response elements

Summary

Summary: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.

Top Publications

  1. doi Transcriptional control of human p53-regulated genes
    Todd Riley
    The Institute for Advanced Study, Princeton, New Jersey, USA
    Nat Rev Mol Cell Biol 9:402-12. 2008
  2. doi The expanding universe of p53 targets
    Daniel Menendez
    Laboratory of Molecular Genetics, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709, USA
    Nat Rev Cancer 9:724-37. 2009
  3. ncbi Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses
    Yoshihiro Narusaka
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 34:137-48. 2003
  4. ncbi Role of histone H3 lysine 27 methylation in Polycomb-group silencing
    Ru Cao
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 298:1039-43. 2002
  5. ncbi The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis
    P H Maxwell
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nature 399:271-5. 1999
  6. ncbi ABFs, a family of ABA-responsive element binding factors
    H Choi
    Kumho Life and Environmental Science Laboratory, Kwangju 500 712, South Korea
    J Biol Chem 275:1723-30. 2000
  7. pmc Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
    F Nikulenkov
    Department of Microbiology, Tumor and Cell Biology MTC, Karolinska Institutet, Stockholm, Sweden
    Cell Death Differ 19:1992-2002. 2012
  8. ncbi Identification and functional characterization of distinct critically important bone morphogenetic protein-specific response elements in the Id1 promoter
    Olexander Korchynskyi
    Division of Cellular Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    J Biol Chem 277:4883-91. 2002
  9. doi A vertebrate Polycomb response element governs segmentation of the posterior hindbrain
    Angela Sing
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, ON, M5G 1X5, Canada
    Cell 138:885-97. 2009
  10. pmc Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins
    Bernadett Papp
    European Molecular Biology Laboratory, Gene Expression Programme, Heidelberg, Germany
    Genes Dev 20:2041-54. 2006

Detail Information

Publications357 found, 100 shown here

  1. doi Transcriptional control of human p53-regulated genes
    Todd Riley
    The Institute for Advanced Study, Princeton, New Jersey, USA
    Nat Rev Mol Cell Biol 9:402-12. 2008
    ..In addition, we present the most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation...
  2. doi The expanding universe of p53 targets
    Daniel Menendez
    Laboratory of Molecular Genetics, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709, USA
    Nat Rev Cancer 9:724-37. 2009
    ..This Review describes the identification and functionality of REs and highlights the inclusion of non-canonical REs that expand the universe of genes and regulation mechanisms in the p53 tumour suppressor network...
  3. ncbi Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses
    Yoshihiro Narusaka
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 34:137-48. 2003
    ..These results indicate that DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A gene in response to ABA in Arabidopsis...
  4. ncbi Role of histone H3 lysine 27 methylation in Polycomb-group silencing
    Ru Cao
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 298:1039-43. 2002
    ..Methylation on H3-K27 facilitates binding of Polycomb (PC), a component of the PRC1 complex, to histone H3 amino-terminal tail. Thus, these studies establish a link between histone methylation and PcG-mediated gene silencing...
  5. ncbi The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis
    P H Maxwell
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nature 399:271-5. 1999
    ..Thus, constitutive HIF-1 activation may underlie the angiogenic phenotype of VHL-associated tumours. The pVHL/HIF-1 interaction provides a new focus for understanding cellular oxygen sensing...
  6. ncbi ABFs, a family of ABA-responsive element binding factors
    H Choi
    Kumho Life and Environmental Science Laboratory, Kwangju 500 712, South Korea
    J Biol Chem 275:1723-30. 2000
    ..Thus, a new family of ABRE binding factors indeed exists that have the potential to activate a large number of ABA/stress-responsive genes in Arabidopsis...
  7. pmc Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
    F Nikulenkov
    Department of Microbiology, Tumor and Cell Biology MTC, Karolinska Institutet, Stockholm, Sweden
    Cell Death Differ 19:1992-2002. 2012
    ..We identified Sp1 as one of the p53 modulators, which confer specificity to p53-mediated transcriptional response upon RITA. Further, we found that STAT3 antagonizes p53-mediated repression of a subset of genes, including AURKA...
  8. ncbi Identification and functional characterization of distinct critically important bone morphogenetic protein-specific response elements in the Id1 promoter
    Olexander Korchynskyi
    Division of Cellular Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    J Biol Chem 277:4883-91. 2002
    ..Our results provide important new insights into how the BMP/Smad pathway can specifically activate target genes...
  9. doi A vertebrate Polycomb response element governs segmentation of the posterior hindbrain
    Angela Sing
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, ON, M5G 1X5, Canada
    Cell 138:885-97. 2009
    ..In Drosophila, PcG/trxG protein complexes are recruited by PcG/trxG response elements (PREs). However, it has been unclear how PcG/trxG are recruited in vertebrates...
  10. pmc Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins
    Bernadett Papp
    European Molecular Biology Laboratory, Gene Expression Programme, Heidelberg, Germany
    Genes Dev 20:2041-54. 2006
    ..PcG protein complexes PhoRC, PRC1, and PRC2 and the Trx protein are all constitutively bound to Polycomb response elements (PREs) in the OFF and ON state...
  11. pmc Polycomb group response elements in Drosophila and vertebrates
    Judith A Kassis
    Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
    Adv Genet 81:83-118. 2013
    ..recruited to the DNA? In Drosophila, there are specific regulatory DNA elements called Polycomb group response elements (PREs) that bring PcG protein complexes to the DNA...
  12. pmc p53 represses c-Myc through induction of the tumor suppressor miR-145
    Mohit Sachdeva
    Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
    Proc Natl Acad Sci U S A 106:3207-12. 2009
    ....
  13. ncbi Hierarchical recruitment of polycomb group silencing complexes
    Liangjun Wang
    Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
    Mol Cell 14:637-46. 2004
    ....
  14. pmc Structure of p73 DNA-binding domain tetramer modulates p73 transactivation
    Abdul S Ethayathulla
    Laboratory of Structural Biochemistry, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive 0378, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 109:6066-71. 2012
    ..How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem...
  15. doi Crystal structure of a multidomain human p53 tetramer bound to the natural CDKN1A (p21) p53-response element
    Soheila Emamzadah
    Department of Molecular Biology, University of Geneva, Geneva, Switzerland
    Mol Cancer Res 9:1493-9. 2011
    ..Thus, the new structure further supports our model that recognition of specific DNA by p53 is associated with conformational changes within the DNA-binding domain of p53...
  16. ncbi DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression
    Yoh Sakuma
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki, 305 8686, Japan
    Biochem Biophys Res Commun 290:998-1009. 2002
    ..The DREB subfamily included three novel DREB1A- and six DREB2A-related proteins. We analyzed expression of novel genes for these proteins and discuss their roles in stress-responsive gene expression...
  17. ncbi Molecular determinants for the tissue specificity of SERMs
    Yongfeng Shang
    Department of Adult Oncology, Dana Farber Cancer Institute, 44 Binney Street, and Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Science 295:2465-8. 2002
    ..Thus cell type- and promoter-specific differences in coregulator recruitment determine the cellular response to SERMs...
  18. ncbi Anatomy of the estrogen response element
    Christian J Gruber
    Division of Gynecologic Endocrinology and Reproductive Medicine, Department of Obstetrics and Gynecology, University of Vienna Medical School, Wahringer Gurtel 18 20, A 1090, Vienna, Austria
    Trends Endocrinol Metab 15:73-8. 2004
    ..A direct nuclear approach is the interaction of estrogen with specific target sequences of DNA, estrogen response elements (ERE) or units...
  19. ncbi Estrogen receptor pathways to AP-1
    P J Kushner
    Metabolic Research Unit, 1119 HSW, University of California, 3rd and Parnassus, 94143 0540, San Francisco, CA, USA
    J Steroid Biochem Mol Biol 74:311-7. 2000
    Estrogen receptor (ER) binds to estrogen response elements in target genes and recruits a coactivator complex of CBP-pl60 that mediates stimulation of transcription...
  20. ncbi Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex
    Chiara Lanzuolo
    Dulbecco Telethon Institute at IGB CNR, Epigenetics and Genome Reprogramming, Via Pietro Castellino 111, 80131 Naples, Italy
    Nat Cell Biol 9:1167-74. 2007
    In Drosophila, the function of the Polycomb group genes (PcGs) and their target sequences (Polycomb response elements (PREs)) is to convey mitotic heritability of transcription programmes--in particular, gene silencing...
  21. ncbi HIF-1 regulates cytochrome oxidase subunits to optimize efficiency of respiration in hypoxic cells
    Ryo Fukuda
    Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 129:111-22. 2007
    ..Thus, mammalian cells respond to hypoxia by altering COX subunit composition, as previously observed in yeast, but by a completely different molecular mechanism...
  22. pmc Glucocorticoid receptor-promoter interactions: energetic dissection suggests a framework for the specificity of steroid receptor-mediated gene regulation
    James P Robblee
    Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
    Biochemistry 51:4463-72. 2012
    ..Finally, simulations show that such partitioning of interaction energetics allows for receptor-specific promoter occupancies, even under conditions where multiple receptors are competing for binding at identical sites...
  23. ncbi RNAi components are required for nuclear clustering of Polycomb group response elements
    Charlotte Grimaud
    Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
    Cell 124:957-71. 2006
    Drosophila Polycomb group (PcG) proteins silence homeotic genes through binding to Polycomb group response elements (PREs). Fab-7 is a PRE-containing regulatory element from the homeotic gene Abdominal-B...
  24. ncbi Predictive base substitution rules that determine the binding and transcriptional specificity of Maf recognition elements
    Tae Yamamoto
    Graduate School of Comprehensive Human Sciences and Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba 305 8577, Japan
    Genes Cells 11:575-91. 2006
    ..This study thus manifests that a clear set of rules pertaining to the cis-acting element determine whether a given MARE preferentially associates with MafG homodimer or with MafG:Nrf2 heterodimer...
  25. pmc VIP1 response elements mediate mitogen-activated protein kinase 3-induced stress gene expression
    Andrea Pitzschke
    Department of Plant Molecular Biology, Max F Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
    Proc Natl Acad Sci U S A 106:18414-9. 2009
    ..a functional bZIP transcription factor that stimulates stress-dependent gene expression by binding to VIP1 response elements (VREs), a DNA hexamer motif...
  26. ncbi DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites
    G B Ehret
    Swiss Institute for Experimental Cancer Research ISREC 1066 Epalinges, Switzerland
    J Biol Chem 276:6675-88. 2001
    ..As previously reported, STAT1 and STAT5 prefer N(3) sites; however, STAT5A, but not STAT1, weakly binds N(4) sites. None of the STATs bound to half-palindromes. There were no specificity differences between STAT5A and STAT5B...
  27. pmc Insulators, not Polycomb response elements, are required for long-range interactions between Polycomb targets in Drosophila melanogaster
    Hua bing Li
    Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ 08854, USA
    Mol Cell Biol 31:616-25. 2011
    ..Fab-7 regulatory elements, we find that these associations are not dependent on or caused by the Polycomb response elements they contain...
  28. pmc Microsatellites as EWS/FLI response elements in Ewing's sarcoma
    Kunal Gangwal
    Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
    Proc Natl Acad Sci U S A 105:10149-54. 2008
    ..These findings illustrate an unprecedented route to specificity for ETS proteins and use of microsatellites in tumorigenesis...
  29. ncbi Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression
    Melanie Wissmann
    Universitäts Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
    Nat Cell Biol 9:347-53. 2007
    ..Thus, our data suggest that specific gene regulation requires the assembly and coordinate action of demethylases with distinct substrate specificities...
  30. doi Widespread negative response elements mediate direct repression by agonist-liganded glucocorticoid receptor
    Milan Surjit
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS UMR7104, INSERM U964, Universite de Strasbourg, College de France, Illkirch, 67404, France
    Cell 145:224-41. 2011
    ..This mechanism suits GR signaling remarkably well, given that adrenal secretion of GC fluctuates in a circadian and stress-related fashion...
  31. ncbi The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator
    Nicolas Preitner
    Department of Molecular Biology, Sciences II, University of Geneva, 30, Quai Ernest Ansermet, CH 1211 4, Geneva, Switzerland
    Cell 110:251-60. 2002
    ..While REV-ERBalpha influences the period length and affects the phase-shifting properties of the clock, it is not required for circadian rhythm generation...
  32. ncbi Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
    ..Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer...
  33. pmc Nrf1 and Nrf2 play distinct roles in activation of antioxidant response element-dependent genes
    Makiko Ohtsuji
    Graduate School of Comprehensive Human Sciences, Japan Science and Technology Corp, 1 1 1 Tennoudai, Tsukuba 305 8577, Japan
    J Biol Chem 283:33554-62. 2008
    ..This study has, thus, identified the first ARE-dependent gene that relies exclusively on Nrf1, suggesting that it plays a distinct functional role in regulating ARE-driven genes...
  34. pmc Pliable DNA conformation of response elements bound to transcription factor p63
    Chen Chen
    W M Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research and the Department of Chemistry and Biochemistry, University of Maryland, Rockville, Maryland 20850, USA
    J Biol Chem 287:7477-86. 2012
    ..p63DBD binding assays to response elements of increasing length complement the structural studies...
  35. ncbi Allosteric regulation of estrogen receptor structure, function, and coactivator recruitment by different estrogen response elements
    Julie M Hall
    Receptor Biology Section, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Mol Endocrinol 16:469-86. 2002
    Hormone-activated ERs (ERalpha and ERbeta) bind with high affinity to specific DNA sequences, estrogen response elements (EREs), located within the regulatory regions of target genes...
  36. doi Regulation of Polycomb group genes Psc and Su(z)2 in Drosophila melanogaster
    Sung Yeon Park
    Department of Molecular Biology and Biochemistry, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
    Mech Dev 128:536-47. 2012
    ..Psc-Su(z)2 locus, a region whose chromatin is enriched for H3K27me3 and contains several putative Polycomb response elements (PREs) that bind PcG proteins...
  37. pmc Redefining the p53 response element
    Bei Wang
    Laboratory of Immunogenetics, Singapore Immunology Network, A STAR, 8A Biomedical Grove, Immunos, Singapore
    Proc Natl Acad Sci U S A 106:14373-8. 2009
    ..Hence this clearer definition of the transcriptional behavior of p53 interaction with its RE will provide better insight toward the understanding of its fundamental role in cellular networks...
  38. ncbi Corepressor SMRT functions as a coactivator for thyroid hormone receptor T3Ralpha from a negative hormone response element
    Hege Berghagen
    Biotechnology Centre of Oslo, University of Oslo, Postboks 1050 Blindern, Oslo 0316, Norway
    J Biol Chem 277:49517-22. 2002
    ..These results suggest that allosteric changes resulting from binding of T3Ralpha to different response elements, i.e. pHREs versus nHREs, dictate whether a cofactor will function as a coactivator or a corepressor...
  39. pmc JASPAR: an open-access database for eukaryotic transcription factor binding profiles
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:D91-4. 2004
    ..JASPAR is available at http://jaspar. cgb.ki.se...
  40. ncbi Experimentally determined sequence requirement of ACGT-containing abscisic acid response element
    Tsukaho Hattori
    Center for Molecular Biology and Genetics, Mie University, Tsu, 514 8507 Japan
    Plant Cell Physiol 43:136-40. 2002
    ..Based on this analysis, the sequence requirement of the ACGT-containing ABRE was determined as ACGTG G/T C, which matched very well with the consensus derived from sequence comparison of ABA-responsive promoters...
  41. pmc Transcriptional regulatory code of a eukaryotic genome
    Christopher T Harbison
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 431:99-104. 2004
    ..We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators...
  42. pmc Identification of a novel Nrf2-regulated antioxidant response element (ARE) in the mouse NAD(P)H:quinone oxidoreductase 1 gene: reassessment of the ARE consensus sequence
    Paul Nioi
    Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, Scotland, UK
    Biochem J 374:337-48. 2003
    ..Furthermore, our results indicate that distinct AREs have differential sequence requirements, and a universally applicable consensus sequence cannot be derived...
  43. ncbi Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax
    Tilman Sanchez-Elsner
    Department of Biochemistry, University of California, Riverside, CA 92521, USA
    Science 311:1118-23. 2006
    Homeotic genes contain cis-regulatory trithorax response elements (TREs) that are targeted by epigenetic activators and transcribed in a tissue-specific manner...
  44. pmc Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9
    Min Wei
    Andrus Gerontology Center, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 4:e13. 2008
    ..Notably, the anti-aging effect caused by the inactivation of both pathways is much more potent than that caused by CR...
  45. ncbi The role of iron regulatory proteins in mammalian iron homeostasis and disease
    Tracey A Rouault
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Building 18T, Room 101, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Chem Biol 2:406-14. 2006
    ..The early death of mouse embryos that lack both IRP1 and IRP2 suggests a central role for IRP-mediated regulation in cellular viability...
  46. pmc TRB3, a novel ER stress-inducible gene, is induced via ATF4-CHOP pathway and is involved in cell death
    Nobumichi Ohoka
    Department of Molecular Health Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho, Nagoya, Japan
    EMBO J 24:1243-55. 2005
    ..In addition, the tunicamycin response region in the TRB3 promoter contains amino-acid response elements overlapping the CHOP-binding site, and CHOP and ATF4 cooperated to activate this promoter activity...
  47. doi Androgen receptor inhibits estrogen receptor-alpha activity and is prognostic in breast cancer
    Amelia A Peters
    Dame Roma Mitchell Cancer Research Laboratories, Discipline of Medicine, University of Adelaide, Hanson Institute, Adelaide, South Australia, Australia
    Cancer Res 69:6131-40. 2009
    ..We conclude that, by binding to a subset of EREs, the AR can prevent activation of target genes that mediate the stimulatory effects of 17beta-estradiol on breast cancer cells...
  48. pmc Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements
    Chen Chen
    William Myron Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 108:6456-61. 2011
    ..of mutations on the structure, we have determined two crystal structures of p63DBD in complex with A/T-rich response elements. One complex contains a 10-bp DNA half-site response element (5'AAACATGTTT3') and the other contains a 22-bp ..
  49. ncbi Sequencing and comparison of yeast species to identify genes and regulatory elements
    Manolis Kellis
    Whitehead MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 423:241-54. 2003
    ..We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human...
  50. pmc Role of Nrf1 in antioxidant response element-mediated gene expression and beyond
    Madhurima Biswas
    Department of Pathology and Laboratory Medicine, University of California, Irvine, D440 Medical Sciences 1, Irvine, CA 92697, USA
    Toxicol Appl Pharmacol 244:16-20. 2010
    ..Herein, we review data derived from cell-based studies and knockout mice in an attempt to define the role and regulation of Nrf1 in oxidative stress response and other functions...
  51. pmc Structural basis for cooperative RNA binding and export complex assembly by HIV Rev
    Matthew D Daugherty
    Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
    Nat Struct Mol Biol 17:1337-42. 2010
    ....
  52. pmc Genetic ablations of iron regulatory proteins 1 and 2 reveal why iron regulatory protein 2 dominates iron homeostasis
    Esther G Meyron-Holtz
    Cell Biology and Metabolism Branch, NIHCD, Bethesda, MD, USA
    EMBO J 23:386-95. 2004
    ..Thus, IRP2 dominates post-transcriptional regulation of iron metabolism in mammals...
  53. ncbi The glucose-6-phosphatase catalytic subunit gene promoter contains both positive and negative glucocorticoid response elements
    Beth T Vander Kooi
    Department of Molecular Physiology and Biophysics, 761 PRB MRB II, Vanderbilt University Medical School, Nashville, TN 37232 0615, USA
    Mol Endocrinol 19:3001-22. 2005
    ..I footprinting analyses show that the glucocorticoid receptor binds to three glucocorticoid response elements (GREs) in the -231 to -129 promoter region and transfection results indicate all three contribute to ..
  54. ncbi Contribution of NAD(P)H:quinone oxidoreductase 1 to protection against carcinogenesis, and regulation of its gene by the Nrf2 basic-region leucine zipper and the arylhydrocarbon receptor basic helix-loop-helix transcription factors
    Paul Nioi
    Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
    Mutat Res 555:149-71. 2004
    ..The XRE recruits the arylhydrocarbon receptor (AhR) and AhR nuclear translocator. Cross-talk may occur between Nrf2 and AhR, but the details of this process remain to be elucidated...
  55. pmc MODY7 gene, KLF11, is a novel p300-dependent regulator of Pdx-1 (MODY4) transcription in pancreatic islet beta cells
    Martin E Fernandez-Zapico
    Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Biol Chem 284:36482-90. 2009
    ..Furthermore, because KLF11 like most MODY-associated transcription factors uses p300, these data further support a role for this coactivator as a critical chromatin link in forms of type 2 diabetes...
  56. pmc C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements
    Lars Grøntved
    Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    EMBO J 32:1568-83. 2013
    ..We suggest that selective targeting of GR in other tissues is likely mediated by the combined action of cell-specific priming proteins and chromatin remodellers...
  57. pmc P53 family members modulate the expression of PRODH, but not PRODH2, via intronic p53 response elements
    Ivan Raimondi
    Department of Biotechnology and Life Sciences, DBSV, University of Insubria, Varese, Italy
    PLoS ONE 8:e69152. 2013
    ..The p53, p63, and p73-dependent transcriptional activation was linked to specific intronic response elements (REs), among those predicted by bioinformatics tools and experimentally validated by a yeast-based ..
  58. ncbi The nuclear pregnane X receptor: a key regulator of xenobiotic metabolism
    Steven A Kliewer
    Nuclear Receptor Discovery Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA
    Endocr Rev 23:687-702. 2002
    ..PXR binds as a heterodimer with the 9-cis retinoic acid receptor (NR2B) to DNA response elements in the regulatory regions of cytochrome P450 3A monooxygenase genes and a number of other genes involved in ..
  59. doi The rules of DNA recognition by the androgen receptor
    Sarah Denayer
    Katholieke Universiteit Leuven, Campus Gasthuisberg, O N1, Herestraat 49, 3000 Leuven, Belgium
    Mol Endocrinol 24:898-913. 2010
    ..receptor (AR) and glucocorticoid, progestagen, and mineralocorticoid receptors all recognize classical DNA response elements that are organized as inverted repeats of 5'-AGAACA-3'-like motifs with a three-nucleotide spacer...
  60. pmc Inhibition of cyclin D1 expression by androgen receptor in breast cancer cells--identification of a novel androgen response element
    Marilena Lanzino
    Dipartimento Farmaco Biologico, University of Calabria, Arcavacata di Rende CS 87036, Italy
    Nucleic Acids Res 38:5351-65. 2010
    ....
  61. pmc The roles of auxin response factor domains in auxin-responsive transcription
    Shiv B Tiwari
    Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
    Plant Cell 15:533-43. 2003
    Auxin response factors (ARFs) are transcription factors that bind to TGTCTC auxin response elements in promoters of early auxin response genes...
  62. pmc Hormone depletion-insensitivity of prostate cancer cells is supported by the AR without binding to classical response elements
    Mesfin Gonit
    Department of Biochemistry and Cancer Biology, Medical University of Ohio, 3035 Arlington Avenue, Toledo, Ohio 43614, USA
    Mol Endocrinol 25:621-34. 2011
    A need for androgen response elements (AREs) for androgen receptor (AR)-dependent growth of hormone depletion-insensitive prostate cancer is generally presumed...
  63. pmc GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response element
    Tokameh Mahmoudi
    Department of Molecular and Cell Biology, Center for Biomedical Genetics, Leiden University Medical Center, PO Box 9503, 2300 RA, Leiden, The Netherlands
    Nucleic Acids Res 31:4147-56. 2003
    Polycomb response elements (PREs) are chromosomal elements, typically comprising thousands of base pairs of poorly defined sequences that confer the maintenance of gene expression patterns by Polycomb group (PcG) repressors and trithorax ..
  64. pmc Hepatitis C virus impairs the induction of cytoprotective Nrf2 target genes by delocalization of small Maf proteins
    Monica Carvajal-Yepes
    Institute of Infection Medicine, Molecular Medical Virology, University of Kiel, D 24105 Kiel, Germany
    J Biol Chem 286:8941-51. 2011
    ..of cytoprotective genes is regulated by short cis-acting elements in their promoters, called antioxidant response elements (AREs). A central regulator of ARE-mediated gene expression is the NF-E2-related factor 2 (Nrf2)...
  65. ncbi Differential responses of the Nrf2-Keap1 system to laminar and oscillatory shear stresses in endothelial cells
    Tomonori Hosoya
    Environmental Response Project ERATO Japan Science and Technology Agency, Graduate School of Comprehensive Human Sciences and Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, 305 8575, Japan
    J Biol Chem 280:27244-50. 2005
    ..These results suggest that O-flow inhibits Nrf2 activity at the DNA binding step, thereby suppressing athero-protective gene expression and hence predisposing the blood vessels to the formation of atherosclerosis...
  66. pmc JunD activates transcription of the human ferritin H gene through an antioxidant response element during oxidative stress
    Yoshiaki Tsuji
    Department of Environmental and Molecular Toxicology, North Carolina State University, Campus Box 7633, Raleigh, NC 27695, USA
    Oncogene 24:7567-78. 2005
    ....
  67. ncbi A role for constitutive androstane receptor in the regulation of human intestinal MDR1 expression
    Oliver Burk
    Dr Margarete Fischer Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, D 70376 Stuttgart, Germany
    Biol Chem 386:503-13. 2005
    ..We demonstrate here by gel shift and transfection experiments that CAR binds to distinct nuclear receptor response elements in the -7...
  68. ncbi Cross-talk between peroxisome proliferator-activated receptor (PPAR) alpha and liver X receptor (LXR) in nutritional regulation of fatty acid metabolism. I. PPARs suppress sterol regulatory element binding protein-1c promoter through inhibition of LXR sig
    Tomohiro Yoshikawa
    Department of Metabolic Diseases, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo ku, Japan
    Mol Endocrinol 17:1240-54. 2003
    ..Deletion and mutation studies demonstrated that the two LXR response elements (LXREs) in the SREBP-1c promoter region are responsible for this inhibitory effect of PPARs...
  69. pmc Functional analysis of p53 binding under differential stresses
    Adam J Krieg
    Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University, Stanford, CA 94303 5152, USA
    Mol Cell Biol 26:7030-45. 2006
    ..Taken together, these experiments describe the identification of novel p53 target genes and the subsequent discovery of distinctly different expression phenomena for p53 target genes under different stress scenarios...
  70. pmc Concerted action of aldehyde dehydrogenases influences depot-specific fat formation
    Barbara Reichert
    Department of Human Nutrition, Ohio State University, Columbus, Ohio, 43210, USA
    Mol Endocrinol 25:799-809. 2011
    ..Our data suggest a paradigm for regulation of fat depots through the concerted action of Aldh1 enzymes that establish RA-dependent tandem regulation of transcription factors ZFP423 and PPARγ in a depot-specific manner...
  71. ncbi Role of basic region leucine zipper transcription factors cyclic AMP response element binding protein (CREB), CREB2, activating transcription factor 2 and CAAT/enhancer binding protein alpha in cyclic AMP response element-mediated transcription
    Gerald Thiel
    Department of Medical Biochemistry and Molecular Biology, University of Saarland Medical Center, Homburg, Germany
    J Neurochem 92:321-36. 2005
    ..Rather, CREB and ATF2 compete for binding to the CRE, and are independently able to up-regulate transcription of genes containing CRE motifs in their regulatory regions...
  72. ncbi Thioredoxin-interacting protein is stimulated by glucose through a carbohydrate response element and induces beta-cell apoptosis
    Alexandra H Minn
    Department of Medicine, University of Wisconsin Madison, Madison, Wisconsin 53792, USA
    Endocrinology 146:2397-405. 2005
    ..Thus, TXNIP is a novel proapoptotic beta-cell gene elevated in insulin resistance/diabetes and up-regulated by glucose through a unique ChoRE and may link glucotoxicity and beta-cell apoptosis...
  73. ncbi Yin Yang-1 inhibits vascular smooth muscle cell growth and intimal thickening by repressing p21WAF1/Cip1 transcription and p21WAF1/Cip1-Cdk4-cyclin D1 assembly
    Fernando S Santiago
    Centre for Vascular Research, Department of Pathology, University of New South Wales, and Department of Haematology, The Prince of Wales Hospital, Sydney, NSW, Australia
    Circ Res 101:146-55. 2007
    ..These findings define a new role for YY1 as both an inducer of p53 instability in smooth muscle cells, and an indirect repressor of p21(WAF1/Cip1) transcription, p21(WAF1/Cip1)-cdk4-cyclin D1 assembly and intimal thickening...
  74. pmc The coordinated p53 and estrogen receptor cis-regulation at an FLT1 promoter SNP is specific to genotoxic stress and estrogenic compound
    Yari Ciribilli
    Unit of Molecular Mutagenesis and DNA Repair, National Institute for Cancer Research, IST, Genoa, Italy
    PLoS ONE 5:e10236. 2010
    ..The transcriptional control required an estrogen receptor (ER) (1/2) site response element (ERE1) 225 nt upstream to the RE-T...
  75. pmc Heterodimer of two bHLH-PAS proteins mediates juvenile hormone-induced gene expression
    Meng Li
    Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
    Proc Natl Acad Sci U S A 108:638-43. 2011
    ..Together, the evidence indicates that Met and FISC form a functional complex on the JHRE in the presence of JH and directly activate transcription of JH target genes...
  76. doi Divalent metal-dependent regulation of hepcidin expression by MTF-1
    Sara Balesaria
    Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
    FEBS Lett 584:719-25. 2010
    ..Here we further reveal that hepcidin transcription also involves interactions between functional metal response elements (MREs) in its promoter, and the MRE-binding transcription factor-1...
  77. pmc Role of Nrf2 in the regulation of the Mrp2 (ABCC2) gene
    Valeska Vollrath
    Department of Gastroenterology, School of Medicine, Catholic University of Chile, Casilla 114 D, Santiago, Chile
    Biochem J 395:599-609. 2006
    ..Thus Nrf2 appears to regulate Mrp2 gene expression via an ARE element located at the proximal region of its promoter in response to exposure to xenobiotics...
  78. pmc Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion
    Yongheng Chen
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital and State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China, Department of Chemistry, Norris Comprehensive Cancer Center, Department of Physics and Astronomy and Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 41:8368-76. 2013
    The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood...
  79. pmc Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view
    Yongping Pan
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, Maryland, United States of America
    PLoS Comput Biol 5:e1000448. 2009
    p53-response elements (p53-REs) are organized as two repeats of a palindromic DNA segment spaced by 0 to 20 base pairs (bp)...
  80. pmc The sigma-1 receptor protects against cellular oxidative stress and activates antioxidant response elements
    Arindam Pal
    Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
    Eur J Pharmacol 682:12-20. 2012
    ..These novel functions of the sigma-1 receptor were sensitive to well-known sigma ligands via their antagonist/agonist properties...
  81. ncbi Mouse sterol response element binding protein-1c gene expression is negatively regulated by thyroid hormone
    Koshi Hashimoto
    Department of Medicine and Molecular Science, Graduate School of Medicine, Gunma University, 3 39 15 Showa machi Maebashi, Gunma 371 8511, Japan
    Endocrinology 147:4292-302. 2006
    ..Thus, we demonstrated that mouse SREBP-1c mRNA is down-regulated by T3 in vivo and that T3 negatively regulates mouse SREBP-1c gene transcription via a novel negative thyroid hormone response element: Site2...
  82. pmc Distinct properties of cell-type-specific and shared transcription factor binding sites
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
    Mol Cell 52:25-36. 2013
    ..Shared sites, bound in multiple cell types, are characterized by high-affinity estrogen response elements (EREs), inaccessible chromatin, and a lack of DNA methylation, while cell-specific sites are characterized ..
  83. ncbi Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity
    Michele Raviscioni
    W M Keck Center for Computational and Structural Biology, Houston TX, USA
    J Mol Biol 350:402-15. 2005
    ..This establishes the existence of evolutionary importance correlation at protein-DNA interfaces, and demonstrates that it is a useful principle for the rational engineering of binding specificity...
  84. pmc The tumor suppressor p53 induces expression of the pregnancy-supporting human chorionic gonadotropin (hCG) CGB7 gene
    Sindy Sohr
    Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
    Cell Cycle 10:3758-67. 2011
    ..With these results we provide a new link between p53 transcriptional activity and human reproduction...
  85. pmc A novel high-throughput cell-based method for integrated quantification of type I interferons and in vitro screening of immunostimulatory RNA drug delivery
    David N Nguyen
    Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
    Biotechnol Bioeng 103:664-75. 2009
    ..We apply this tool to investigate isRNA drug delivery, but it may also find use in other applications for which high-throughput detection of type 1 IFN is desired...
  86. pmc Proinflammatory cytokines enhance estrogen-dependent expression of the multidrug transporter gene ABCG2 through estrogen receptor and NF{kappa}B cooperativity at adjacent response elements
    Madhumita Pradhan
    Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois 60612, USA
    J Biol Chem 285:31100-6. 2010
    ..The result of this cooperative binding of ER and p65 at adjacent response elements leads to a major increase in both ABCG2 mRNA and protein expression...
  87. pmc Genome-wide in silico identification of new conserved and functional retinoic acid receptor response elements (direct repeats separated by 5 bp)
    Sébastien Lalevée
    Department of Functional Genomics and Cancer, Universite de Strasbourg, F_67404 Illkirch Cedex, France
    J Biol Chem 286:33322-34. 2011
    The nuclear retinoic acid receptors interact with specific retinoic acid (RA) response elements (RAREs) located in the promoters of target genes to orchestrate transcriptional networks involved in cell growth and differentiation...
  88. doi atRA Regulation of NEDD9, a gene involved in neurite outgrowth and cell adhesion
    D C Knutson
    Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706 1544, USA
    Arch Biochem Biophys 477:163-74. 2008
    ..Finally, chromatin immunoprecipitation (ChIP) assays demonstrate that RAR and RXR are bound to the RARE in cells...
  89. pmc ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1
    M Li
    Department of Biochemistry and Molecular Biology, and the USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California 90089 9176, USA
    Mol Cell Biol 20:5096-106. 2000
    ..The requirement for a high-affinity NF-Y site for ATF6 but not human Ire1p activity suggests that they stimulate the ERSE through diverse pathways...
  90. pmc Enhanced expression of the transcription factor Nrf2 by cancer chemopreventive agents: role of antioxidant response element-like sequences in the nrf2 promoter
    Mi Kyoung Kwak
    Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Mol Cell Biol 22:2883-92. 2002
    ....
  91. pmc ALU repeats in promoters are position-dependent co-response elements (coRE) that enhance or repress transcription by dimeric and monomeric progesterone receptors
    Britta M Jacobsen
    Department of Medicine Endocrinology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
    Mol Endocrinol 23:989-1000. 2009
    We have conducted an in silico analysis of progesterone response elements (PRE) in progesterone receptor (PR) up-regulated promoters...
  92. ncbi Targeted deletion of the gene encoding iron regulatory protein-2 causes misregulation of iron metabolism and neurodegenerative disease in mice
    T LaVaute
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
    Nat Genet 27:209-14. 2001
    ..Thus, misregulation of iron metabolism leads to neurodegenerative disease in Ireb2(-/-) mice and may contribute to the pathogenesis of comparable human neurodegenerative diseases...
  93. ncbi Effect of ethanol on the regulation of corticotropin-releasing factor (CRF) gene expression
    Zhongqi Li
    The Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
    Mol Cell Neurosci 29:345-54. 2005
    ..Finally a PKA inhibitor and a cAMP antagonist both decreased ethanol-induced CRF peptide secretion, gene expression, and transcription. These results suggest that ethanol upregulates CRF expression through cAMP/PKA-dependent pathways...
  94. ncbi Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1
    J C Yoon
    Dana Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 413:131-8. 2001
    ..These results implicate PGC-1 as a key modulator of hepatic gluconeogenesis and as a central target of the insulin-cAMP axis in liver...
  95. pmc Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer
    Joanna Zawacka-Pankau
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsvag 16, Stockholm, SE 171 77, Sweden
    J Biol Chem 286:41600-15. 2011
    ..e. their dependence on glycolysis), which could contribute to the tumor-selective killing of cancer cells by pharmacologically activated p53...
  96. pmc High-resolution DNA-binding specificity analysis of yeast transcription factors
    Cong Zhu
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:556-66. 2009
    ..These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes...
  97. pmc A unique DNA binding domain converts T-cell factors into strong Wnt effectors
    Fawzia A Atcha
    Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA
    Mol Cell Biol 27:8352-63. 2007
    ..Wnt regulation of gene expression requires binding of LEF/T-cell factor (LEF/TCF) transcription factors to Wnt response elements (WREs) and recruitment of the activator beta-catenin...
  98. pmc Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc
    Hasmik Yepiskoposyan
    Institute of Molecular Biology, University of Zurich CH 8057 Zurich, Switzerland
    Nucleic Acids Res 34:4866-77. 2006
    ..mRNA studies in MTF-1 overexpressing or null mutant flies and in silico search for metal response elements (binding sites for MTF-1) confirmed novel MTF-1 regulated genes such as ferritins, the ABC transporter ..
  99. ncbi Transcriptional regulation of the heme oxygenase-1 gene via the stress response element pathway
    J Alam
    Department of Molecular Genetics, Ochsner Clinic Foundation, New Orleans, LA 70121, USA
    Curr Pharm Des 9:2499-511. 2003
    ..In principle, the multiplicity of StRE binding proteins also provides for a range of pharmaceutical targets for controlled production of the potentially therapeutic HO-1 protein...
  100. pmc A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs
    Nate P Hoverter
    Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
    Mol Cell Biol 32:3648-62. 2012
    ..LEF/TCFs have a DNA sequence-specific high-mobility group (HMG) box that binds Wnt response elements (WREs)...
  101. doi Nucleosome-driven transcription factor binding and gene regulation
    Cecilia Ballaré
    Gene Regulation Stem Cells and Cancer Program, Centre for Genomic Regulation CRG, 08003 Barcelona, Spain
    Mol Cell 49:67-79. 2013
    ..Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes are crucial for PR binding and hormonal gene regulation...

Research Grants71

  1. MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSION
    Carole R Mendelson; Fiscal Year: 2013
    ..1) and nuclear factor (B (NF-(B), upstream stimulatory factors (USFs) 1 and 2, and Sp1 to critical response elements upstream of the SP-A gene...
  2. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..compete in trans with the liganded vitamin D receptor (VDR) and estrogen receptor 1 (ER1) for their cognate response elements, identifying them as nucleic acid binding proteins in the heterogeneous nuclear ribonucleoprotein C (hnRNPC) ..
  3. Preclinical drug trial in mouse models of inflammation
    Kanneboyina Nagaraju; Fiscal Year: 2011
    ..and side effects (metabolic and hormonal) are thought to be predominantly mediated by transactivation via GC response elements in the nucleus...
  4. Regulation of insulins by the Rhox5 homeobox gene supports spermatogenesis
    James Maclean; Fiscal Year: 2009
    ..This was a breakthrough discovery for our laboratory, as no putative Rhox5-response elements had ever discovered...
  5. INTERACTION OF THE ESTROGEN RECEPTOR WITH DNA
    ANN NARDULLI; Fiscal Year: 2013
    ..are initiated by binding to the estrogen receptor (ER) and inducing the receptor to bind to estrogen response elements (EREs) residing in target genes...
  6. Transcriptional Regulation of Natriuetic Sensitivity in Diabetes Mellitus
    PATIENCE O OBIH; Fiscal Year: 2012
    ..Because PPAR3 and PPAR1 share the same peroxisome response elements and can be transactivated by the same ligands, we hypothesize therefore, that PPAR3 will play a defined role ..
  7. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
    ..modulates the inflammatory response through a variety of mechanisms, including DNA binding of glucocorticoid response elements (GREs)...
  8. Preclinical drug trial in mouse models of inflammation
    Kanneboyina Nagaraju; Fiscal Year: 2013
    ..and side effects (metabolic and hormonal) are thought to be predominantly mediated by transactivation via GC response elements in the nucleus...
  9. ATRIAL NATRIURETIC PEPTIDE AND RECEPTOR GENES IN HYPOXIA
    Yiu Fai Chen; Fiscal Year: 2010
    ..and binding (via complex formation with transcription factors) of pSmad2 and pSmad3 to TGF-B-Smad response elements in the promoter regions of ECM genes...
  10. Epigenetic Changes in the Glucocorticoid Receptor Gene Due to Arsenic Exposure
    Andrea M Allan; Fiscal Year: 2013
    ..in glucocorticoid receptor level and a decrease in several proteins whose promoters contain glucocorticoid response elements (GREs) and are activated by GR binding...
  11. PTH-RELATED PEPTIDE AND VIT D IN PROSTATE CANCER GROWTH
    Miriam Falzon; Fiscal Year: 2009
    ..3) The vitamin D response elements via which vitamin D regulates PTHrP gene expression will be identified by PTHrP gene promoter deletions and ..
  12. Feedback and Hormonal Regulation of Hepatic HMG-CoA Reductase
    GENE CHARLES NESS; Fiscal Year: 2010
    ..Candidate insulin response elements will be investigated by introducing HMGR DNA regions ligated to luciferase directly into livers of diabetic ..
  13. Mechanisms that Regulate Neonatal Lung Heme Oxygenase in Hyperoxia
    Phyllis A Dennery; Fiscal Year: 2013
    ..The cyotoplasmic and active form of HO-1 may modulate the regulation of genes with antioxidant response elements (ARE) through pathways involving p38 MAP kinase and NrF2...
  14. De novo establishment of Polycomb-group-mediated repression
    Richard S Jones; Fiscal Year: 2010
    ..g., Pleiohomeotic) bind to sequences within Polycomb Response Elements (PREs) and recruit additional PcG protein complexes, such as PRC2, which in turn methylates histone H3 at ..
  15. Dynamics of Transcriptional Regulation
    Elena Zelin; Fiscal Year: 2011
    ..studies have revealed that many regulatory proteins are highly mobile, and exist in a rapid equilibrium with response elements within cells...
  16. Negative regulation by thyroid hormone
    Anthony N Hollenberg; Fiscal Year: 2010
    ..On positively regulated genes TH interacts with thyroid hormone receptor isoforms (TRs) on TH response elements (TREs) to initially relieve repression caused by the unliganded receptor's ability to recruit a ..
  17. Nuclear Receptor Networks in Human Disease
    Frances M Sladek; Fiscal Year: 2010
    ..A complementary approach that has not been fully exploited is a computational one based on the DNA response elements that recruit the nuclear receptors to the regulatory regions of their target genes...
  18. Direct Regulation of Mitochondrial Transcription by Thyroid Hormone and Receptor
    MEGAN LYNN BESTWICK; Fiscal Year: 2012
    ..In fact some OXPHOS genes in the nucleus have hormone response elements in their promoter regions, as well as other nuclear genes that encode mtDNA regulatory factors...
  19. The Role of Nuclear Receptor PPARbeta in the Regulation of Muscle Fuel Metabolism
    EMILY YVONNE SMITH; Fiscal Year: 2013
    ..nuclear receptor PPAR?, serve as key transcriptional regulators of lipid metabolism by binding conserved DNA response elements in target gene promoters...
  20. GCL-M Regulation of Angiogenesis
    CHRISTOPHER BRUCE PATTILLO; Fiscal Year: 2010
    ..defense mechanisms are activated, among these are E2-related factor-2 (Nrf-2) which binds to DNA antioxidant response elements (ARE) on several genes including GCL-M...
  21. HYPOXIA AND GENE REPRESSION
    Amato J Giaccia; Fiscal Year: 2013
    ..Hypoxia-induced p53 is nuclear and associates with p53-response elements in target genes, such as mdm2 and p21...
  22. DNA LESIONS AND GENE EXPRESSION IN HYPOXIC LUNG DISEASE
    Mark N Gillespie; Fiscal Year: 2013
    ..ROS generated in hypoxia cause transient oxidative DNA modifications that cluster in the hypoxic response elements (HREs) of multiple hypoxia-inducible genes, with specific bases near the HIF-1-DNA recognition sequence ..
  23. Crosstalk between estrogen receptor and NFkB in target gene regulation
    Jonna Frasor; Fiscal Year: 2013
    ..and NF?B synergistically regulate gene transcription, we will first examine whether a unique combination of response elements in the 5'flanking region of synergistically regulated genes contributes to synergy through cooperative ..
  24. Regulation of Periostin by TGFbeta and BMP in Heart Development
    Thomas Doetschman; Fiscal Year: 2010
    ..9kb promoter. Consistent with our model, this sequence contains both Tgf2 (TRE) and Bmp (BRE) response elements. That promoter will be used in Aim 2 to test whether the aberrant valve muscularization seen in human ..
  25. Study of an iron-responsive E3 ligase regulating mammalian iron homeostasis
    Richard K Bruick; Fiscal Year: 2013
    ..When cellular free iron availability is low, Iron Regulatory Proteins 1 and 2 (IRP1 and 2) bind Iron Response Elements (IREs) within the 5'or 3'untranslated regions of these mRNAs to affect their subsequent ..
  26. Defining the role of mast cells during influenza A virus infection
    Joshua J Obar; Fiscal Year: 2012
    ..This proposal will examine the early host response elements to IAV infection, specifically examining the role that mast cells and protease- activated receptors play in ..
  27. Notch and Wnt signaling in protection by nandrolone against disuse atrophy
    Christopher Cardozo; Fiscal Year: 2012
    ..and nuclear translocation of the transcriptional regulator ss-catenin, as well as possible androgen receptor response elements;the androgen receptor is a ligand-activated transcription factor that binds to such sites to upregulate gene ..
  28. Mechanism of Gene Repression in the Kidney
    Sanjeevkumar R Patel; Fiscal Year: 2013
    ..Such inductive signals can phosphorylate the Pax2 protein and promote transcriptional activation of Pax2 response elements. In the kidney, Pax2 is likely to regulate hundreds of loci that respond to inductive signaling and as such ..
  29. Endocrine Disruptors: Assessment of endocrine disruption activity, mechanism and
    Subhrangsu Mandal; Fiscal Year: 2010
    ..HOXC13 promoter contains multiple estrogen response elements (EREs) to which estrogen receptors (ER: ERa and ER[unreadable]) bind during E2-mediated gene activation...
  30. Role of oxidative modifications to D-loop region in mTDNA replication in hypoxia
    Mykhaylo Ruchko; Fiscal Year: 2012
    ..In lung vascular cells, for example, hypoxia causes ROS- dependent base modifications within hypoxic response elements (HREs) of hypoxia inducible genes...
  31. Defining the thyroid hormone receptor Cistrome in vivo
    Anthony N Hollenberg; Fiscal Year: 2012
    ..lines, it has been presumed that the effects of the TR on gene expression are dictated by the presence of TR response elements (TREs) in the regulatory regions of targeted genes...
  32. Mechanisms of Oxygen Sensing
    Navdeep S Chandel; Fiscal Year: 2013
    ..HIFs bind to hypoxia-response elements in the promoter/enhance regions of a large number of target genes resulting in activation of a genetic ..
  33. Imaging Nuclear Receptor LRH-1 in Functional Transcriptional Assemblies
    Robert J Fletterick; Fiscal Year: 2010
    ..Specific DNA fragments representing known response elements of LRH-1 will be included in evaluation of our assemblies...
  34. Mechanisms of Immunosuppressive Actions of Glucocorticoids
    Inez Rogatsky; Fiscal Year: 2011
    ..1) dissect the GRIP1:IRF3 interaction in vitro, in cells and in IRF3 complexes bound at the IFN-Stimulated Response Elements;(2)corroborate the relevance of this interaction by examining the cross-talk between GRand IRF3 in primary ..
  35. A Novel Role of the Aryl Hydrocarbon Receptor in Hepatic Steatosis
    Wen Xie; Fiscal Year: 2013
    ..AhR regulates the expression of xenobiotic enzymes by binding to the dioxin response elements (DREs) present in target gene promoters...
  36. Human Osteoprogenitor Control by Hepatocyte Growth Factor and Vitamin D
    Guy Howard; Fiscal Year: 2013
    ..ChIP assays will identify specific binding of 1,25OHD activated VDR to putative response elements on the TA vs deltaNp63 promoters, as well as identify p63 isoform(s) binding to the VDR promoter...
  37. Molecular Mechanisms in Retinal Degeneration
    Debora B Farber; Fiscal Year: 2011
    ..that the 15A15 protein binds to several DNA fragments containing the core consensus sequences for hormone response elements and that it has several features characteristic of coactivators/ co-repressors of nuclear hormone receptors (..
  38. Functional Vitamin D Receptor Gene Variants and Racial/Ethnic Cancer Disparities
    Robin Taylor Wilson; Fiscal Year: 2010
    ..VDR acts to promote or prevent downstream gene signaling through vitamin D response elements (VDRE) located in the promoter region of vitamin D-responsive genes...
  39. Nell-1, A Cbfa 1 Downstream Target, In Bone Formation
    Kang Ting; Fiscal Year: 2009
    ..that: 1) runt-related transcription factor 2 (Runx2) regulates LNell-1 through cis-acting element 2 (OSE2) response elements (REs);2) LNell-1 increases osteoblastic differentiation and can partially compensate for Runx2 ..
  40. The switch between epigenetically silenced and active chromatin states
    Vincenzo Pirrotta; Fiscal Year: 2013
    ..extended distribution of these complexes is striking and suggests a functional link between Polycomb Response Elements and transcriptional activity...
  41. Nutritional Copper Signaling and Homeostasis
    Sabeeha Merchant; Fiscal Year: 2013
    ..Its target genes are associated with copper response elements, which serve as binding sites for the DNA binding domain of CRR1...
  42. Molecular mechanism of cytochrome P4501A1 expression.
    Bhagavatula Moorthy; Fiscal Year: 2013
    ..g., AHR response elements (AHREs)], leading to a novel mechanism by which MC-DNA adduct(s) will suppress CYP1A1 gene expression...
  43. ESAT-6 primes dendritic cells with reduced IL-12 and increased IL-23 production
    Buka Samten; Fiscal Year: 2013
    ..To identify the molecular mechanisms underlying these important effects, we propose to: 1. Identify ESAT-6 response elements (EREs) in the promoters of p35 and p19...
  44. Anti-angiogenic Barriers to Tumor Development
    Susan E Crawford; Fiscal Year: 2010
    ..The interaction of PEDF and PPARgamma will be investigated by evaluating the functional activity of PPAR response elements in the PEDF gene and the nuclear signaling pathways explored...
  45. Phase I enzymes as part of an epigenetic switch
    Elwood Albert Linney; Fiscal Year: 2013
    ..This would occur in a subset of genes that have retinoic acid response elements (RAREs) in their regulatory DNA...
  46. Regulation of Hepatic Excretion of Xenobiotics by Mrps
    Curtis D Klaassen; Fiscal Year: 2010
    ..Moreover, using in-silico analysis, we identified putative Nrf2-responsive sequences, known as electrophile response elements (EpREs), in the 5'flanking regions of the Mrp2, 3, and 4 genes...
  47. PHARMACOGENETICS OF HUMAN CARBONYL REDUCTASES
    JAVIER GUILLERMO BLANCO; Fiscal Year: 2013
    ..prototypical antioxidant tert-butylhydroquinone and that the CBR3 promoter contains 2 conserved antioxidant response elements (AREs)...
  48. Innate Immune Recognition of Candida albicans Infection in a C. elegans Model
    Read Pukkila-Worley; Fiscal Year: 2013
    ..for novel immune response genes using a tool that will maximize the yield for uncharacterized innate immune response elements (Aim 3). These experiments offer the first assessment of the C...
  49. Control of redox regulators by the ubiquitin system
    Scott M Plafker; Fiscal Year: 2013
    ..Test the hypotheses that UbcM2 regulates Keap1 nuclear import and the affinity of Nrf2 for its cognate response elements in the promoters of anti-oxidant genes...
  50. Regulation of Rhodopsin Expression
    Donald J Zack; Fiscal Year: 2012
    ..together with libraries of transcription factor expression clones to identify factors that regulate the response elements identified in "2";and 4) use a combined bioinformatic and experimental approach to identify genes that are ..
  51. Generation of Retinoid Signals during Development
    GREGG L DUESTER; Fiscal Year: 2013
    ..RA directly regulates transcription of key genes by serving as a ligand for nuclear RA receptors bound to RA response elements (RAREs)...
  52. PROGESTERONE RECEPTOR BINDING TO SPECIFIC DNA SEQUENCES
    Dean P Edwards; Fiscal Year: 2013
    ..The short CTE interacts with coregulatory proteins and binds DNA flanking progesterone response elements (PRE) to extend the protein-DNA interface and stabilize interactions mediated by the core DBD...
  53. Mechanistic studies of a PPAR-g mutation that causes lipodystrophy &diabetes
    OLGA IGOR ASTAPOVA; Fiscal Year: 2013
    ..PPARg is a ligand-activated nuclear receptor with a well-characterized structure that binds PPAR response elements and regulates transcription of target genes by recruiting coactivators and/or corepressors...
  54. Modifying SF-1 Transcriptional Programs by Sumoylation
    EMILY JEAN FAIVRE; Fiscal Year: 2010
    ..Because our preliminary survey of response elements affected by SF-1 sumoylation appear to be noncanonical, low-affinity sites, I will use chromatin ..
  55. Environmental Estrogen Induced Epigenetic Alteration of Uterine Stem Cells
    Hugh S Taylor; Fiscal Year: 2013
    ..investigators have previously shown that fetal exposure to these agents alters the methylation of estrogen response elements (EREs) in the endometrium...
  56. The Role of Mu-opioid Receptor Splice Variants in the HIV Disease
    SETH MICHAEL DEVER; Fiscal Year: 2013
    ..signaling assays will use plasmid constructs with which luciferase expression is under the control of response elements for various cellular signaling pathways. Morphine binding will be assessed using GTP gamma S binding assays...
  57. Establishment of Adiponectin as a PPARgamma Cofactor
    KATHRYN ELLEN DAVIS; Fiscal Year: 2010
    ..that low molecular weight adiponectin can translocate to the nucleus and associate with PPAR gamma on PPAR response elements. In this study I propose to analyze the role of adiponectin in activating PPAR gamma target gene expression...
  58. Nuclear Receptor DNA Binding in Human Physiology and Disease
    Frances M Sladek; Fiscal Year: 2013
    ..They do so in large part by first binding specific DNA response elements (RE) in regulatory regions of genes...
  59. Transcriptional Regulation by the HTLV-1 Tax Protein
    Jennifer K Nyborg; Fiscal Year: 2013
    ..Three enhancer elements, called viral cyclic AMP response elements (vCREs), are located in the HTLV-1 transcriptional control region and are critical to Tax-activated ..
  60. SPECIFICITY IN HOMEOTIC RESPONSE ELEMENTS
    WILLIAM JAMES MCGINNIS; Fiscal Year: 2013
    ..This research will also increase our knowledge of the genetic circuitry that controls which cells in the developing head of embryos become different regions of the brain. ..
  61. Selective Ah Receptor Ligands Repress Acute-Phase Response
    Gary H Perdew; Fiscal Year: 2013
    ..traditionally studied in terms of its ability to mediate transcriptional effects through binding to dioxin-response elements (DRE)...
  62. Mechanisms of Xenoestrogen Stress: A Proteomic and Functional Genomic Approach
    TARA L contact SABO ATTWOOD; Fiscal Year: 2010
    ..and to quantitate the ligand-dependence of binding kinetics and affinity of the ER complexes with various response elements. Once co-accessory proteins are identified, we will test the hypothesis that (Specific Aim 3) a subset of ..
  63. REGULATION OF BILE ACID SYNTHESIS
    JOHN CHIANG; Fiscal Year: 1999
    ..Multiple bile acid response elements and potential transcription factors binding sites have been mapped...
  64. MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSION
    CAROLE MENDELSON; Fiscal Year: 2007
    ..activity is critically dependent upon cooperative interactions of at[unreadable] least four identified DNA response elements which lie within 400 bp[unreadable] upstream of the SP-A transcription initiation site...
  65. INTERLEUKIN 5 GENE EXPRESSION AND LUNG INFLAMMATION
    Anuradha Ray; Fiscal Year: 2000
    ..In a Th2 clone, antigen- and mitogen-stimulated IL-5 gene expression involves GATA, CLE0 and additional cis- response elements in the IL-5 promoter...
  66. NF-kappaB Regulation by Androgen Receptor
    ALBERT BALDWIN JR; Fiscal Year: 2004
    ..with transcriptional coactivators, and control of gene expression through binding to androgen receptor response elements (AREs) in the promoters of relevant genes to stimulate specific gene expression...
  67. JUVENILE HORMONE REGULATION OF GENE EXPRESSION
    WALTER GOODMAN; Fiscal Year: 2003
    ..by which JH increases levels of fat body hJHBP mRNA in bl larvae; (2) identify and sequence putative response elements using mobility shift assays and DNase I footprinting analysis; and (3) demonstrate the putative response ..
  68. VITAMIN D MEDIATED GENE REGULATION IN B LYMPHOCYTES
    John Morgan; Fiscal Year: 2000
    ..hormone with specific intracellular receptors and their subsequent interaction with cis-acting regulatory response elements within the promoter of the target gene...
  69. COREPRESSORS AND NEGATIVE REGULATION BY THYROID HORMONE
    Ronald Cohen; Fiscal Year: 2002
    DESCRIPTION (Taken from the applicant's Abstract): Thyroid hormone receptors (TRs) bind to thyroid hormone response elements (TREs) in the regulatory regions of genes to stimulate or inhibit gene transcription...
  70. Induction of FSH-beta by TGF-Beta Family Members
    William Miller; Fiscal Year: 2007
    ..transcriptional event regulating FSHB, and its corollary is that this induction depends on discrete response elements in the FSHB proximal promoter...
  71. REGULATION OF TISSUE FACTOR PATHWAY INHIBITOR EXPRESSION
    MADHU BAJAJ; Fiscal Year: 2000
    ..In this proposal, the applicant will define the adhesion response elements in the TFPI gene that upregulate TFPI expression in monocytes and U937 cells...