CpG methylation within the 5′ regulatory region of the BRCA1 gene is tumor specific and includes a putative CREB binding site

The alcohol dehydrogenase 2 (ADH2) gene of Saccharomyces cerevisiae is under stringent glucose repression. Two cis-acting upstream activation sequences (UAS) that function synergistically in the derepression of ADH2 gene expression have been identified. UAS1 is the binding site for the transcriptional regulator Adr1p. UAS2 has been shown to be important for ADH2 expression and confers glucose-regulated, ADR1-independent activity to a heterologous reporter gene. An analysis of point mutations within UAS2, in the context of the entire ADH2 upstream regulatory region, showed that the specific sequence of UAS2 is important for efficient derepression of ADH2, as would be expected if UAS2 were the binding site for a transcriptional regulatory protein. In the context of the ADH2 upstream regulatory region, including UAS1, working in concert with the ADH2 basal promoter elements, UAS2-dependent gene activation was dependent on orientation, copy number, and helix phase. Multimerization of UAS2, or its presence in reversed orientation, resulted in a decrease in ADH2 expression. In contrast, UAS2-dependent expression of a reporter gene containing the ADH2 basal promoter and coding sequence was enhanced by multimerization of UAS2 and was independent of UAS2 orientation. The reduced expression caused by multimerization of UAS2 in the native promoter was observed only in the presence of ADR1. Inhibition of UAS2-dependent gene expression by Adr1p was also observed with a UAS2-dependent ADH2 reporter gene. This inhibition increased with ADR1 copy number and required the DNA-binding activity of Adr1p. Specific but low-affinity binding of Adr1p to UAS2 in vitro was demonstrated, suggesting that the inhibition of UAS2-dependent gene expression observed in vivo could be a direct effect due to Adr1p binding to UAS2.

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Roles of Transcription Factor Mot3 and Chromatin in Repression of the Hypoxic Gene ANB1 in Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.20.19.7088-7098.2000 ◽

2000 ◽

Vol 20 (19) ◽

pp. 7088-7098 ◽

Cited By ~ 41

Author(s):

Alexander J. Kastaniotis ◽

Thomas A. Mennella ◽

Christian Konrad ◽

Ana M. Rodriguez Torres ◽

Richard S. Zitomer

Keyword(s):

Binding Site ◽

Regulatory Region ◽

Direct Interaction ◽

Minor Effect ◽

Histone H4 ◽

Coding Region ◽

Basal Transcriptional Machinery ◽

In The Wild ◽

A Minor

ABSTRACT The hypoxic genes of Saccharomyces cerevisiae are repressed by a complex consisting of the aerobically expressed, sequence-specific DNA-binding protein Rox1 and the Tup1-Ssn6 general repressors. The regulatory region of one well-studied hypoxic gene,ANB1, is comprised of two operators, OpA and OpB, each of which has two strong Rox1 binding sites, yet OpA represses transcription almost 10 times more effectively than OpB. We show here that this difference is due to the presence of a Mot3 binding site in OpA. Mutations in this site reduced OpA repression to OpB levels, and the addition of a Mot3 binding site to OpB enhanced repression. Deletion of the mot3 gene also resulted in reduced repression of ANB1. Repression of two other hypoxic genes in which Mot3 sites were associated with Rox1 sites was reduced in the deletion strain, but other hypoxic genes were unaffected. In addition, the mot3Δ mutation caused a partial derepression of the Mig1–Tup1-Ssn6-repressed SUC2 gene, but not the α2–Mcm1–Tup1-Ssn6-repressed STE2 gene. The Mot3 protein was demonstrated to bind to the ANB1 OpA in vitro. Competition experiments indicated that there was no interaction between Rox1 and Mot3, indicating that Mot3 functions either in Tup1-Ssn6 recruitment or directly in repression. A great deal of evidence has accumulated suggesting that the Tup1-Ssn6 complex represses transcription through both nucleosome positioning and a direct interaction with the basal transcriptional machinery. We demonstrate here that under repressed conditions a nucleosome is positioned over the TATA box in the wild-type ANB1promoter. This nucleosome was absent in cells carrying arox1, tup1, or mot3 deletion, all of which cause some degree of derepression. Interestingly, however, this positioned nucleosome was also lost in a cell carrying a deletion of the N-terminal coding region of histone H4, yet ANB1expression remained fully repressed. A similar deletion in the gene for histone H3, which had no effect on repression, had only a minor effect on the positioned nucleosome. These results indicate that the nucleosome phasing on the ANB1 promoter caused by the Rox1–Mot3–Tup1-Ssn6 complex is either completely redundant with a chromatin-independent repression mechanism or, less likely, plays no role in repression at all.

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Effect of variation in miRNA-binding site (rs8176318) of the BRCA1 gene in breast cancer patients

TURKISH JOURNAL OF MEDICAL SCIENCES ◽

10.3906/sag-1905-17 ◽

2019 ◽

Vol 49 (5) ◽

pp. 1433-1438 ◽

Cited By ~ 1

Author(s):

Mushtaq AHMAD ◽

Fazal JALIL ◽

Mutiul HAQ ◽

Aftab Ali SHAH

Keyword(s):

Breast Cancer ◽

Binding Site ◽

Cancer Patients ◽

Brca1 Gene ◽

Mirna Binding Site ◽

Breast Cancer Patients

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Identification of Ste4 as a potential regulator of Byr2 in the sexual response pathway of Schizosaccharomyces pombe.

Molecular and Cellular Biology ◽

10.1128/mcb.16.10.5597 ◽

1996 ◽

Vol 16 (10) ◽

pp. 5597-5603 ◽

Cited By ~ 56

Author(s):

M M Barr ◽

H Tu ◽

L Van Aelst ◽

M Wigler

Keyword(s):

Saccharomyces Cerevisiae ◽

Schizosaccharomyces Pombe ◽

Binding Site ◽

Sexual Differentiation ◽

Leucine Zipper ◽

Regulatory Region ◽

Map Kinase Cascade ◽

Kinase Cascade ◽

Two Hybrid ◽

Erk Kinase

A conserved MAP kinase cascade is central to signal transduction in both simple and complex eukaryotes. In the yeast Schizosaccharomyces pombe, Byr2, a homolog of mammalian MAPK/ERK kinase kinase and Saccharomyces cerevisiae STE11, is required for pheromone-induced sexual differentiation. A screen for S. pombe proteins that interact with Byr2 in a two-hybrid system led to the isolation of Ste4, a protein that is known to be required for sexual function. Ste4 binds to the regulatory region of Byr2. This binding site is separable from the binding site for Ras1. Both Ste4 and Ras1 act upstream of Byr2 and act at least partially independently. Ste4 contains a leucine zipper and is capable of homotypic interaction. Ste4 has regions of homology with STE50, an S. cerevisiae protein required for sexual differentiation that we show can bind to STE11.

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Regulatory region of metastasis-inducing DNA is the binding site for T cell factor-4

Oncogene ◽

10.1038/sj.onc.1204358 ◽

2001 ◽

Vol 20 (14) ◽

pp. 1793-1797 ◽

Cited By ~ 26

Author(s):

Mohamed K El-Tanani ◽

Roger Barraclough ◽

Mark C Wilkinson ◽

Philip S Rudland

Keyword(s):

T Cell ◽

Binding Site ◽

Regulatory Region ◽

T Cell Factor

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A Pair of Highly Conserved Two-Component Systems Participates in the Regulation of the Hypervariable FIR Proteins in Different Legionella Species

Journal of Bacteriology ◽

10.1128/jb.01742-06 ◽

2007 ◽

Vol 189 (9) ◽

pp. 3382-3391 ◽

Cited By ~ 10

Author(s):

Michal Feldman ◽

Gil Segal

Keyword(s):

Binding Site ◽

Legionella Pneumophila ◽

Response Regulator ◽

Regulatory Element ◽

Expression System ◽

Regulatory Region ◽

Regulatory Elements ◽

Mobility Shift ◽

Type Iv ◽

Essential Components

ABSTRACT Legionella pneumophila and other pathogenic Legionella species multiply inside protozoa and human macrophages by using the Icm/Dot type IV secretion system. The IcmQ protein, which possesses pore-forming activity, and IcmR, which functions as its chaperone, are two essential components of this system. It was previously shown that in 29 Legionella species, a large hypervariable-gene family (fir genes) is located upstream from a conserved icmQ gene, but although nonhomologous, the FIR proteins were found to function similarly together with their corresponding IcmQ proteins. Alignment of the regulatory regions of 29 fir genes revealed that they can be divided into three regulatory groups; the first group contains a binding site for the CpxR response regulator, which was previously shown to regulate the L. pneumophila fir gene (icmR); the second group, which includes most of the fir genes, contains the CpxR binding site and an additional regulatory element that was identified here as a PmrA binding site; and the third group contains only the PmrA binding site. Analysis of the regulatory region of two fir genes, which included substitutions in the CpxR and PmrA consensus sequences, a controlled expression system, as well as examination of direct binding with mobility shift assays, revealed that both CpxR and PmrA positively regulate the expression of the fir genes that contain both regulatory elements. The change in the regulation of the fir genes that occurred during the course of evolution might be required for the adaptation of the different Legionella species to their specific environmental hosts.

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The octamer binding site in the HPV16 regulatory region produces opposite effects on gene expression in cervical and non-cervical cells

Nucleic Acids Research ◽

10.1093/nar/21.4.1019 ◽

1993 ◽

Vol 21 (4) ◽

pp. 1019-1023 ◽

Cited By ~ 21

Author(s):

Peter J. Morris ◽

Carolyn L. Dent ◽

Christopher J. Ring ◽

David S. Latchman

Keyword(s):

Gene Expression ◽

Binding Site ◽

Regulatory Region ◽

Cervical Cells

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A functional interferon regulatory factor-1 (IRF-1)-binding site in the upstream regulatory region (URR) of human papillomavirus type 16

Virology ◽

10.1016/s0042-6822(03)00138-7 ◽

2003 ◽

Vol 310 (2) ◽

pp. 280-286 ◽

Cited By ~ 9

Author(s):

Istvan Arany ◽

Kenneth J Grattendick ◽

William E Whitehead ◽

Istvan A Ember ◽

Stephen K Tyring

Keyword(s):

Human Papillomavirus ◽

Binding Site ◽

Regulatory Region ◽

Interferon Regulatory Factor ◽

Upstream Regulatory Region ◽

Regulatory Factor ◽

Human Papillomavirus Type 16 ◽

Interferon Regulatory Factor 1

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An ATF/CREB-binding site is essential for cell-specific and inducible transcription of the murine MIP-1β cytokine gene

Gene ◽

10.1016/0378-1119(94)00701-s ◽

1995 ◽

Vol 152 (2) ◽

pp. 173-179 ◽

Cited By ~ 29

Author(s):

J. Proffitt ◽

G. Crabtree ◽

M. Grove ◽

P. Daubersies ◽

B. Bailleul ◽

...

Keyword(s):

Binding Site ◽

Cytokine Gene ◽

Creb Binding Site

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Alterations in the binding site of the cyclic AMP receptor protein at the Escherichia coli galactose operon regulatory region

Biochemical Journal ◽

10.1042/bj2530809 ◽

1988 ◽

Vol 253 (3) ◽

pp. 809-818 ◽

Cited By ~ 10

Author(s):

K Gaston ◽

B Chan ◽

A Kolb ◽

J Fox ◽

S Busby

Keyword(s):

Escherichia Coli ◽

Cyclic Amp ◽

Binding Site ◽

Consensus Sequence ◽

Regulatory Region ◽

Receptor Protein ◽

Binding Assays ◽

Cyclic Amp Receptor Protein ◽

Stimulation Of

Gene manipulation techniques have been used to alter the binding site for the cyclic AMP-cyclic AMP receptor protein complex (cAMP-CRP) at the regulatory region of the Escherichia coli galactose (gal) operon. The effects of these changes on CRP-dependent stimulation of expression from the galP1 promoter in vivo have been measured, and gel binding assays have been used to measure the affinity of cAMP-CRP for the modified sites. Firstly we have deleted progressively longer sequences from upstream of the gal CRP site in order to locate the functional limit of the site. A deletion to -49, removing the first base that corresponds to the consensus sequence for a CRP binding site, is sufficient to reduce CRP binding and block CRP-dependent stimulation of P1. Secondly, we used synthetic oligonucleotides to invert the asymmetric nucleotide sequence at the gal CRP binding site or to make the sequence symmetric. Inversion of the site has little effect on CRP binding, the architecture of open complexes at P1 revealed by DNAase I footprinting, or the stimulation of transcription from P1. Making the site symmetric increases the affinity for CRP by over 50-fold and leads to increased transcription from P1, whilst hardly altering the DNAase I footprint of open complexes. Our results confirm that the strength of binding of CRP depends on the nature of the site and show that it is this that principally accounts for differences in CRP-dependent stimulation of transcription.

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