transcriptional regulatory elements

Summary

Alias: regulator genes
Summary: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.

Top Publications

  1. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
  2. pmc Core transcriptional regulatory circuitry in human embryonic stem cells
    Laurie A Boyer
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:947-56. 2005
  3. ncbi Transcriptional regulatory elements in the human genome
    Glenn A Maston
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Annu Rev Genomics Hum Genet 7:29-59. 2006
  4. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
  5. pmc Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Raja Jothi
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:5221-31. 2008
  6. pmc Gene regulatory networks for development
    Michael Levine
    Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:4936-42. 2005
  7. ncbi Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1
    Christopher R Vakoc
    Division of Hematology, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
    Mol Cell 17:453-62. 2005
  8. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
  9. ncbi Exploring the metabolic and genetic control of gene expression on a genomic scale
    J L DeRisi
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Science 278:680-6. 1997
  10. pmc From DNA sequence to transcriptional behaviour: a quantitative approach
    Eran Segal
    Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 10:443-56. 2009

Detail Information

Publications270 found, 100 shown here

  1. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
    ..Our data provide new insights into the function of histone methylation and chromatin organization in genome function...
  2. pmc Core transcriptional regulatory circuitry in human embryonic stem cells
    Laurie A Boyer
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:947-56. 2005
    ..These results provide new insights into the transcriptional regulation of stem cells and reveal how OCT4, SOX2, and NANOG contribute to pluripotency and self-renewal...
  3. ncbi Transcriptional regulatory elements in the human genome
    Glenn A Maston
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Annu Rev Genomics Hum Genet 7:29-59. 2006
    ..Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and ..
  4. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
    ..JASPAR is available at http://jaspar.genereg.net...
  5. pmc Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Raja Jothi
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:5221-31. 2008
    ..Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding...
  6. pmc Gene regulatory networks for development
    Michael Levine
    Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:4936-42. 2005
    ..Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal-ventral patterning in the Drosophila embryo...
  7. ncbi Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1
    Christopher R Vakoc
    Division of Hematology, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
    Mol Cell 17:453-62. 2005
    ..Together, these data demonstrate that GATA-1 and FOG-1 are essential anchors for a tissue-specific chromatin loop, providing general insights into long-range enhancer function...
  8. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  9. ncbi Exploring the metabolic and genetic control of gene expression on a genomic scale
    J L DeRisi
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Science 278:680-6. 1997
    ..These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns...
  10. pmc From DNA sequence to transcriptional behaviour: a quantitative approach
    Eran Segal
    Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 10:443-56. 2009
    ..It can also be used to model more complex phenomena such as transcriptional noise and the evolution of transcriptional regulation...
  11. ncbi Dissecting the regulatory circuitry of a eukaryotic genome
    F C Holstege
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Cell 95:717-28. 1998
    ....
  12. ncbi Inferring genetic networks and identifying compound mode of action via expression profiling
    Timothy S Gardner
    Center for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Science 301:102-5. 2003
    ..This approach, which is experimentally and computationally scalable, provides a framework for elucidating the functional properties of genetic networks and identifying molecular targets of pharmacological compounds...
  13. ncbi Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses
    Jennifer L Nemhauser
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Cell 126:467-75. 2006
    ..Instead, different hormones appear to regulate distinct members of protein families. We conclude that there is not a core transcriptional growth-regulatory module in young Arabidopsis seedlings...
  14. ncbi REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis
    Nurit Ballas
    Howard Hughes Medical Institute, Dept of Neurology and Behavior, The State University of New York at Stony Brook, Stony Brook, NY 11794, USA
    Cell 121:645-57. 2005
    ..Thus, a multistage repressor mechanism controls the orderly expression of genes during development while still permitting fine tuning in response to specific stimuli...
  15. ncbi Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    Eran Segal
    Computer Science Department, Stanford University, Stanford, California, 94305, USA
    Nat Genet 34:166-76. 2003
    ..We present microarray experiments supporting three novel predictions, suggesting regulatory roles for previously uncharacterized proteins...
  16. pmc ORegAnno: an open-access community-driven resource for regulatory annotation
    Obi L Griffith
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
    Nucleic Acids Res 36:D107-13. 2008
    ..All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org...
  17. ncbi A genomic regulatory network for development
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 295:1669-78. 2002
    ..Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time...
  18. ncbi Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6
    D A Kleinjan
    MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
    Hum Mol Genet 10:2049-59. 2001
    ..Components of this downstream regulatory region drive reporter expression in distinct partial PAX6 patterns, indicating that the functional PAX6 gene domain extends far beyond the transcription unit...
  19. pmc Phosphorylation-independent activity of atypical response regulators of Helicobacter pylori
    Jennifer Schär
    Theodor Boveri Institut für Biowissenschaften, Lehrstuhl fur Mikrobiologie, Universitat Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    J Bacteriol 187:3100-9. 2005
    ..Two of the response regulator genes, hp1043 and hp166, proved to be essential for cell growth, and inactivation of the response regulator gene ..
  20. ncbi Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis
    R Gardan
    Unite de Biochimie, Microbienne, France
    J Mol Biol 249:843-56. 1995
    ..These sequences are probably the target of RocR. Analysis of a rocR'-'lacZ fusion strain showed that the expression of rocR is not induced by arginine and is negatively autoregulated...
  21. ncbi Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation
    Steven A McCarroll
    Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143 USA
    Curr Biol 15:347-52. 2005
    ..This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system...
  22. ncbi Trichomes: different regulatory networks lead to convergent structures
    Laura Serna
    Environmental Sciences Faculty, University of Castilla La Mancha, 45071 Toledo, Spain
    Trends Plant Sci 11:274-80. 2006
    ....
  23. pmc Long-range control of gene expression: emerging mechanisms and disruption in disease
    Dirk A Kleinjan
    MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, United Kingdom
    Am J Hum Genet 76:8-32. 2005
    ..Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes...
  24. pmc Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex
    Esther Bae
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:16847-52. 2002
    ..These observations suggest that the intergenic RNAs may play a role in initiating cis regulation at the BX-C early in development...
  25. ncbi Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    Jean Valery Turatsinze
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, Belgium
    Nat Protoc 3:1578-88. 2008
    ..This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour...
  26. ncbi Homeostatic regulation of MeCP2 expression by a CREB-induced microRNA
    Matthew E Klein
    Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
    Nat Neurosci 10:1513-4. 2007
    ..This feedback loop may provide a mechanism for homeostatic control of MeCP2 expression...
  27. pmc StuAp is a sequence-specific transcription factor that regulates developmental complexity in Aspergillus nidulans
    J R Dutton
    Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, ID 83844, USA
    EMBO J 16:5710-21. 1997
    ..nidulans. The budding pattern of sterigmata may involve processes related to those controlling pseudohyphal growth in budding yeast...
  28. pmc An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    Kenzie D Macisaac
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    BMC Bioinformatics 7:113. 2006
    ..Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data...
  29. pmc Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression
    Guoyu Ling
    Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
    Mol Cell Biol 30:5531-44. 2010
    ..This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions...
  30. ncbi Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana
    Weixiong Zhang
    Department of Computer Science and Engineering, Washington University in Saint Louis Saint Louis, MO 63130, USA
    Bioinformatics 21:3074-81. 2005
    ....
  31. ncbi Mapping global histone acetylation patterns to gene expression
    Siavash K Kurdistani
    Department of Biological Chemistry, UCLA School of Medicine and the Molecular Biology Institute, Boyer Hall, Los Angeles, CA 90095, USA
    Cell 117:721-33. 2004
    ..Thus, certain acetylation patterns may be used as surfaces for specific protein-histone interactions, providing one mechanism for coordinate regulation of chromatin processes that are biologically related...
  32. ncbi The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
    Reka Albert
    School of Mathematics, University of Minnesota, 127 Vincent Hall, Minneapolis, MN 55455, USA
    J Theor Biol 223:1-18. 2003
    ..The model gives important insights into the functioning of the segment polarity gene network, such as the crucial role of the wingless and sloppy paired genes, and the network's ability to correct errors in the pre-pattern...
  33. ncbi Discovery of regulatory elements in vertebrates through comparative genomics
    Amol Prakash
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:1249-56. 2005
    ..The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques...
  34. pmc A group of scs elements function as domain boundaries in an enhancer-blocking assay
    R Kellum
    Department of Biology, Moffett Labs, Princeton University, New Jersey 08544
    Mol Cell Biol 12:2424-31. 1992
    ..In contrast, a MAR/SAR DNA segment and another spacer DNA segment had no apparent effect on enhancer activity...
  35. ncbi The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand
    Irina Artsimovitch
    Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI 53706, USA
    Cell 109:193-203. 2002
    ..This activity predicts a cumulative antitermination model for RfaH's regulation of ops-containing operons in vivo...
  36. pmc Quantifying the relationship between co-expression, co-regulation and gene function
    Dominic J Allocco
    Informatics Program, Children s Hospital, Boston, MA, USA
    BMC Bioinformatics 5:18. 2004
    ....
  37. ncbi GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12
    Zhuo Ma
    Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL 36688, USA
    Mol Microbiol 49:1309-20. 2003
    ..The number of regulatory proteins (five), sigma factors (two) and regulatory feedback loops focused on gadA/BC expression make this one of the most intensively regulated systems in E. coli...
  38. pmc Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
    Tae Young Roh
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genes Dev 19:542-52. 2005
    ..TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements...
  39. pmc RSAT: regulatory sequence analysis tools
    Morgane Thomas-Chollier
    Laboratoire de Bioinformatique des Génomes et des Réseaux BiGRe, Universite Libre de Bruxelles, Campus Plaine, CP 263 Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 36:W119-27. 2008
    ..Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published...
  40. ncbi Genome-wide map of nucleosome acetylation and methylation in yeast
    Dmitry K Pokholok
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:517-27. 2005
    ..These maps provide the foundation for further understanding the roles of chromatin in gene expression and genome maintenance...
  41. pmc Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis
    K I Yoshida
    Department of Biotechnology, Faculty of Engineering, Fukuyama University, Hiroshima, Japan
    J Bacteriol 179:4591-8. 1997
    ..The promoter assignments of the iol and iolRS operons were confirmed in vivo with a lacZ fusion integrated into the amyE locus...
  42. pmc Functional conservation of Pax6 regulatory elements in humans and mice demonstrated with a novel transgenic reporter mouse
    David A Tyas
    Genes and Development Group, Centre for Integrative Physiology, University of Edinburgh, Edinburgh EH8 9XD, UK
    BMC Dev Biol 6:21. 2006
    ..The sequence of the Pax6/PAX6 protein is identical in mice and humans and previous studies have shown structural conservation of the gene's regulatory regions...
  43. ncbi The molecular elements that underlie developmental evolution
    Claudio R Alonso
    Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Nat Rev Genet 6:709-15. 2005
    ..We also explain why these alternative regulatory levels might have been neglected, and briefly discuss ways to test our hypothesis...
  44. ncbi In silico representation and discovery of transcription factor binding sites
    Giulio Pavesi
    University of Milan, Milano, Italy
    Brief Bioinform 5:217-36. 2004
    ..This paper provides a survey of existing methods proposed for the problem, focusing both on the ideas underlying them and their availability to the scientific community...
  45. ncbi Topology of the network integrating salicylate and jasmonate signal transduction derived from global expression phenotyping
    Jane Glazebrook
    Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
    Plant J 34:217-28. 2003
    ..This work allowed modeling of network topology, definition of co-regulated genes, and placement of previously uncharacterized regulatory genes in the network...
  46. ncbi The genomics of gene expression
    John A Stamatoyannopoulos
    Department of Molecular Biology, Regulome, Canal View Building, Seattle, WA 98103, USA
    Genomics 84:449-57. 2004
    ..A number of recent studies employing these methods provide insight into questions of central importance to our understanding of the larger role of transcriptional regulation in the organization of the human and other complex genomes...
  47. ncbi Human CREM gene: evolutionary conservation, chromosomal localization, and inducibility of the transcript
    D Masquilier
    Laboratoire de Genetique Moleculaire des Eucaryotes, Centre National de la Recherche Scientifique, Institut National de la Sante et de la Recherche Medicale INSERM, Faculte de Medecine, Strasbourg, France
    Cell Growth Differ 4:931-7. 1993
    ..Finally, we show the conservation of CREM cyclic AMP transcriptional inducibility in humans and establish that the induced transcripts correspond to the mouse ICER products...
  48. pmc Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 16:123-31. 2006
    ..This strategy, which can be applied to any cell line or tissue, will enable a better understanding of how chromatin structure dictates cell function and fate...
  49. pmc Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus
    G Lakshmanan
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
    Mol Cell Biol 19:1558-68. 1999
    ..of the integrated YAC transgenes allowed the general localization of a number of very distant transcriptional regulatory elements (putative central nervous system-, endocardium-, and urogenital system-specific enhancers)...
  50. pmc Proteolytic release of the carboxy-terminal fragment of proHB-EGF causes nuclear export of PLZF
    Daisuke Nanba
    Department of Medical Biochemistry, Ehime University School of Medicine, Onsen gun, Ehime 791 0295, Japan
    J Cell Biol 163:489-502. 2003
    ..These results indicate that released HB-EGF-C functions as an intracellular signal and coordinates cell cycle progression with HB-EGF...
  51. ncbi cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae
    Martha Kirouac
    Howard Hughes Medical Institute and Division of Biology, Mail Code 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 257:85-103. 2003
    ..By using the cis-regulatory analysis and phylogenetic footprinting, we have identified overrepresented sequences involved in conferring vulval and AC expression...
  52. pmc A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
    Brian T Naughton
    Department of Biochemistry, Stanford University, CA 94305, USA
    Nucleic Acids Res 34:5730-9. 2006
    ..We elucidate the reasons why we expect graph-based methods to perform well on motif data. Our MotifScan algorithm shows greatly improved performance over the prevalent PSSM-based method for the detection of eukaryotic motifs...
  53. ncbi Methylation of histones: playing memory with DNA
    Antoine H F M Peters
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
    Curr Opin Cell Biol 17:230-8. 2005
    ..Thus, in addition to having great in vivo complexity, this modification appears more dynamic then was previously thought...
  54. ncbi Genome-wide transcription and the implications for genomic organization
    Philipp Kapranov
    Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
    Nat Rev Genet 8:413-23. 2007
    ..What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?..
  55. ncbi Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs
    Maude Guillier
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Microbiol 59:231-47. 2006
    ..Taken together, these data suggest that OmrA and OmrB participate in the regulation of outer membrane composition in response to environmental conditions...
  56. ncbi On the selection and evolution of regulatory DNA motifs
    Ulrich Gerland
    Department of Physics, University of California, San Diego, La Jolla, CA 92093 0319, USA
    J Mol Evol 55:386-400. 2002
    ..We discuss possible experimental approaches to resolve open questions raised by our study...
  57. pmc Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene
    I Sá-Nogueira
    Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
    J Bacteriol 179:1598-608. 1997
    ..We demonstrate that the araR gene codes for a negative regulator of the ara operon and that the expression of araR is repressed by its own product...
  58. ncbi The three 'C' s of chromosome conformation capture: controls, controls, controls
    Job Dekker
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 519, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nat Methods 3:17-21. 2006
    ..The general guidelines presented here should help experimental design and minimize misinterpretation of 3C experiments...
  59. pmc Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction
    Xiao Qing Gan
    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    J Cell Biol 180:1087-100. 2008
    ..Our results reveal a mechanism by which nuclear Dvl cooperates with c-Jun to regulate gene transcription stimulated by the canonical Wnt signaling pathway...
  60. pmc Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation
    Pooja Rawal
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
    Genome Res 16:644-55. 2006
    ..We also predict G4 motif-induced supercoiling sensitivity for >30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli...
  61. pmc Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
    Elizabeth D Wederell
    Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
    Nucleic Acids Res 36:4549-64. 2008
    ..Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function...
  62. ncbi Graded and areal expression patterns of regulatory genes and cadherins in embryonic neocortex independent of thalamocortical input
    Y Nakagawa
    Molecular Neurobiology Laboratory, The Salk Institute, La Jolla, California 92037, USA
    J Neurosci 19:10877-85. 1999
    ..These findings show that TCAs are not required for the establishment or maintenance of the graded and areal expression patterns of these genes and strongly suggest that their regulation is intrinsic to the developing neocortex...
  63. pmc A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, School of Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
    Genome Biol 6:R110. 2005
    ....
  64. ncbi Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals
    Masanori Uchikawa
    Graduate School of Frontier Biosciences, Osaka University, 1 3 Yamadaoka, Suita, Osaka 565 0871, Japan
    Dev Cell 4:509-19. 2003
    ..These functionally identified Sox2 enhancers exactly correspond to the extragenic sequence blocks conspicuously conserved between chicken and mammals, which are not discernible by sequence comparison among mammals...
  65. ncbi Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer
    Hsuan Pu Chen
    Department of Biomedical Engineering, University of California, Los Angeles, CA 90095, USA
    Genomics 92:292-300. 2008
    ..Our results suggest a wider variety of mammalian transcriptional regulatory sequences than is currently recognized and that these may include coding region SNPs...
  66. pmc A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    Marcus B Noyes
    Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 36:2547-60. 2008
    ....
  67. ncbi Tsix, a gene antisense to Xist at the X-inactivation centre
    J T Lee
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02115, USA
    Nat Genet 21:400-4. 1999
    ..Tsix is not found on the inactive X once cells enter the X-inactivation pathway. Tsix has features suggesting a role in regulating the early steps of X inactivation, but not the silencing step...
  68. ncbi ATF4 is a substrate of RSK2 and an essential regulator of osteoblast biology; implication for Coffin-Lowry Syndrome
    Xiangli Yang
    Department of Molecular and Human Genetics and Bone Disease Program of Texas, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 117:387-98. 2004
    ..These findings identify ATF4 as a critical regulator of osteoblast differentiation and function, and indicate that lack of ATF4 phosphorylation by RSK2 may contribute to the skeletal phenotype of CLS...
  69. pmc Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves
    Kenneth W Berendzen
    Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D 50829 Köln, Germany
    BMC Bioinformatics 7:522. 2006
    ..Surprisingly little is known about the nature of cis-regulatory element (CRE) distribution in promoters...
  70. ncbi Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    Albertha J M Walhout
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 16:1445-54. 2006
    ....
  71. ncbi Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53
    Woojin An
    Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10021, USA
    Cell 117:735-48. 2004
    ..These studies thus define diverse cofactor functions, as well as underlying mechanisms involving distinct histone modifications, in p53-dependent gene activation...
  72. ncbi Transient homologous chromosome pairing marks the onset of X inactivation
    Na Xu
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School Boston, MA 02114, USA
    Science 311:1149-52. 2006
    ..Thus, Tsix and Xite function both in cis and in trans. We propose that Tsix and Xite regulate counting and mutually exclusive choice through X-X pairing...
  73. pmc Positive and negative elements regulate a melanocyte-specific promoter
    P Lowings
    Eukaryotic Transcription Laboratory, Marie Curie Research Institute, Oxted, Surrey, United Kingdom
    Mol Cell Biol 12:3653-62. 1992
    ..The possible mechanisms underlying melanocyte-specific gene expression are discussed...
  74. ncbi Genomic analysis of essentiality within protein networks
    Haiyuan Yu
    Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
    Trends Genet 20:227-31. 2004
    ..Although transcription factors with many targets tend to be essential, surprisingly, we find that genes that are regulated by many transcription factors are usually not essential...
  75. ncbi Gene regulatory networks and the evolution of animal body plans
    Eric H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Science 311:796-800. 2006
    ..Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts...
  76. pmc Microphthalmia gene product as a signal transducer in cAMP-induced differentiation of melanocytes
    C Bertolotto
    Institut National de la Sante et de la Recherche Medicale U385, Biologie et Physiopathologie de la Peau, Faculte de Medecine, Paris, France
    J Cell Biol 142:827-35. 1998
    ..These findings disclose the mechanism by which cAMP stimulates tyrosinase expression and melanogenesis and emphasize the critical role of microphthalmia as signal transducer in cAMP-induced melanogenesis and pigment cell differentiation...
  77. pmc DiRE: identifying distant regulatory elements of co-expressed genes
    Valer Gotea
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:W133-9. 2008
    ..Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org...
  78. pmc The spoIIJ gene, which regulates early developmental steps in Bacillus subtilis, belongs to a class of environmentally responsive genes
    C Antoniewski
    Institut de Microbiologie, Universite Paris Sud, Orsay, France
    J Bacteriol 172:86-93. 1990
    ..Thus, spoIIj, which is transcribed during vegetative growth, presumably under the control of sigma H, encodes a protein that could interact with major regulators of early sporulation stages, such as SpoOA and/or SpoOF...
  79. ncbi A Drosophila GATA family member that binds to Adh regulatory sequences is expressed in the developing fat body
    T Abel
    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
    Development 119:623-33. 1993
    ..Together with the established role of GATA factors during mammalian development, these results suggest that ABF may play a key role in the organogenesis of the fat body...
  80. ncbi Topological and causal structure of the yeast transcriptional regulatory network
    Nabil Guelzim
    ATelier de Génomique Cognitive, Centre National de la Recherche Scientifique ESA 8071, Genopole R, 523 Terrasses de l Agora, 91000 Evry, France
    Nat Genet 31:60-3. 2002
    ..This deviation from randomness probably reflects functional constraints that include biosynthetic cost, response delay and differentiative and homeostatic regulation...
  81. ncbi Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity
    Hiromi Okawa
    Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba 305 8577, Japan
    Biochem Biophys Res Commun 339:79-88. 2006
    ..These results demonstrate that chronic activation of Nrf2 confers animals with resistance to xenobiotics without affecting the morphological and physiological integrity of hepatocytes...
  82. ncbi Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase
    P R Dohrmann
    Department of Cellular, Viral, and Molecular Biology, University of Utah Medical Center, Salt Lake City 84132
    Genes Dev 6:93-104. 1992
    ..Chimeric SWI5/ACE2 protein fusion experiments suggest that promoter specificity resides in a domain distinct from the zinc finger domain...
  83. ncbi Sp1/Sp3 and the myeloid zinc finger gene MZF1 regulate the human N-cadherin promoter in osteoblasts
    S Le Mee
    Laboratory of Osteoblast Biology and Pathology, INSERM U606, Lariboisiere Hospital, 75475 Cedex 10 Paris, France
    Exp Cell Res 302:129-42. 2005
    ..These results indicate that Sp1/Sp3 and MZF1 are important transcription factors regulating N-cadherin promoter activity and expression in osteoblasts...
  84. ncbi Combinatorial synthesis of genetic networks
    Calin C Guet
    Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Science 296:1466-70. 2002
    ..Combinatorial synthesis provides an alternative approach for studying biological networks, as well as an efficient method for producing diverse phenotypes in vivo...
  85. ncbi Tbx genes and limb identity in chick embryo development
    A Isaac
    Department of Anatomy and Developmental Biology, University College London, London WC1E 6BT, UK
    Development 125:1867-75. 1998
    ..The ectopic limb always displays a limb-like Tbx-3 expression. Thus Tbx-4 and Tbx-5 are strong candidates for encoding 'wingness' and 'legness'...
  86. pmc Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region
    Santiago Garcia-Vallve
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain
    BMC Evol Biol 6:20. 2006
    ..It is believed that there is a core of transcription factor binding sites (TFBS) common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses...
  87. ncbi Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    Maumita Mandal
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Cell 113:577-86. 2003
    ..Furthermore, it is now apparent that riboswitches contribute to the regulation of numerous fundamental metabolic pathways in certain bacteria...
  88. ncbi Finding optimal degenerate patterns in DNA sequences
    Daisuke Shinozaki
    Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
    Bioinformatics 19:ii206-14. 2003
    ..Our aim is to devise a heuristic algorithm to find a degenerate pattern which is optimal for positive and negative string sets w.r.t. a given score function...
  89. ncbi Conservation of regulatory elements controlling hairy pair-rule stripe formation
    J A Langeland
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, Madison 53706
    Development 117:585-96. 1993
    ..Other, as yet unidentified, proteins are certain to play a role in stripe activation, presumably acting through other conserved sequence tracts...
  90. pmc Identification of C. elegans DAF-12-binding sites, response elements, and target genes
    Yuriy Shostak
    Program in Biochemistry and Molecular Biology, University of California, San Francisco, California 94143 2280, USA
    Genes Dev 18:2529-44. 2004
    ..DAF-12 target gene regulation was developmental program and stage specific, potentially predicting a fit of these targets into regulatory networks governing aspects of C. elegans reproductive development and dauer formation...
  91. ncbi Preliminary identification and analysis of point mutations correlated with response to interferon-alpha in hepatitis B virus post-transcriptional regulatory elements
    Tong jing Xing
    Department of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
    Chin Med J (Engl) 118:56-61. 2005
    ..This study was designed to explore the heterogeneity of HBV post-transcriptional regulatory elements (HPRE) and the relationship between the diversity of HPRE and the response to IFN-alpha treatment.
  92. pmc A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth
    Vandana Yadav
    National Centre for Plant Genome Research, New Delhi 110067, India
    Plant Cell 17:1953-66. 2005
    ..Taken together, these results demonstrate that AtMYC2 is a common transcription factor of light, ABA, and JA signaling pathways in Arabidopsis...
  93. pmc The product of the Drosophila zeste gene binds to specific DNA sequences in white and Ubx
    M Benson
    EMBO J 6:1387-92. 1987
    ..At least two independent zeste binding sites are found in a 250-bp interval of the white regulatory region that contains also the sites of wsp mutations, which are known to be deficient in zeste interaction...
  94. pmc Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    Nak Kyeong Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Bioinformatics 9:262. 2008
    ..Although some programs for identifying sequence motifs exploit positional information, most of them model it only implicitly and with ad hoc methods, making them unsuitable for general motif searches...
  95. ncbi Identification of transcriptional regulatory elements in the human somatostatin receptor sst2 promoter and regions including estrogen response element half-site for estrogen activation
    Nobuko Kimura
    Tokyo Metropolitan Institute for Neuroscience, Tokyo Metropolitan Organization for Medical Research, 2 6 Musashidai, Fuchu, Tokyo 183 8526, Japan
    J Mol Endocrinol 40:75-91. 2008
    ..The present results should provide a molecular basis for transcriptional regulation in a variety of physiological and pathological contexts of sst2-expressing tissues...
  96. ncbi Imaginal disc silencers from Ultrabithorax: evidence for Polycomb response elements
    B Christen
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Mech Dev 48:255-66. 1994
    ..Since silencing by BXD also requires Pc function, this suggests that BXD contains target sites for Pc or for Pc-like proteins. We propose that stable silencing of Ubx is achieved through cooperation between hb and Pc target sites...
  97. pmc Functional interaction of CP2 with GATA-1 in the regulation of erythroid promoters
    Francesca Bosè
    Dipartimento di Biotecnologie e Bioscienze, Universita di Milano Bicocca, P za della Scienza 2, 20126 Milano, Italy
    Mol Cell Biol 26:3942-54. 2006
    ..This may contribute to the functional cooperation between these factors and provide an explanation for the important role of ubiquitous CP2 in the regulation of erythroid genes...
  98. ncbi New computational approaches for analysis of cis-regulatory networks
    C Titus Brown
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:86-102. 2002
    ..Several of the tools discussed in this paper are still in active development and some are available as open source...
  99. ncbi Modeling DNA sequence-based cis-regulatory gene networks
    Hamid Bolouri
    Science and Technology Research Centre, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
    Dev Biol 246:2-13. 2002
    ..Successful network models lead to direct tests of key architectural features by targeted cis-regulatory analysis...
  100. pmc A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors
    Hongkai Ji
    Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138, USA
    Nucleic Acids Res 34:e146. 2006
    ....
  101. pmc PReMod: a database of genome-wide mammalian cis-regulatory module predictions
    Vincent Ferretti
    McGill University and Genome Quebec Innovation Center, 740 Dr Penfield, Montreal, QC, Canada H3A 1A4
    Nucleic Acids Res 35:D122-6. 2007
    ..It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod...

Research Grants63

  1. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  2. Innovative approach for high-volume production of endogenous reporter cells
    ROBERT E FINNEY; Fiscal Year: 2012
    ..reporter gene such as a fluorescent protein or luciferase downstream to cloned promoter and transcriptional regulatory elements. In an exogenous reporter, the vector is introduced into recipient cells where expression proceeds ..
  3. Role of POZ-zinc finger proteins in tumorigenesis.
    Pier Paolo Pandolfi; Fiscal Year: 2013
    ..In view of the critical role exerted by this protein in tumorigenesis and embryonic development the further elucidation of POKEMON/LRF function and role in human cancer is of great relevance to biomedical research. ..
  4. Functional Assessment of the Locus for Atrial Fibrillation on Chromosome 4q25
    PATRICK THOMAS ELLINOR; Fiscal Year: 2010
    ..2C. Characterizing the identified transcriptional regulatory elements using a mammalian expression system...
  5. The Role of TAF4b in Spermatogonial Stem Cell Maintenance and Self-Renewal
    Eric Gustafson; Fiscal Year: 2013
    ..While recent work has identified master transcriptional regulator genes controlling pluripotency in mouse and human embryonic stem (ES) cells, it is still unclear whether similar ..
  6. NOVEL MODULATORS OF ALCOHOL INDUCED METABOLIC AND LIVER INJURY
    Raj M Lakshman; Fiscal Year: 2013
    ..abstract_text> ..
  7. RANKL and Inflammation-associated Bone Loss
    CHARLES A O'BRIEN; Fiscal Year: 2012
    ..cells, but not in activated T cells, and stimulation of RANKL expression is mediated by distant transcriptional regulatory elements. The studies in Specific Objective 1 will determine whether RANKL expression in lymphocytes ..
  8. Heme, Iron and Oxidative Stress: Regulation of Iron Homeostasis in H. Influenzae
    Robert S Munson; Fiscal Year: 2013
    ..abstract_text> ..
  9. Tissue-specific regulation of a gene essential for airway epithelial function
    Ann Harris; Fiscal Year: 2012
    ..Translational opportunities that may arise from this work include modulating CFTR expression in vivo and the construction of efficient, tissue-specific gene therapy vectors. ..
  10. Genome-wide Light-inducible Tuning of Transcriptional Network Dynamic
    Feng Zhang; Fiscal Year: 2013
    ..Application of this novel technology will enable high throughput discovery of the upstream transcriptional regulatory elements of any endogenous gene, as well as temporally precise modulation of gene expression in the native ..
  11. Deciphering Principles of Regulatory Genomics
    Gabriela G Loots; Fiscal Year: 2010
    ..we aim to elucidate sequence signatures, genomic location and the functional activity of transcriptional regulatory elements that drive tissue specific gene expression during embryonic vertebrate development...
  12. A Unified Model of Gene Regulatory Circuit Evolution
    Victor Hanson-Smith; Fiscal Year: 2013
    ..C. albicans control biofilm formation using a complex circuit with six master-regulator genes and thousands of downstream target genes. It is not known how biofilm formation evolved, or if the C...
  13. Using combinatorial control to improve transgene expression specificity in plants
    Tedd D Elich; Fiscal Year: 2012
    ..expression cassettes that are combinatorially controlled by transcriptional promoters and post-transcriptional regulatory elements. Selection of miRNA binding elements will be based on recently published data demonstrating cell ..
  14. AXONAL PATHWAY SELECTION IN THE ZEBRAFISH EMBRYO
    Michael Granato; Fiscal Year: 2013
    ....
  15. Role of the Foxn4 Gene during Retinogenesis
    Mengqing Xiang; Fiscal Year: 2009
    ..approaches, we aim to investigate in Foxn4 null retinas the expression profiles of photoreceptor and ganglion regulator genes, and the generation and distribution patterns of photoreceptor cells, as well as to examine the effect of ..
  16. C. elegans transcriptional regulatory elements
    Barbara J Wold; Fiscal Year: 2013
    ..We will attempt to solve this problem by extensive, reiterated experimental tests of computational predictions in a simple animal genome. ..
  17. Adaptive protein evolution of_Drosophila_germline stem cell genes_bam_and_bgcn_
    Daniel A Barbash; Fiscal Year: 2013
    ..and the evolutionary forces responsible for driving high rates of protein divergence at two key GSC regulator genes, bam and bgcn...
  18. Gene Network Perturbations in Alcohol Dependence - A Systems Biology Approach
    Pietro P Sanna; Fiscal Year: 2013
    ..The CNSi will be used to identify the master regulator genes (MRs) that activate specific gene signatures associated with the transition from moderate to excessive ..
  19. TRANSCRIPTIONAL CONTROL OF INTERFERON-GAMMA IN T AND NK CELLS
    AMY SUSAN WEINMANN; Fiscal Year: 2010
    ..Aim 3: Identify the mechanisms bv which the transcriptional regulatory elements within the Ifng locus influence IFN-? expression and the key transcription factors that act at ..
  20. Functional genomic analysis of the CD8 T cell response to HIV vaccines in
    MARGARET JULIANA MCELRATH; Fiscal Year: 2013
    ..in a mouse model, and supplemented with new data from Aim 1, we will evaluate the role of up to 96 candidate regulator genes that are increased in Ad5/HIV-induced CD8 T cells using functional genomic approaches...
  21. Modeling MicroRNA-Target Functional Networks for Acute Myeloid Leukemia Prognosis
    Xinan Holly Yang; Fiscal Year: 2013
    ..Both the abundance of available AML patient profiles and the proven ability of our proposed methods suggest that we will achieve our aim to build an LSC-driven prognostic model. ..
  22. Genetic Studies of Loci Associated with Atrial Fibrillation
    SHAMONE ROBINETTE GORE PANTER; Fiscal Year: 2013
    ..this hypothesis, in vitro and in vivo experiments will be performed to identify and test functional transcriptional regulatory elements in the 4q25 region determine their effects on gene expression of Pitx2 and neighboring genes.
  23. MicroRNA Expression Profiling Circuits for Detection and Destruction of Cancer
    Ron Weiss; Fiscal Year: 2013
    ..The circuits use a combination of transcriptional and post-transcriptional regulatory elements that respond to the microRNA markers and together control expression of the "killer" protein...
  24. FUNCTIONAL DOMAINS AND EXPRESSION OF OLFACTORY RECEPTORS
    Timothy S McClintock; Fiscal Year: 2010
    ..We will test whether targeted knockout of six of these regulator genes, all expressed by immature olfactory sensory neurons, causes deficits in either the production of mature ..
  25. Efficient Algorithms for Motif Search
    Sanguthevar Rajasekaran; Fiscal Year: 2013
    ..principal paradigms that have been previously used for identifying short functional peptide motifs, transcriptional regulatory elements, composite regulatory patterns, DNA motifs, similarity between families of proteins, etc...
  26. Evaluation of RNA transport elements in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2007
    DESCRIPTION (provided by applicant): Post-transcriptional regulatory elements (PTREs) effect various aspects of RNA function: transport of RNAs from the nucleus to the cytoplasm, localization of the RNA in specific cellular compartments,..
  27. ENDOTHELIAL CELL DIVERSITY DURING FETAL DEVELOPMENT
    Eugene Levin; Fiscal Year: 2001
    ..be tested is that tPA expression in specific arterial endothelial cells is controlled by a set of transcriptional regulatory elements and factors that are "activated" in response to the conditions within the developing fetal arterial ..
  28. DOXORUBICIN BIOSYNTHESIS AND RESISTANCE
    CHARLES SIH; Fiscal Year: 2000
    ..If not, then the applicants will determine if the expression of selected dnr structural genes is controlled by phosphate level, with or without dnrN or dnrI involvement. ..
  29. The role of microRNAs in Schwann cell development and disease
    Rajeshwar B Awatramani; Fiscal Year: 2013
    ..The experiments proposed will impact our understanding of both Schwann cell differentiation during development, as well as dedifferentiation in nerve injury and demyelinating diseases. ..
  30. BIOCHEMISTRY OF MAST CELL SECRETORY GRANULE ENZYMES
    Lawrence Schwartz; Fiscal Year: 1999
    ..tryptase, existence of common polymorphisms, organization of the tryptase genome and presence of transcriptional regulatory elements will be addressed...
  31. The meiotic role of dtopors in male Drosophila
    JOHN TOMKIEL; Fiscal Year: 2007
    ..proposed to function by establishing chromatin domains that restrict the activities of cis-acting transcriptional regulatory elements. The Dtopors protein associates with insulator proteins and lamin and has been hypothesized to play ..
  32. TWO-COMPONENT SIGNAL PROTEINS OF ASPERGILLUS FUMIGATUS
    Richard Calderone; Fiscal Year: 2003
    ..If determined to be important to this organism, our studies may suggest that 2-component proteins are relevant targets for the development of broad-spectrum antifungals. ..
  33. Induction of Macrophage iNOS by Salmonella
    BOBBY CHERAYIL; Fiscal Year: 2006
    ..and characterizing their influence on TRAF-dependent signals, (c) identifying cis-acting transcriptional regulatory elements in the iNOS promoter that respond to Salmonella infection, and to Sop-induced signals, and (d) ..
  34. MOLECULAR BIOLOGY OF TRANSALDOLASE
    Andras Perl; Fiscal Year: 2004
    ..We have identified two distinct transcriptional regulatory elements, an upstream promoter and an enhancer, the latter contributed by a TAL-associated repetitive ..
  35. ACTIVATION OF VANS IN VITRO
    Bernard Weisblum; Fiscal Year: 2000
    ..Testing such intermediates will only be feasible in a cell-free system, where it is possible to have assurance that the effectors have access to their proposed targets. ..
  36. GENETIC POLYMORPHISM OF DIHYDROPYRIMIDINE DEHYDROGENASE
    Robert Diasio; Fiscal Year: 2006
    ..The specific aims will include: Spec. Aim 1) - Identify and clarify the role of additional transcriptional regulatory elements affecting DPYD gene expression including identification of a...
  37. AUTONOMOUS PARVOVIRUS VECTORS FOR CANCER THERAPY
    IAN MAXWELL; Fiscal Year: 1992
    ..Expression can be controlled by cis -acting transcriptional regulatory elements so as to kill specific target cells in culture, and in transgenic mice...
  38. Regulation of rRNA transcription in Entamoeba histolyti*
    William Petri; Fiscal Year: 2003
    ..The sequences upstream of the two rDNA units which normally contain the transcriptional regulatory elements are completely different from each other...
  39. RESPONSE REGULATOR GENE (CASSK1) OF CANDIDA ALBICANS
    Richard Calderone; Fiscal Year: 2004
    ..To this end, we have identified a 2-component, histidine kinase (CaHKI) and response regulator genes (CaSSKl), both of which are essential for virulence of the organism, since knock-out strains in each gene ..
  40. TRANSCRIPTIONAL REGULATION OF CARDIOMYOCYTE DEVELOPMENT
    Gordon Huggins; Fiscal Year: 2003
    ..the GATA4 zinc finger protein that binds to and trans-activates a wide variety of cardiac specific transcriptional regulatory elements. Using a gene targeting approach we showed that GATA4 is necessary for the formation of the ..
  41. GENE EXPRESSION AND REGULATION IN P. FALCIPARUM
    DAVID BZIK; Fiscal Year: 1992
    ..b>Transcriptional regulatory elements that control the synthesis and stability of mRNA and mark genes for stage- specific expression will ..
  42. Models of X-Linked Retinitis Pigmentosa
    GUSTAVO AGUIRRE; Fiscal Year: 2007
    ....
  43. TWO-STAGE SKIN CARCINOGENESIS & HA-RAS GENE EXPRESSION
    Jill Pelling; Fiscal Year: 1992
    ..regulation in cis of the mouse c-Ha-ras gene in vitro, by identifying and characterizing cis-transcriptional regulatory elements of the Ha- ras oncogene, using the transient gene expression assay for chloramphenicol ..
  44. MOLECULAR GENETICS OF LOW RENIN HYPERTENSION
    Perrin White; Fiscal Year: 2001
    ..The investigators will identify and characterize transcriptional regulatory elements in HSD11K...
  45. GENE THERAPY FOR DUCHENNE MUSCULAR DYSTROPHY
    JEFFREY LEIDEN; Fiscal Year: 1999
    ..Our proposed studies will make use of skeletal muscle- and cardiac-specific transcriptional regulatory elements previously cloned and characterized by our laboratory to restrict expression of the dystrophin gene ..
  46. REGULATION OF HUMAN ALDOSTERONE SYNTHASE
    Perrin White; Fiscal Year: 2002
    ..The proposed studies will extend the applicants' ongoing collaborative project that has defined transcriptional regulatory elements in the proximal 5' flanking region of CYP11B2...
  47. CFTR GENOTYPING BY PEPTIDE MASS-SIGNATURE GENOTYPING
    Edwin Naylor; Fiscal Year: 2001
    ..Establishing a CFTR genotyping service will set a precedent to expand PMSG services to other disorders where genotype analysis is a valuable tool. ..
  48. REGULATION OF BETA-POLYMERASE IN PREMALIGNANT CONDITIONS
    Craig Tendler; Fiscal Year: 1992
    ..or oncogene expressing plasmids to determine if these nuclear proteins act as positive or negative transcriptional regulatory elements on the expression of beta-polymerase...
  49. Transcriptional Regulation of Keratocan and Mimecan
    GARY CONRAD; Fiscal Year: 2004
    ..The overall objective of this project is to analyze the cis-acting transcriptional regulatory elements of keratocan and mimecan genes, to identify corneal proteins that interact with these elements, and ..
  50. NEURONAL-GLIAL DIFFERENTIATION
    Noboru Sueoka; Fiscal Year: 1992
    ..proteins that bind to the elements and their corresponding genes, and studying the control mechanisms of the regulator genes themselves...
  51. NON-ACUTE RETROVIRUSES AND DETERMINANTS OF ONCOGENICITY
    Susan Ross; Fiscal Year: 2004
    ..Project 2 will delineate the transcriptional regulatory elements within the TBLV long terminal repeat that alter its cell type tropism from mammary to T cells, the ..
  52. MOLECULAR BIOLOGY OF CARDIAC SODIUM/CALCIUM EXCHANGE
    KENNETH PHILIPSON; Fiscal Year: 2001
    ..3. Gene structure. Transcriptional regulatory elements and intron/exon boundaries will be analyzed...
  53. SIGNAL TRANSDUCTION PATHWAYS IN HEMATOPOIESIS
    Bernard Mathey Prevot; Fiscal Year: 2003
    ..cDNAs for both receptors have been placed under the control of Gal4 transcriptional regulatory elements, and injected into Drosophila embryos...
  54. REACTIVATION OF HERPES EYE DISEASE
    David Fink; Fiscal Year: 1999
    ..neurotransmitter phenotype, expression of high affinity growth factor receptor, and the presence of transcriptional regulatory elements. (2) To define the mechanisms responsible for reactivation of HSV from latency on a cell specific ..
  55. Chromatin modifications that regulate transcription at the neuromuscular synapse
    Larry Fromm; Fiscal Year: 2006
    ..NRG-1-induced AChR transcription requires two transcriptional regulatory elements, one that binds GA-binding protein (GABP) and another that binds early growth respone-1 (Egr-1), ..
  56. Vitamin D3 inducible Genes Mediating Differentiation
    Stephen Nimer; Fiscal Year: 2004
    ..regulation of the p21 promoter, and its possible role as a transcriptional modulator of other cell cycle regulator genes, will be addressed. A screen for novel HoxAlO target genes using array technology will also be generated. 3...
  57. Neuregulin signaling at the neuromuscular synapse
    Larry Fromm; Fiscal Year: 2004
    ..NRG-1-induced AChR transcription requires two transcriptional regulatory elements, one that binds GA-binding protein (GABP), a heterodimer of the Ets protein GABP alpha and GABP ..
  58. The role of SIR4 in Ty1 retrotransposition
    JILL KEENEY; Fiscal Year: 2002
    ..SIR4 complexes with other Silent Information Regulator genes do transcriptionally regulate the mating loci and telomeres by creating a silenced chromatin region...
  59. ACTIVATION OF HIV-1 IN MACROPHAGES BY LUNG CELLS
    Maureen Goodenow; Fiscal Year: 2000
    ..The hypothesis is that natural genetic variation of transcriptional regulatory elements in the long terminal repeat (LTR) sequences of the HIV-1 genome modulate activation and quiescence ..
  60. Computational discovery of cis-regulatory sequences
    John Stamatoyannopoulos; Fiscal Year: 2007
    ..DNaseI hypersensitivity in vivo is the sine qua non of a diverse cast of transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions...
  61. ENDOTHELIAL GENE REGULATION BY BIOMECHANICAL FORCES
    MICHAEL GIMBRONE; Fiscal Year: 2003
    ....
  62. GATA TRANSCRIPTION FACTOR FUNCTION IN DEVELOPMENT
    JAMES ENGEL; Fiscal Year: 2004
    ..In the first strategy, we propose to define the transcriptional regulatory elements that confer tissue-specific regulation to the GATA factor genes, and to then generate partially ..