In our previous study, we demonstrated a major positive regulatory role for GATA-1 and a negative regulatory role for GATA-2 in MBP gene transcription. Further analysis of the MBP promoter region identified a C/EBP (CCAAT/enhancer-binding protein) consensus binding site 6 bp upstream of the functional GATA-binding site in the MBP gene. In the cell line HT93A, which is capable of differentiating towards both the eosinophil and neutrophil lineages in response to retinoic acid (RA), C/EBP mRNA expression decreased significantly concomitant with eosinophilic and neutrophilic differentiation, whereas C/EBPβ expression was markedly increased. Electrophoretic mobility shift assays (EMSAs) showed that recombinant C/EBPβ protein could bind to the potential C/EBP-binding site (bp −90 to −82) in the MBP promoter. Furthermore, we have demonstrated that both C/EBPβ and GATA-1 can bind simultaneously to the C/EBP- and GATA-binding sites in the MBP promoter. To determine the functionality of both the C/EBP- and GATA-binding sites, we analyzed whether C/EBPβ and GATA-1 can stimulate the MBP promoter in the C/EBPβ and GATA-1 negative Jurkat T-cell line. Cotransfection with C/EBPβ and GATA-1 expression vectors produced a 5-fold increase compared with cotransfection with the C/EBPβ or GATA-1 expression vectors individually. In addition, GST pull-down experiments demonstrated a physical interaction between human GATA-1 and C/EBPβ. Expression of FOG (F̲riendo̲fG̲ATA), which binds to GATA-1 and acts as a cofactor for GATA-binding proteins, decreased transactivation activity of GATA-1 for the MBP promoter in a dose-dependent manner. Our results provide the first evidence that both GATA-1 and C/EBPβ synergistically transactivate the promoter of an eosinophil-specific granule protein gene and that FOG may act as a negative cofactor for the eosinophil lineage, unlike its positively regulatory function for the erythroid and megakaryocyte lineages.

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The role of NeuroD1 in the upregulation of SMYD3 by HBx.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.4_suppl.183 ◽

2012 ◽

Vol 30 (4_suppl) ◽

pp. 183-183

Author(s):

Junyao Xu ◽

Qingqi Hong ◽

Chuanchao He ◽

Jie Wang

Keyword(s):

Gene Expression ◽

Binding Site ◽

Promoter Region ◽

Gene Transfection ◽

Histone Methyltransferase ◽

Proximal Promoter ◽

Luciferase Reporter ◽

Mobility Shift ◽

Cis Element ◽

E Box

183 Background: SET and MYND Domain-Containing Protein 3 (SMYD3) is frequently overexpressed in hepatocellular carcinoma (HCC) exhibiting increased malignant phenotypes. It has also been known that the hepatitis B virus x protein (HBx) is strongly associated with HCC development and progression. Although overexpression of both proteins is related to HCC, the relationship between the two has not been well studied. Methods: Immunohistochemical staining was used to detect the expression of HBx and SMYD3 in HCC tumor tissues. HBx gene transfection, RNAi, and histone methyltransferase(H3-K4) activity assay were performed to reveal the transcrpitionally activation of HBx on functional SMYD3 gene expression. Chromatin immunoprecipitation (ChIP), Co-immunoprecipitation (Co-IP), Electrophoretic mobility shift assay (EMSA) were applied to investigate the underlying mechanism. Dual-luciferase reporter assay was used to search for the HBx responsive cis-element of SMYD3 gene. Results: Immunohistochemistry identified the positive correlation between HBx and SMYD3 expression in 42 HCC tissues. Up-regulation of HBx on SMYD3 expression was validated through experiments involving overexpression or knock-down of HBx in different HCC cell lines. And up-regulated SMYD3 is functionally active as histone methyltransferase. Next we found that HBx transcriptionally regulated SMYD3 gene expression by interacting with RNA polymerase IIand altering its binding site to a proximal promoter region(SD2) from a distant promoter region(SD6) of SMYD3. Truncated and mutant reporter assays revealed that the cis-element mapped in -178~-203bp in SMYD3 promotor is responsive for HBx-transactivation. And this 25bp cis-element contains a E-box 3 unit, which is a binding site for the transcriptional factor Neurogenic differentiation 1(NeuroD1). EMSA and Chip showed that HBx increased NeuroD1 binding to SMYD3 proximal promotor, however transcient expression of antisense NeuroD1 abolished HBx-induced SMYD3 expression. Conclusions: HBx transcriptionally up-regulates SMYD3 and that this process is mediated by NeuroD1 through binding to the E-box 3 site of SMYD3 promotor.

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PP7 A novel protein-binding site (agre) in human collagenase-3 proximal promoter region is involved in repression of transcription

Osteoarthritis and Cartilage ◽

10.1016/s1063-4584(01)80213-2 ◽

2001 ◽

Vol 9 ◽

pp. S3

Keyword(s):

Protein Binding ◽

Binding Site ◽

Promoter Region ◽

Proximal Promoter ◽

Protein Binding Site ◽

Proximal Promoter Region ◽

Novel Protein

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Characterization of Transcriptional Regulatory Elements in the Promoter Region of the Murine Blood Coagulation Factor VII Gene

Journal of Biological Chemistry ◽

10.1074/jbc.273.4.2277 ◽

1998 ◽

Vol 273 (4) ◽

pp. 2277-2287 ◽

Cited By ~ 16

Author(s):

Daniel R. Stauffer ◽

Beatrice N. Chukwumezie ◽

Julie A. Wilberding ◽

Elliot D. Rosen ◽

Francis J. Castellino

Keyword(s):

Blood Coagulation ◽

Promoter Region ◽

Coagulation Factor ◽

Regulatory Elements ◽

Factor Vii ◽

Transcriptional Regulatory Elements ◽

Coagulation Factor Vii ◽

Transcriptional Regulatory

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Cell type-specific protein-DNA interactions in the human zeta-globin upstream promoter region: displacement of Sp1 by the erythroid cell-specific factor NF-E1.

Molecular and Cellular Biology ◽

10.1128/mcb.10.1.282 ◽

1990 ◽

Vol 10 (1) ◽

pp. 282-294 ◽

Cited By ~ 23

Author(s):

C Y Yu ◽

J Chen ◽

L I Lin ◽

M Tam ◽

C K Shen

Keyword(s):

Binding Site ◽

Binding Sites ◽

Promoter Region ◽

Globin Gene ◽

Cell Type ◽

Upstream Promoter ◽

Protein Dna Interactions ◽

Cell Type Specific ◽

Upstream Promoter Region ◽

Zeta Globin Gene

The protein-DNA interactions of the upstream promoter region of the human embryonic zeta-globin gene in nuclear extracts of erythroid K562 cells and nonerythroid HeLa cells were analyzed by DNase I footprinting, gel mobility shift assay, methylation interference, and oligonucleotide competition experiments. There are mainly two clusters of nuclear factor-binding sites in the zeta promoter. The proximal cluster spans the DNA sequence from -110 to -60 and consists of binding sites for CP2, Sp1, and NF-E1. NF-E1 binding is K562 specific, whereas CP2 binding is common to both types of cells. Overlapping the NF-E1- and CP2-binding sites is a hidden Sp1-binding site or CAC box, as demonstrated by binding studies of affinity-purified Sp1. In the distal promoter region at -250 to -220, another NF-E1-binding site overlaps a CAC box or Sp1-binding site. Extract-mixing experiments demonstrated that the higher affinity of NF-E1 binding excluded the binding of Sp1 in the K562 extract. NF-E1 factors could also displace prebound Sp1 molecules. Between the two clusters of multiple-factor-binding sites are sequences recognized by other factors, including zeta-globin factors 1 and 2, that are present in both HeLa and K562 extracts. We discuss the cell type-specific, competitive binding of multiple nuclear factors in terms of functional implications in transcriptional regulation of the zeta-globin gene.

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