Negative Androgen-Response Elements in Androgen Target Genes

2013 ◽  
pp. 29-41
Author(s):  
Wei Qi ◽  
Zhengxin Wang
Keyword(s):  
Target Genes ◽  
Response Elements

ZFARED: A Database of the Antioxidant Response Elements in Zebrafish

2020 ◽  
Vol 15 (5) ◽  
pp. 415-419
Author(s):  
Azhwar Raghunath ◽  
Raju Nagarajan ◽  
Ekambaram Perumal
Keyword(s):  
Target Genes ◽  
Antioxidant Response ◽  
Zebrafish Genome ◽  
Promoter Regions ◽  
Protein Coding ◽  
Response Elements ◽  
Toxic Agents ◽  
Upstream Promoter ◽  
Its Gene ◽  
Antioxidant Response Elements

Background: Antioxidant Response Elements (ARE) play a key role in the expression of Nrf2 target genes by regulating the Keap1-Nrf2-ARE pathway, which offers protection against toxic agents and oxidative stress-induced diseases. Objective: To develop a database of putative AREs for all the genes in the zebrafish genome. This database will be helpful for researchers to investigate Nrf2 regulatory mechanisms in detail. Methods: To facilitate researchers functionally characterize zebrafish AREs, we have developed a database of AREs, Zebrafish Antioxidant Response Element Database (ZFARED), for all the protein-coding genes including antioxidant and mitochondrial genes in the zebrafish genome. The front end of the database was developed using HTML, JavaScript, and CSS and tested in different browsers. The back end of the database was developed using Perl scripts and Perl-CGI and Perl- DBI modules. Results: ZFARED is the first database on the AREs in zebrafish, which facilitates fast and efficient searching of AREs. AREs were identified using the in-house developed Perl algorithms and the database was developed using HTML, JavaScript, and Perl-CGI scripts. From this database, researchers can access the AREs based on chromosome number (1 to 25 and M for mitochondria), strand (positive or negative), ARE pattern and keywords. Users can also specify the size of the upstream/promoter regions (5 to 30 kb) from transcription start site to access the AREs located in those specific regions. Conclusion: ZFARED will be useful in the investigation of the Keap1-Nrf2-ARE pathway and its gene regulation. ZFARED is freely available at http://zfared.buc.edu.in/.

Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements

2006 ◽  
Vol 339 (1) ◽  
pp. 99-106 ◽  
Author(s):  
Kuniko Horie-Inoue ◽  
Kenichi Takayama ◽  
Hidemasa U. Bono ◽  
Yasuyoshi Ouchi ◽  
Yasushi Okazaki ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Target Genes ◽  
Hormone Response ◽  
Response Elements ◽  
Hormone Response Elements

scholarly journals Rapid Effects of Retinoic Acid on CREB and ERK Phosphorylation in Neuronal Cells

2004 ◽  
Vol 15 (12) ◽  
pp. 5583-5592 ◽  
Author(s):  
Estela Cañón ◽  
Jose Miguel Cosgaya ◽  
Sona Scsucova ◽  
Ana Aranda
Keyword(s):  
Retinoic Acid ◽  
Transcriptional Activity ◽  
Target Genes ◽  
Primary Cultures ◽  
Neuronal Cells ◽  
Neuronal Cell ◽  
Direct Stimulation ◽  
Creb Phosphorylation ◽  
Response Elements ◽  
Stimulation Of

Retinoic acid (RA) is a potent regulator of neuronal cell differentiation. RA normally activates gene expression by binding to nuclear receptors that interact with response elements (RAREs) in regulatory regions of target genes. We show here that in PC12 cell subclones in which the retinoid causes neurite extension, RA induces a rapid and sustained phosphorylation of CREB (cyclic AMP response element binding protein), compatible with a nongenomic effect. RA also causes a rapid increase of CREB phosphorylation in primary cultures of cerebrocortical cells and of dorsal root ganglia neurons from rat embryos. RA-mediated phosphorylation of CREB leads to a direct stimulation of CREB-dependent transcriptional activity and to activation of the expression of genes such as c-fos, which do not contain RAREs but contain cAMP response elements (CREs) in their promoters. CREB is a major target of extracellular signal regulated kinase ERK1/2 signaling in neuronal cells, and we demonstrate here that RA induces an early stimulation of ERK1/2, which is required both for CREB phosphorylation and transcriptional activity. These results demonstrate that RA, by a nongenomic mechanism, stimulates signaling pathways that lead to phosphorylation of transcription factors, which in turn activate the transcription of genes involved in neuronal differentiation.

scholarly journals Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Elina Ly ◽  
Jennifer F. Kugel ◽  
James A. Goodrich
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Target Genes ◽  
Population Distribution ◽  
Kinetic Stability ◽  
Full Length ◽  
Dna Complexes ◽  
Response Elements ◽  
Cell Fate Decisions ◽  
Half Site

Abstract The tumor suppressor protein p53 is critical for cell fate decisions, including apoptosis, senescence, and cell cycle arrest. p53 is a tetrameric transcription factor that binds DNA response elements to regulate transcription of target genes. p53 response elements consist of two decameric half-sites, and data suggest one p53 dimer in the tetramer binds to each half-site. Despite a broad literature describing p53 binding DNA, unanswered questions remain, due partly to the need for more quantitative and structural studies with full length protein. Here we describe a single molecule fluorescence system to visualize full length p53 tetramers binding DNA in real time. The data revealed a dynamic interaction in which tetrameric p53/DNA complexes assembled and disassembled without a dimer/DNA intermediate. On a wild type DNA containing two half sites, p53/DNA complexes existed in two kinetically distinct populations. p53 tetramers bound response elements containing only one half site to form a single population of complexes with reduced kinetic stability. Altering the spacing and helical phasing between two half sites affected both the population distribution of p53/DNA complexes and their kinetic stability. Our real time single molecule measurements of full length p53 tetramers binding DNA reveal the parameters that define the stability of p53/DNA complexes, and provide insight into the pathways by which those complexes assemble.

scholarly journals Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites

2019 ◽  
Author(s):  
Elina Ly ◽  
Jennifer F. Kugel ◽  
James A. Goodrich
Keyword(s):  
Real Time ◽  
Cell Fate ◽  
Single Molecule ◽  
Target Genes ◽  
Full Length ◽  
Forward Rate ◽  
Kinetic Measurements ◽  
Response Elements ◽  
Cell Fate Decisions ◽  
Half Site

AbstractThe tumor suppressor protein p53 is at the nexus of cell fate decisions, including apoptosis, senescence, and cell cycle arrest. p53 is a tetrameric transcription factor that binds to DNA response elements to regulate transcription of its target genes, a process activated by cellular stress. p53 response elements consist of two decameric half-sites, and most data suggest one p53 dimer in the tetramer binds to each half-site. Despite a broad literature describing p53 binding to DNA, unanswered questions remain, due in part to the need for more quantitative and structural studies with the full length protein. Here we describe a single molecule fluorescence system to visualize full length p53 tetramers binding to DNA in real time. The data reveal a dynamic interaction with many p53 binding and dissociation events occurring on single DNA molecules over minutes. We found that p53 tetramers bound to response elements containing only a single half site. The kinetic stability of tetramer/DNA complexes depended on the number of half sites and the helical phasing between them, with the most stable complexes forming on DNA containing two adjacent half sites. The forward rate of binding was not strongly impacted when one half site was mutated. These studies provide real time kinetic measurements of full length p53 tetramers binding to single molecules of DNA, and reveal new insight into the mechanisms by which this nucleoprotein complex forms.

scholarly journals Genome reading by the NF-κB transcription factors

2019 ◽  
Vol 47 (19) ◽  
pp. 9967-9989 ◽  
Author(s):  
Maria Carmen Mulero ◽  
Vivien Ya-Fan Wang ◽  
Tom Huxford ◽  
Gourisankar Ghosh
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Sequences ◽  
Target Genes ◽  
Target Selection ◽  
Structural Features ◽  
Response Elements ◽  
Target Binding

Abstract The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5′-GGGRNNNYCC-3′ (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.

scholarly journals Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes

2005 ◽  
Vol 281 (2) ◽  
pp. 210-226 ◽  
Author(s):  
Andreas von Bubnoff ◽  
Daniel A. Peiffer ◽  
Ira L. Blitz ◽  
Tadayoshi Hayata ◽  
Souichi Ogata ◽  
...  
Keyword(s):  
Target Genes ◽  
Phylogenetic Footprinting ◽  
Response Elements ◽  
Genome Scanning

scholarly journals Retinoic Acid Receptor Isotype Specificity in F9 Teratocarcinoma Stem Cells Results from the Differential Recruitment of Coregulators to Retinoic Acid Response Elements

2007 ◽  
Vol 282 (46) ◽  
pp. 33421-33434 ◽  
Author(s):  
Robert F. Gillespie ◽  
Lorraine J. Gudas
Keyword(s):  
Stem Cells ◽  
Retinoic Acid ◽  
Target Genes ◽  
Retinoic Acid Receptor ◽  
Polycomb Group ◽  
Polycomb Group Protein ◽  
Response Elements ◽  
Acid Receptor ◽  
Group Protein ◽  
F9 Teratocarcinoma

The retinoic acid receptor (RAR) α, β2, and γ isotypes each regulate specific subsets of target genes in F9 teratocarcinoma stem cells. We used chromatin immunoprecipitation assays to monitor the association of RARγ, retinoic X receptor (RXR) α, and coregulators with the RARβ2, Hoxa1, and Cyp26A1 retinoic acid response elements (RAREs) in F9 wild type and RARα, -β2, and -γ null cells. Additionally we quantitatively monitored expression of the corresponding mRNAs. We demonstrated that the association of RARγ and/or RXRα with a RARE was not sufficient for retinoic acid (RA)-mediated transcription of the corresponding target gene. However, the ability of RARγ and/or RXRα to recruit pCIP (AIB1/ACTR/RAC-3/TRAM-1/SRC-3) and p300 to a RARE did correlate with RA-associated transcription of target mRNAs. Therefore, the specific functions of the RAR isotypes do not manifest at the level of their DNA binding but rather from a differential ability to recruit specific components of the transcriptional machinery. We also demonstrated that RA-mediated displacement of the polycomb group protein SUZ12 from a RARE was inhibited in the absence of RARγ. Thus, transcriptional components of the RAR signaling pathway are specifically required for displacement of SUZ12 from RAREs during RA-mediated differentiation of F9 cells.

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