transcription factors


Summary: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

Top Publications

  1. ncbi Induction of pluripotent stem cells from adult human fibroblasts by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 131:861-72. 2007
  2. 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
  3. pmc Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    Sven Heinz
    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Mol Cell 38:576-89. 2010
  4. pmc Histone modifications at human enhancers reflect global cell-type-specific gene expression
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 459:108-12. 2009
  5. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
  6. ncbi Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    H Niwa
    Centre for Genome Research, The University of Edinburgh, King s Buildings, Edinburgh, UK
    Nat Genet 24:372-6. 2000
  7. doi Transcription factors: from enhancer binding to developmental control
    Francois Spitz
    Developmental Biology Unit, European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nat Rev Genet 13:613-26. 2012
  8. pmc JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    Elodie Portales-Casamar
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
    Nucleic Acids Res 38:D105-10. 2010
  9. ncbi Hypoxia--a key regulatory factor in tumour growth
    Adrian L Harris
    Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
    Nat Rev Cancer 2:38-47. 2002
  10. pmc An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
    Ittai Ben-Porath
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:499-507. 2008

Detail Information

Publications352 found, 100 shown here

  1. ncbi Induction of pluripotent stem cells from adult human fibroblasts by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 131:861-72. 2007
    ..iPS) cells, capable of germline transmission, from mouse somatic cells by transduction of four defined transcription factors. Here, we demonstrate the generation of iPS cells from adult human dermal fibroblasts with the same four ..
  2. 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
  3. pmc Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    Sven Heinz
    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Mol Cell 38:576-89. 2010
    Genome-scale studies have revealed extensive, cell type-specific colocalization of transcription factors, but the mechanisms underlying this phenomenon remain poorly understood...
  4. pmc Histone modifications at human enhancers reflect global cell-type-specific gene expression
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 459:108-12. 2009
    ..Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression...
  5. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
    ..Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease...
  6. ncbi Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    H Niwa
    Centre for Genome Research, The University of Edinburgh, King s Buildings, Edinburgh, UK
    Nat Genet 24:372-6. 2000
    Cell fate during development is defined by transcription factors that act as molecular switches to activate or repress specific gene expression programmes...
  7. doi Transcription factors: from enhancer binding to developmental control
    Francois Spitz
    Developmental Biology Unit, European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nat Rev Genet 13:613-26. 2012
    ..Views of how transcription factors regulate gene expression are changing owing to recent genome-wide studies of transcription factor binding ..
  8. pmc JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    Elodie Portales-Casamar
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
    Nucleic Acids Res 38:D105-10. 2010 is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner...
  9. ncbi Hypoxia--a key regulatory factor in tumour growth
    Adrian L Harris
    Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
    Nat Rev Cancer 2:38-47. 2002
    ..Many elements of the hypoxia-response pathway are therefore good candidates for therapeutic targeting...
  10. pmc An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
    Ittai Ben-Porath
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:499-507. 2008
  11. doi Genome sequence of the palaeopolyploid soybean
    Jeremy Schmutz
    HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Nature 463:178-83. 2010
    ..An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties...
  12. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  13. ncbi Resveratrol improves mitochondrial function and protects against metabolic disease by activating SIRT1 and PGC-1alpha
    Marie Lagouge
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, 67404 Illkirch, France
    Cell 127:1109-22. 2006
    ..These pharmacological effects of RSV combined with the association of three Sirt1 SNPs and energy homeostasis in Finnish subjects implicates SIRT1 as a key regulator of energy and metabolic homeostasis...
  14. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
  15. 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...
  16. pmc Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension
    G L Wang
    Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287 3914, USA
    Proc Natl Acad Sci U S A 92:5510-4. 1995
  17. pmc The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2
    Manav Korpal
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    J Biol Chem 283:14910-4. 2008
    ..These results suggested that loss of expression of the miR-200 family members may play a critical role in the repression of E-cadherin by ZEB1 and ZEB2 during EMT, thereby enhancing migration and invasion during cancer progression...
  18. pmc Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
    Alexander Marson
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 134:521-33. 2008
    ..We find that the key ES cell transcription factors are associated with promoters for miRNAs that are preferentially expressed in ES cells and with promoters ..
  19. ncbi Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation
    P Jaakkola
    The Henry Wellcome Building of Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Science 292:468-72. 2001
    ..An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor...
  20. ncbi Activation of beta-catenin-Tcf signaling in colon cancer by mutations in beta-catenin or APC
    P J Morin
    Howard Hughes Medical Institute and Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
    Science 275:1787-90. 1997
    ..These results indicate that regulation of beta-catenin is critical to APC's tumor suppressive effect and that this regulation can be circumvented by mutations in either APC or beta-catenin...
  21. doi WRKY transcription factors
    Paul J Rushton
    Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
    Trends Plant Sci 15:247-58. 2010
    WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes...
  22. pmc RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
    Socorro Gama-Castro
    Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, AP 565 A, Cuernavaca, Morelos 62100, Mexico
    Nucleic Acids Res 39:D98-105. 2011
    ..A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format...
  23. ncbi Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells
    Ian Chambers
    Institute for Stem Cell Research, University of Edinburgh, King s Buildings, West Mains Road, Edinburgh EH9 3JQ, Scotland
    Cell 113:643-55. 2003
    ..A unique network of transcription factors may characterize self-renewal and simultaneously suppress differentiation...
  24. doi Breaking the code of DNA binding specificity of TAL-type III effectors
    Jens Boch
    Department of Genetics, Institute of Biology, Martin Luther University Halle Wittenberg, Weinbergweg 10, D 06099 Halle Saale Germany
    Science 326:1509-12. 2009
    ..Our study describes the functionality of a distinct type of DNA binding domain and allows the design of DNA binding domains for biotechnology...
  25. ncbi The transcription factor snail controls epithelial-mesenchymal transitions by repressing E-cadherin expression
    A Cano
    Instituto de Investigaciones Biomedicas, Arturo Duperier 4, 28029 Madrid, Spain
    Nat Cell Biol 2:76-83. 2000
    The Snail family of transcription factors has previously been implicated in the differentiation of epithelial cells into mesenchymal cells (epithelial-mesenchymal transitions) during embryonic development...
  26. ncbi Prolonged rapamycin treatment inhibits mTORC2 assembly and Akt/PKB
    Dos D Sarbassov
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Cell 22:159-68. 2006
    ..Our work describes an unforeseen mechanism of action for rapamycin that suggests it can be used to inhibit Akt/PKB in certain cell types...
  27. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    ..This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks...
  28. doi The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1
    Philip A Gregory
    Hanson Institute and Division of Human Immunology, Institute of Medical and Veterinary Science, Adelaide, SA 5000, Australia
    Nat Cell Biol 10:593-601. 2008
    ..Expression of the miR-200 family was also lost in regions of metaplastic breast cancer specimens lacking E-cadherin. These data suggest that downregulation of the microRNAs may be an important step in tumour progression...
  29. pmc Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
    Feng Zhang
    Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:149-53. 2011
    ..We synthesized 17 TALEs that are customized to recognize specific DNA-binding sites, and demonstrate that they can specifically modulate transcription of endogenous genes (SOX2 and KLF4) in human cells...
  30. 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
    The transcription factors OCT4, SOX2, and NANOG have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture...
  31. 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...
  32. ncbi Induced pluripotent stem cell lines derived from human somatic cells
    Junying Yu
    Genome Center of Wisconsin, Madison, WI 53706 1580, USA
    Science 318:1917-20. 2007
  33. pmc Architecture of the human regulatory network derived from ENCODE data
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Nature 489:91-100. 2012
    b>Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell...
  34. ncbi Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
    ..The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory ..
  35. ncbi XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor
    H Yoshida
    Graduate School of Biostudies, Kyoto University, Kyoto 606 8304, Japan
    Cell 107:881-91. 2001
    ..Our results reveal features of the UPR conserved during evolution and clarify the relationship between IRE1- and ATF6-dependent pathways...
  36. pmc Master transcription factors and mediator establish super-enhancers at key cell identity genes
    Warren A Whyte
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 153:307-19. 2013
    Master transcription factors Oct4, Sox2, and Nanog bind enhancer elements and recruit Mediator to activate much of the gene expression program of pluripotent embryonic stem cells (ESCs)...
  37. pmc Systematic localization of common disease-associated variation in regulatory DNA
    Matthew T Maurano
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Science 337:1190-5. 2012
    ..Our results suggest pervasive involvement of regulatory DNA variation in common human disease and provide pathogenic insights into diverse disorders...
  38. pmc Genomic expression programs in the response of yeast cells to environmental changes
    A P Gasch
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5428, USA
    Mol Biol Cell 11:4241-57. 2000
    ..Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while ..
  39. ncbi The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
    Mitsutoshi Yoneyama
    Department of Tumor Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Nat Immunol 5:730-7. 2004
    ..The caspase recruitment domain transmitted 'downstream' signals, resulting in the activation of transcription factors NF-kappaB and IRF-3...
  40. pmc Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma
    Ignacio Varela
    Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
    Nature 469:539-42. 2011
    ..4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology...
  41. ncbi IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA
    Marcella Calfon
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Nature 415:92-6. 2002
    ..Our findings suggest that physiological ER load regulates a developmental decision in higher eukaryotes...
  42. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFkappaB, Sox2, Oct4 (also known as Pou5f1) and Nanog...
  43. ncbi Targeted disruption of Cbfa1 results in a complete lack of bone formation owing to maturational arrest of osteoblasts
    T Komori
    Department of Medicine III, Osaka University Medical School, Suita, Japan
    Cell 89:755-64. 1997
  44. doi DNA-binding specificities of human transcription factors
    Arttu Jolma
    Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
    Cell 152:327-39. 2013
    Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize...
  45. ncbi The role of chromatin during transcription
    Bing Li
    Stowers Medical Research Institute, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 128:707-19. 2007
    ..In this Review, we highlight advances in our understanding of chromatin regulation and discuss how such regulation affects the binding of transcription factors as well as the initiation and elongation steps of transcription.
  46. pmc An expansive human regulatory lexicon encoded in transcription factor footprints
    Shane Neph
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 489:83-90. 2012
  47. pmc A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells
    Ulrike Burk
    Department of Visceral Surgery, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
    EMBO Rep 9:582-9. 2008
    ..Alternatively, depending on the environmental trigger, this loop might switch and induce epithelial differentiation, and thus explain the strong intratumorous heterogeneity observed in many human cancers...
  48. ncbi Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3
    Rashu B Seth
    Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Cell 122:669-82. 2005
    Viral infection triggers host innate immune responses through activation of the transcription factors NF-kappaB and IRF 3, which coordinately regulate the expression of type-I interferons such as interferon-beta (IFN-beta)...
  49. pmc Identification of functional elements and regulatory circuits by Drosophila modENCODE
    Sushmita Roy
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 330:1787-97. 2010
    ..modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and ..
  50. pmc Direct conversion of fibroblasts to functional neurons by defined factors
    Thomas Vierbuchen
    Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University School of Medicine, 1050 Arastradero Road, Palo Alto, California 94304, USA
    Nature 463:1035-41. 2010
    ..that mouse and human fibroblasts can be reprogrammed to a pluripotent state with a combination of four transcription factors. This raised the question of whether transcription factors could directly induce other defined somatic ..
  51. doi DNA-binding factors shape the mouse methylome at distal regulatory regions
    Michael B Stadler
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
    Nature 480:490-5. 2011
    ..methylomes confirms this dependency, as cell-type-specific LMRs are occupied by cell-type-specific transcription factors. This study provides methylome references for the mouse and shows that DNA-binding factors locally ..
  52. ncbi Regulated translation initiation controls stress-induced gene expression in mammalian cells
    H P Harding
    Skirball Institute of Biomolecular Medicine The Department of Medicine, Kaplan Cancer Center New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 6:1099-108. 2000
    ..Mammalian cells thus utilize an ancient pathway to regulate gene expression in response to diverse stress signals...
  53. ncbi Cellular survival: a play in three Akts
    S R Datta
    Division of Neuroscience, Children s Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115 USA
    Genes Dev 13:2905-27. 1999
  54. pmc Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+ T regulatory cells
    Angela M Thornton
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Immunol 184:3433-41. 2010
    ..Collectively, these results demonstrate that Helios is potentially a specific marker of thymic-derived Treg cells and raises the possibility that a significant percentage of Foxp3(+) Treg cells are generated extrathymically...
  55. pmc Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes
    Joseph H Taube
    Department of Molecular Pathology, University of Texas M D Anderson Cancer Center, Houston, TX 77054, USA
    Proc Natl Acad Sci U S A 107:15449-54. 2010
    ..Inducers of the EMT include several transcription factors (TFs), such as Goosecoid, Snail, and Twist, as well as the secreted TGF-beta1...
  56. pmc XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
    Ann Hwee Lee
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Mol Cell Biol 23:7448-59. 2003
    ..We have investigated here the contribution of the UPR transcription factors XBP-1, ATF6alpha, and ATF6beta to UPR target gene expression...
  57. ncbi Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer
    Scott A Tomlins
    Department of Pathology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, MI 48109 0602, USA
    Science 310:644-8. 2005
    ..Two ETS transcription factors, ERG and ETV1, were identified as outliers in prostate cancer...
  58. pmc A map of the cis-regulatory sequences in the mouse genome
    Yin Shen
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 488:116-20. 2012
    ..We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type...
  59. ncbi Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia
    Andrew P Weng
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Science 306:269-71. 2004
    ..These findings greatly expand the role of activated NOTCH1 in the molecular pathogenesis of human T-ALL and provide a strong rationale for targeted therapies that interfere with NOTCH signaling...
  60. ncbi IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction
    Taro Kawai
    Exploratory Research for Advanced Technology, Japan Science and Technology Agency
    Nat Immunol 6:981-8. 2005
    ..induced type I interferon and interferon-inducible genes through activation of IRF3, IRF7 and NF-kappaB transcription factors. TBK1 and IKKi protein kinases were required for the IPS-1-mediated interferon induction...
  61. doi In vivo reprogramming of adult pancreatic exocrine cells to beta-cells
    Qiao Zhou
    Department of Stem Cell and Regenerative Biology, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 455:627-32. 2008
    ..of re-expressing key developmental regulators in vivo, we identify a specific combination of three transcription factors (Ngn3 (also known as Neurog3) Pdx1 and Mafa) that reprograms differentiated pancreatic exocrine cells in ..
  62. ncbi Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    Cesar Llave
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 297:2053-6. 2002
    ..interacts with mRNA targets encoding several members of the Scarecrow-like (SCL) family of putative transcription factors. miRNA 39 is complementary to an internal region of three SCL mRNAs...
  63. pmc Foxo transcription factors induce the atrophy-related ubiquitin ligase atrogin-1 and cause skeletal muscle atrophy
    Marco Sandri
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 117:399-412. 2004
    ..myotubes undergoing atrophy, the activity of the PI3K/AKT pathway decreases, leading to activation of Foxo transcription factors and atrogin-1 induction. IGF-1 treatment or AKT overexpression inhibits Foxo and atrogin-1 expression...
  64. doi SWI/SNF nucleosome remodellers and cancer
    Department of Pediatric Oncology, Dana Farber Cancer Institute, Division of Hematology Oncology, Children s Hospital Boston, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
    Nat Rev Cancer 11:481-92. 2011
    ..In this Review we discuss the contributions of SWI/SNF mutations to cancer formation, examine their normal functions and discuss opportunities for novel therapeutic interventions for SWI/SNF-mutant cancers...
  65. 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 a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns...
  66. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    ..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.
  67. ncbi An integrated stress response regulates amino acid metabolism and resistance to oxidative stress
    Heather P Harding
    Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 11:619-33. 2003
    ..A signaling pathway initiated by eIF2alpha phosphorylation protects cells against metabolic consequences of ER oxidation by promoting the linked processes of amino acid sufficiency and resistance to oxidative stress...
  68. pmc A unique chromatin signature uncovers early developmental enhancers in humans
    Alvaro Rada-Iglesias
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nature 470:279-83. 2011
    ..Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis...
  69. ncbi Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
    Coleen T Murphy
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
    Nature 424:277-83. 2003
  70. pmc TGF-beta-induced epithelial to mesenchymal transition
    Jian Xu
    Department of Cell and Tissue Biology, Programs in Cell Biology and Developmental Biology, University of California San Francisco, San Francisco, CA, USA
    Cell Res 19:156-72. 2009
    ..In this review, we will discuss the induction of EMT in response to TGF-beta, and focus on the underlying signaling and transcription mechanisms...
  71. pmc p63 is a suppressor of tumorigenesis and metastasis interacting with mutant p53
    G Melino
    Medical Research Council, Toxicology Unit, Hodgkin Building, Leicester University, Leicester, UK
    Cell Death Differ 18:1487-99. 2011
    ..This demonstrates an important role for p63 in cancer development and its progression, and the aim of this review is to set this new evidence that links p63 to metastasis within the context of the long conserved other functions of p63...
  72. ncbi Roles of CHOP/GADD153 in endoplasmic reticulum stress
    S Oyadomari
    Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860 8556, Japan
    Cell Death Differ 11:381-9. 2004
    ..Here, we summarize the current understanding of the roles of CHOP/GADD153 in ER stress-mediated apoptosis and in diseases including diabetes, brain ischemia and neurodegenerative disease...
  73. ncbi Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus
    Etienne Meylan
    Department of Biochemistry, University of Lausanne, BIL Biomedical Research Center, Chemin des Boveresses 155, CH 1066 Epalinges, Switzerland
    Nature 437:1167-72. 2005
    ..their protein-interacting CARD domains, relay an undefined signal resulting in the activation of the transcription factors interferon regulatory factor 3 (IRF3) and NF-kappaB...
  74. pmc Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    Jie Wang
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 22:1798-812. 2012
    ..We present the results of our analysis in a TF-centric web repository Factorbook ( and will continually update this repository as more ENCODE data are generated...
  75. doi MYB transcription factors in Arabidopsis
    Christian Dubos
    Institut Jean Pierre Bourgin, UMR1318 INRA AgroParisTech, 78026 Versailles Cedex, France
    Trends Plant Sci 15:573-81. 2010
    ..Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA...
  76. doi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    b>Transcription factors (TFs) and their specific interactions with targets are crucial for specifying gene-expression programs...
  77. pmc An efficient algorithm for large-scale detection of protein families
    A J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 30:1575-84. 2002
    ..The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins...
  78. ncbi Identification of c-MYC as a target of the APC pathway
    T C He
    Howard Hughes Medical Institute and Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
    Science 281:1509-12. 1998
    ..These results provide a molecular framework for understanding the previously enigmatic overexpression of c-MYC in colorectal cancers...
  79. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome ..
  80. ncbi Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase
    Anne Brunet
    Division of Neuroscience, Children s Hospital, and Department of Neurobiology, Center for Blood Research CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA
    Science 303:2011-5. 2004
    ..homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of ..
  81. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
  82. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
    ..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...
  83. doi A census of human transcription factors: function, expression and evolution
    Juan M Vaquerizas
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Nat Rev Genet 10:252-63. 2009
    b>Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment...
  84. ncbi Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor
    A Brunet
    Children s Hospital and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cell 96:857-68. 1999, we demonstrate that Akt also regulates the activity of FKHRL1, a member of the Forkhead family of transcription factors. In the presence of survival factors, Akt phosphorylates FKHRL1, leading to FKHRL1's association with 14-3-..
  85. pmc Selective inhibition of BET bromodomains
    Panagis Filippakopoulos
    Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
    Nature 468:1067-73. 2010
    ..These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chemical scaffold for the development of chemical probes more broadly throughout the bromodomain family...
  86. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at
  87. ncbi Targeting HIF-1 for cancer therapy
    Gregg L Semenza
    McKusick Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 3914, USA
    Nat Rev Cancer 3:721-32. 2003
    ..In preclinical studies, inhibition of HIF-1 activity has marked effects on tumour growth. Efforts are underway to identify inhibitors of HIF-1 and to test their efficacy as anticancer therapeutics...
  88. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various ..
  89. pmc Activation of vascular endothelial growth factor gene transcription by hypoxia-inducible factor 1
    J A Forsythe
    Department of Physiology, University of Maryland School of Medicine, Baltimore, 21201, USA
    Mol Cell Biol 16:4604-13. 1996
    ..VEGF mRNA was not induced by hypoxia in mutant cells that do not express the HIF-1beta (ARNT) subunit. These findings implicate HIF-1 in the activation of VEGF transcription in hypoxic cells...
  90. pmc c-Myc regulates transcriptional pause release
    Peter B Rahl
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 141:432-45. 2010
    ..of the RNA polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA-binding transcription factors is well recognized as a key regulatory step in gene expression...
  91. ncbi Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1
    Z Wu
    Dana Farber Cancer Institute, and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cell 98:115-24. 1999
    ..These data elucidate a pathway that directly links external physiological stimuli to the regulation of mitochondrial biogenesis and function...
  92. pmc Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
    L M Guzman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Bacteriol 177:4121-30. 1995
    ..We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system...
  93. ncbi The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    B J Reinhart
    Department of Molecular Biology, Massachusetts General Hospital, and Harvard Medical School, Boston 02114, USA
    Nature 403:901-6. 2000
    ..We propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory RNAs triggers transitions in the complement of heterochronic regulatory proteins to coordinate developmental timing...
  94. pmc AMPK phosphorylation of raptor mediates a metabolic checkpoint
    Dana M Gwinn
    Molecular and Cell Biology Laboratory, Dulbecco Center for Cancer Research, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Mol Cell 30:214-26. 2008
    ..These findings uncover a conserved effector of AMPK that mediates its role as a metabolic checkpoint coordinating cell growth with energy status...
  95. pmc An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression
    Jindan Yu
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Cancer Cell 17:443-54. 2010
    ..These findings provide a working model in which TMPRSS2-ERG plays a critical role in cancer progression by disrupting lineage-specific differentiation of the prostate and potentiating the EZH2-mediated dedifferentiation program...
  96. pmc DREME: motif discovery in transcription factor ChIP-seq data
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 27:1653-9. 2011
    ..Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF...
  97. pmc Pioneer transcription factors: establishing competence for gene expression
    Kenneth S Zaret
    Epigenetics Program, Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, USA
    Genes Dev 25:2227-41. 2011
    b>Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression...
  98. pmc RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia
    Johannes Zuber
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 478:524-8. 2011
  99. pmc An atlas of combinatorial transcriptional regulation in mouse and man
    Timothy Ravasi
    The FANTOM Consortium, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Cell 140:744-52. 2010
    Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression...
  100. pmc Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases
    Dirk Hockemeyer
    The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Biotechnol 27:851-7. 2009
    ..Finally, we targeted the PITX3 gene, demonstrating that ZFNs can be used to generate reporter cells by targeting non-expressed genes in hESCs and hiPSCs...
  101. ncbi Twist, a master regulator of morphogenesis, plays an essential role in tumor metastasis
    Jing Yang
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 117:927-39. 2004
    ..These results establish a mechanistic link between Twist, EMT, and tumor metastasis...

Research Grants123 found, 100 shown here

  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. NIH Director's Pioneer Award
    ERICH JARVIS; Fiscal Year: 2009
    ..Repairing the pathway in vocal learners, when damaged, would have profound impact for correcting neurological disorders of speech. ..
  3. Transcription factors regulating sensory gene expression and pain pathways
    Eric E Turner; Fiscal Year: 2011
    ..In these studies we have focused on the roles of the transcription factors Brn3a and Islet1, and have shown these factors to be "master regulators" of sensory neuron development and ..
  4. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..The long-term goal is to identify the regulatory mechanisms to assist in the development of novel therapeutic protocols for better treatments. ..
  5. Bone Deficits and Excess Adiposity after Pediatric Bone Marrow Transplantation
    Sogol Mostoufi-Moab; Fiscal Year: 2013
    ..from the inverse relation between bone and fat formation within the bone marrow cavity, where hormones and transcription factors regulate mesenchyme stem cell (MSC) differentiation into osteoblasts or osteocytes...
  6. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..transgene expression, DNA methylation status of the TSPY promoter and exon 1, and identification of transcription factors and repressors affected by such epigenetic changes...
  7. Identification of Genetic and Epigenetic Alterations in Spondyloarthritis
    Tibor T Glant; Fiscal Year: 2013
    Carole R Mendelson; Fiscal Year: 2013
    ..Using chromatin immunoprecipitation, we will analyze temporal changes in in vivo recruitment of key transcription factors and coregulators to the SP-A promoter in lung tissues and cells of fetal and neonatal mice and in human ..
  9. Vitamin D3, Interference with Androgen Signal and Inhibition of Prostate Cancer
    Bandana Chatterjee; Fiscal Year: 2013
    ..AR and VDR were present at the regulated promoter during both induction and de-induction of E2F1. Transcription factors WSTF and E47 occupied regulated chromatin in response to androgen...
  10. Regulation of ER stress-induced cell death
    Randal J Kaufman; Fiscal Year: 2013
    ..The proposed studies on protein synthesis will provide vital information that should encourage the development of novel therapeutics to treat diabetes. ..
  11. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2013
    ..level by examining Cd modulation of the LO promoter activation regulated by metal and redox-sensitive transcription factors and their cognate cis-elements, and determining LO promoter methylation to provide evidence for Cd ..
  12. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..Additionally, insight will be gained into the regulation of T cell function in both health and disease with relevance to an array of immune and neoplastic diseases. ..
  13. Med1 in Liver Metabolism, Regeneration and Cancer
    Janardan K Reddy; Fiscal Year: 2013
    ..Given that nuclear receptors and transcription factors CEBPB and forkhead box protein M1 (FOXM1), play critical roles in metabolism and proliferation of ..
  14. Targeted siRNA nanotechnology for intravesical treatment of urologicaldiseases
    Robert M Weiss; Fiscal Year: 2010
    ..Our first test of these nanoparticles will use a mouse model of bladder cancer. Thus, we can determine the therapeutic potential of siRNA for treatment of urologic diseases. ..
  15. Induction and maintenance of regulatory T cells
    Mitchell Kronenberg; Fiscal Year: 2013
    ..This proposal will study the mechanisms by which the immune responses are properly controlled. Such knowledge will eventually facilitate the design of novel therapeutic approaches for immunological diseases. ..
  16. Targeting Inflammation for the Amelioration of Cisplatin-Hearing Loss
    Vickram Ramkumar; Fiscal Year: 2011
    ..We believe the information gained from this study will lead to potentially new treatments for treating hearing loss. ..
  17. Role of IKK in NSCLC: Modulation of SMRT and NF-kappaB
    Marty W Mayo; Fiscal Year: 2012
    ..The induction of EMT stimulates the expression of master-switch transcription factors, including Twist, and increases the expression of the polycomb repressive complex (PRC) proteins, which ..
  18. Skeletal Muscle. Ca Release Control Inside the Sarcoplasmic Reticulum.
    Eduardo Rios; Fiscal Year: 2013
    ..decays when muscles fatigue- is sustained by SOCE, a universal Ca2+ entry pathway, crucial for mobilizing transcription factors that control gene expression...
    Pi Wan Cheng; Fiscal Year: 2010
    ..2. Characterize C2GnT-M gene regulation by mapping cis-regulatory elements and identifying the cognate transcription factors under basal conditions...
    JERROLD MICHAEL OLEFSKY; Fiscal Year: 2013
    ..These studies should lead to an improved understanding of the basic causes of Type 2 diabetes mellitus and hold the potential for new therapeutic modalities. ..
  21. Tat and CDK9 on gene expression alterations coupled to HIV-1 Associated Dementia
    Xavier Grana; Fiscal Year: 2010
    ..Among the genes downregulated we have identified various transcription factors. Our data also show that inhibition of CDK9 results in the upregulation of a subset of genes including ..
    DHAN V KALVAKOLANU; Fiscal Year: 2013
    ..Previously, we have identified a novel IFN-regulated element and its cognate transcription factors. One such protein is CCAAT/Enhancer Binding protein-beta (C/EBP-2), a transcription factor known to ..
  23. Prevention of UV-induced carcinogenesis by cyanidin-3-glucoside
    Xianglin Shi; Fiscal Year: 2013 antioxidant by inhibiting the generation of reactive oxygen species and inducing antioxidant-regulative transcription factors. These preliminary studies indicate that C3G may function as a potential chemopreventive and ..
  24. Role of CD44 in experimental Multiple Sclerosis
    Mitzi Nagarkatti; Fiscal Year: 2013
    ..abstract_text> ..
  25. The role of IKK beta in cardiomyocytes at baseline and following stress
    MATTHEW PETER COGGINS; Fiscal Year: 2013
    ..The Nuclear Factor of kappa B cells (NF-kB) family of transcription factors regulates a wide range of essential processes in multiple tissues, from inflammation to cell survival...
  26. Molecular Regulation of Progesterone Synthesis
    John S Davis; Fiscal Year: 2013
    ..Considering the importance sex steroids in health and disease, we must have a better understanding of the mechanisms controlling the synthesis of steroid hormones. ..
  27. Fatty acid related regulation of enteric infectious disease
    FREDRICK JON KULL; Fiscal Year: 2012
  28. Systemic Inflammation and Central Nervous System Dysfunction
    Laura L Dugan; Fiscal Year: 2013
    ..abstract_text> ..
  29. New insights in mechanisms of renal injury
    Balakuntalam S Kasinath; Fiscal Year: 2013
    ..B. Downstream effects of GSK3 beta: Transcriptional regulation of fibronectin. GSK 3beta regulates three transcription factors for fibronectin: beta catenin, NFkB and AP1...
  30. Steroid Responsive Mechanisms in the Ear
    DENNIS ROYAL TRUNE; Fiscal Year: 2012
    ..Of particular interest are immune suppression of inflammatory cytokines and related transcription factors compared to the regulation of ion transport pathways that control fluid homeostasis.
  31. Notch and Regulators of Notch Signaling Impact Both Glucose and Lipid Metabolism
    UTPAL BHAGIRATH PAJVANI; Fiscal Year: 2013
    ..Pajvani will need in order to become an independent translational medical researcher and a productive member of the academic medical community. ..
  32. Regulation of Cell Signaling by Human Biliverdin Reductase
    Mahin D Maines; Fiscal Year: 2013
    ..In addition, the enzyme activity is necessary for protection against the fatal "green jaundice". Our work has revealed a novel approach for development of therapeutic interventions in a range of human diseases. ..
  33. Sirtuin/FOXO Signaling in the Regulation of Bone Mass
    Stavroula Kousteni; Fiscal Year: 2012
    ..of ROS by mechanisms that involve dephosphorylation and subsequent activation of a family of ubiquitous transcription factors known as FOXOs...
  34. Analysis of gene regulation of Vibrio cholerae during infection
    Jun Zhu; Fiscal Year: 2013
    ..cholerae in vivo survival strategies and shed new light on the host-pathogen interactions that underpin infections by related enteric bacterial pathogens. ..
  35. Interdisciplinary Research Training in Reproduction for Indian Fellows
    John C Herr; Fiscal Year: 2010
    ..between membrane receptors, sperm capacitation and the acrosome reaction, protein transcription, nuclear transcription factors, molecular physiology of ion channels, neuroendocrine control of mechanisms in reproduction, molecular ..
  36. Regulation of Type 1 Interferon Production by Autoimmunity-Associated PTPN22
    Yaya Wang; Fiscal Year: 2013
    ..In this grant I wil study the function of a genetic variant associated with multiple autoimmune diseases, the PTPN22 1858T variant, to examine its role in immune responses and disease pathogenesis. ..
  37. FOXP3-microRNA146-NFkB Axis in Tumor Suppression
    Lizhong Wang; Fiscal Year: 2013
    ..abstract_text> ..
  38. A quantitative proteomics approach to understand viral immune evasion strategies
    Michele E Hardy; Fiscal Year: 2010
    ..Understanding these pathways and the mechanisms by which viruses evade the innate immune response may lead new approaches to attenuated vaccines or antiviral drug targets specifically designed to bypass viral evasion strategies. ..
  39. ER stress: role in myocyte apoptosis and myocardial remodeling
    Krishna Singh; Fiscal Year: 2013
    ..The proposed studies investigating the role of ER stress in cardiac myocyte apoptosis and myocardial remodeling may uncover novel therapeutic strategies for the treatment of heart failure. ..
  40. PUFA Synthesis and the Control of Hepatic Metabolism
    Donald B Jump; Fiscal Year: 2013
    ..Defining the mechanistic linkage between PUFA synthesis, TAG hydrolysis, FoxO1, GNG &stress pathways will identify novel methods to manage diabetic complications, like hyperglycemia &fatty liver. ..
  41. Human Beta-Defensin-1 in HSV-1 Innate Immunity
    LISA KATHLEEN RYAN; Fiscal Year: 2010
    ..induces relevant amounts of hBD-1 in PDC via stimulation of Toll-like receptor 9 and activation of transcription factors subsequently increasing hBD-1 gene transcription...
    Alvaro Puga; Fiscal Year: 2013
  43. Role of Mitochondria in the Regulation of Iron metabolism by Alcohol
    ..adenine nucleotide transport, cytochrome c oxidase activity or the dimerization of hypoxia-inducible transcription factors to study the regulation of hepcidin transcription by alcohol-mediated oxidative stress...
  44. Cell signaling as a leukemia biomarker
  45. An Aldosterone-Endothelin Feedback Mechanism on Sodium Homeostasis
    Charles S Wingo; Fiscal Year: 2012
    ..Importantly, these studies will lend understanding into a novel signaling pathway that may explain the role of aldosterone in the progression of cardiovascular and renal disease. ..
  46. Plant-Derived Estrogens and Cell Proliferation
    Emma Shtivelman; Fiscal Year: 2011
    ..Molecular studies have found that a variety of transcription factors and coregulatory proteins are required for ERs to regulate genes and produce biological effects...
  47. Molecular Mechanisms of Disease Progression in Myeloid Malignancy
    ELIZABETH ANN EKLUND; Fiscal Year: 2013
    ..Targeting these mechanisms may lead to cure in CML by abolishing the CSC/LSC, and suggest therapeutic approaches to other forms of cancer with dysregulation of Fas and bcatenin. ..
    Rafi Ahmed; Fiscal Year: 2013
    ..The following specific aims are proposed to achieve our goals: 1) To identify transcription factors that regulate naive to effector CD8 T cell differentiation...
    Howard B Lieberman; Fiscal Year: 2013
  50. Integrated signaling of eicosanoids in HSC formation and regeneration
    Trista E North; Fiscal Year: 2013
    ..These results are expected to reveal deeper insight into interactive roles of inflammatory mediators in marrow regeneration and have relevance for combinatorial targeting to direct clinical outcome in transfusion biology. ..
  51. Targeting AP-1 proteins in COPD
    SEKHAR M POTHIREDDY; Fiscal Year: 2010
    ..b-ZIP proteins are the Jun (c-Jun, Jun-B, and Jun-D) and Fos (c-Fos, Fos-B, Fra-1, and Fra-2) families of transcription factors. Through homo- and heterodimerization, these b-ZIP proteins form a dimeric complex known as the activator ..
    RAMON E PARSONS; Fiscal Year: 2012
    ..In aim 3, we will investigate how PTEN regulates FOXO transcription factors to activate a target gene. DNA elements will be identified on the promoter that coordinate gene activation...
  53. Regulation of LPS-mediated HMGB1 Release by Poly (ADP-ribose) Polymerase-1
    RAJESH K ANEJA; Fiscal Year: 2013
    ..Additional studies will be performed to determine the therapeutic window for use of PARP-1 inhibitors in murine sepsis. ..
  54. Nuclear-Cytoplasmic Shuttling of Foxc2 via 14-3-3 Determines Proximal Tubule Cell
    DIANA LYNNE GOLDEN; Fiscal Year: 2012
    ..Foxc2 is a member of the Forkhead box (Fox) transcription factors known to be involved in cardiovascular, skeletal, and kidney development, playing a role in specifying ..
  55. The Role of Vascular MR-Regulated Genes in Vascular Function and Disease
    Iris Z Jaffe; Fiscal Year: 2013
    ..abstract_text> ..
    Raymond F Novak; Fiscal Year: 2010
  57. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..association with gene-specific protein complexes, inducing displacement of gene-selective coregulators and transcription factors. This hypothesis will be pursued in the following Specific Aims: SPECIFIC AIM 1...
  58. Runx Proteins and Sex Steroid Signaling in Bone
    Baruch Frenkel; Fiscal Year: 2009
    ..They will decipher cryptic mechanisms of action of existing SERMs, and support the rationale development of novel ones, based on their influence on Runx proteins. ..
  59. The mechanisms by which alcohol and HIV render the lung susceptible to injury
    DAVID MARSHALL GUIDOT; Fiscal Year: 2013
    ..This research project is designed to determine how alcohol and HIV-1 interact to make the lung susceptible to injury, and to develop effective treatments that can improve the health of these vulnerable individuals. ..
  60. Role of MicroRNA mi R-33 in Controlling Cholesterol/Lipid Homeostasis
    Anders M Naar; Fiscal Year: 2010
    The sterol response element binding protein (SREBP) transcription factors have been identified as key regulators of genes involved in both cholesterol and lipid homeostasis...
  61. Molecular Mechanisms of Chemoprevention: NRF2 Signaling
    Thomas W Kensler; Fiscal Year: 2013
  62. Impaired mitochondrial fusion in pulmonary arterial hypertension
    Stephen L Archer; Fiscal Year: 2010
    ..This proposal seeks to understand the role of the HIF-1a and mitofusin in PAH and develop therapies (inhibition of HIF-1 a and supplementation of mitofusin-2) to restore mitochondrial form and function and cure PAH. ..
    Michael R Green; Fiscal Year: 2013
    ..Transcription initiation by RNA polymerase II involves the assembly of general transcription factors on the core promoter to form a preinitiation complex (PIC)...
  64. Mechanism(s) of Alcoholic Pancreatitis
    Bhupendra S Kaphalia; Fiscal Year: 2011
    ..regulated protein 78 and related cell death pathways, and inflammatory responses by proinflammatory transcription factors and cytokines in the pancreas and/or plasma...
  65. Genistein and Prostate Cancer
    Rajvir Dahiya; Fiscal Year: 2010
    ..6) To analyze transcription factors which mediate the effects of genistein on prostate cancer. Specific Aim # 3...
  66. Pluripotent stem cell-derived HSCs: improvements and molecular mechanisms
    Patrick Cahan; Fiscal Year: 2013
    ..An extensive program of formal training, course-work, meetings with the advisory committee, and dedicated supervision and mentorship by Dr. Daley will ensure that these goals are achieved. ..
  67. The PKCepsilon-regulated oncogenic and tumor suppressor roles of ATF2 in melanoma
    ERIC KIRK LAU; Fiscal Year: 2013
    ..abstract_text> ..
  68. Epigenetic downregulation of the antibody response and inhibition of autoimmunity
    Paolo Casali; Fiscal Year: 2013
    ..upregulate miR-155, miR-181b, miR-93 to downregulate AID (central to CSR/SHM), miR- 146a to downregulate transcription factors Irf5 and (through Stat1) T-bet (important in CSR to IgG2a and lupus), miR-127 and miR-125b to downregulate ..
  69. Role of Membrane Modifications in the Bioactivities of Conjugated Linoleic Acids
    Papasani V Subbaiah; Fiscal Year: 2013
    ..inflammation are due to the altered membrane composition of ER, which in turn affects the activation of transcription factors including sterol regulatory element binding proteins (SREBPs), the master regulators of lipid metabolism...
  70. Role of poly (ADP-ribose) polymerase 1 (PARP-1) in experimental colitis
    Claire Larmonier; Fiscal Year: 2013 regulate the expression of diverse proinflammatory mediators, through its interaction with numerous transcription factors such as NF-kB and AP-1...
  71. Mechanisms of Cochlear Oxidative Stress Injury and Strategies to Protect Hearing
    Michael J Brenner; Fiscal Year: 2013
    ..This work will better define the role of cell membrane channels, transcription factors, and other molecular targets in gentamicin-induced hearing loss...
  72. Characterization of an essential mitochondrial rRNA methyltransferase
    Kip E Guja; Fiscal Year: 2013
    ..The goal of this proposal is to provide a more complete understanding of how TFB proteins influence disease pathogenesis by elucidating the roles that they play in mitochondrial gene expression. ..
  73. Regulation of Human Papillomavirus Replication via Cell Signaling Pathways
    ANASTACIA GRIEGO; Fiscal Year: 2013
    ..Based on previous studies indicating AP-1 transcription factors regulate HPV gene expression, we hypothesize that HPV infection establishes an intracellular feed-forward ..
  74. Mechanism of CREB dysregulation in Alzheimer brain
    Subbiah Pugazhenthi; Fiscal Year: 2013
    ..In this model, transcription factors provide a crucial link between signaling pathways and gene expression...
  75. Role of natural indoles in experimental autoimmune encephalomyelitis
    Mitzi Nagarkatti; Fiscal Year: 2013
    ..These studies should provide novel insights into the basic mechanisms through which plant indoles exhibit anti- inflammatory properties so that they can be used against a wide range of autoimmune and inflammatory diseases. ..
  76. Mechanisms in transcriptional regulation during cardiac hypertrophy
    Maha Abdellatif; Fiscal Year: 2013
    ..2) Determine the role of TFIIB in gene transcription and the development of cardiac hypertrophy. 3) Determine the role of Cdk9 in gene transcription and the development of cardiac hypertrophy. ..
    Yoshio Yamaoka; Fiscal Year: 2013
    ..Binding sites for the transcription factors nuclear factor-:B (NF-:B), activator protein 1 (AP-1), interferon-stimulated responsive element (ISRE)-..
  78. Dopamine D1 Receptor in mouse models of primary dystonia
    Laurie J Ozelius; Fiscal Year: 2013
    ..Identification of a final common pathway in different forms of EOTD will aid in directing discovery of therapeutic targets for this currently incurable disorder. ..
  79. New pathways regulating bile acid homeostasis and cholestatic liver diseases
    Li Wang; Fiscal Year: 2013
    ..Fully defining the regulation of bile acid metabolism, including bile acid synthesis and catabolism, is essential for further advances in diagnosis, management, and prevention of cholestatic liver diseases. ..
  80. Post-translational regulation of MLL in leukemogenesis
    ANDREW GEORGE MUNTEAN; Fiscal Year: 2013
    ..These studies focus on the MLL-PAFc interaction and ubiquitination of MLL which are directly relevant to MLL and HOX dependent leukemias and may prove as effective therapeutic targets. ..
  81. The RAGE of COPD
    John R Hoidal; Fiscal Year: 2013
    ..pathways that include NADPH oxidase(s) (Nox)-generated reactive oxygen species (ROS) activate key transcription factors including NF-B and EGR-1 to propagate the inflammation, apoptosis and lung destruction leading to ..
  82. Functional Studies of Variants of the Bipolar Risk Gene CACNA1C in Human Neurons
    JEN PAN; Fiscal Year: 2013
    ..fibroblasts have been directly converted to functional neuronal cells through ectopic expression of three transcription factors (ASCL1, MYT1L, BRN2)...
  83. Pluripotent Stem Cells: Modeling syncytiotrophoblast development and pathogenesis
    Danny J Schust; Fiscal Year: 2013 examine the molecular events controlling STB formation and lifespan, with an emphasis on the roles of transcription factors, such as GCM1 &GATA2, fusogenic proteins such syncytin-1 &-2 (ERVW1, ERVFRD-1, respectively) and a ..
  84. Mitochondrial Metabolism and ROS Regulate Lung Cancer
    Navdeep S Chandel; Fiscal Year: 2013
    ..serve as signaling molecules to activate numerous signaling pathways, including PI3K, ERK1/2 MAPK, and the transcription factors hypoxia inducible factors (HIFs), which promote tumor cell proliferation, angiogenesis, and metastasis...
  85. Regulation of ENaC Transcription
    Bruce C Kone; Fiscal Year: 2013
    ..The central hypothesis is that these responses depend on the dynamic and orchestrated action of key transcription factors and changes in the profile of chromatin modifiers and modifications that ultimately lead to expression of ?..
  86. Ligands and cofactors required for RORgt function in the immune system
    Dan Littman; Fiscal Year: 2013
    ..Together, these studies will provide a better understanding of the mechanism of action of RORyt and will facilitate new strategies for therapy in autoimmune diseases. ..
    Jason C Mills; Fiscal Year: 2013
    ..Thus, the experiments proposed may help us begin to understand stem cell response to injury in multiple tissues and diseases. Finally, our new finding that the key drug tamoxifen causes gastric toxicity warrants further study in humans. ..
  88. Mechanisms to restrain social cheating from quorum sensing in Pseudomonas aerugin
    AJAI DANDEKAR; Fiscal Year: 2013
    ..My project seeks to understand aspects of the evolution of the quorum sensing system, with an eye to manipulation of bacterial populations in chronic infections, particularly those of the disease cystic fibrosis. ..
  89. Role of Central Neural NFkB and ER Stress in Obesity-induced Hypertension
    COLIN NEAL YOUNG; Fiscal Year: 2013
    ..gene expression in central nervous system (CNS) cardiovascular neurons through the activation of inducible transcription factors, including nuclear factor kappa-B (NF?B)...
  90. Steroid-Based Contrast Agents for Magnetic Resonance Imaging of Endocrine Disease
    Thomas J Meade; Fiscal Year: 2013
    ..Progesterone and estrogen are steroid hormones that bind to their receptors and function as a transcription factors in the nucleus...
    Sally A Camper; Fiscal Year: 2013
    ..Addressing each of these hypotheses will lead to better molecular diagnoses and provide fundamental information on pituitary precursor cell generation and proliferation. ! ..
    Domenico Accili; Fiscal Year: 2013
    ..delve into the pathophysiology of hepatic insulin resistance, and specifically into the identification of transcription factors that cause the paradoxical admixture of increased glucose production and triglyceride synthesis that ..
    MARIA INES MORANO; Fiscal Year: 2013
    ..CYPs due to preferential nuclear receptor binding or interactions with other nuclear receptors or transcription factors. During Phase I of this study, we established SEAP reporter constructs for CYP1A2, CYP2B6, and CYP3A4 each ..
  94. FOXO1 Inhibition in Genotoxic Stress Response and Prostate Cancer Survival
    Haojie Huang; Fiscal Year: 2013
    ..Findings from this study will not only enhance our understanding of age-related prostate cancinogenesis, but could also provide new molecular targets to devise strategies for prostate cancer prevention and therapy. ..
  95. Epigenic Control of ENaC Transcription and Sodium Transport
    Wenzheng Zhang; Fiscal Year: 2013
  96. Mechanisms of ER stress - induced fatty liver
    D Thomas Rutkowski; Fiscal Year: 2013 will be placed into a hierarchy based on the ability of in vivo overexpression of key metabolic transcription factors to partially or fully rescue steatosis in Atf6[unreadable]-null mice...
  97. Epigenetic regulation in neuropathic pain
    Zhonghui Guan; Fiscal Year: 2013
    ..Indeed, in mice in which the CBP KIX domain is mutated so that the binding between CBP and transcription factors, including ATF, is greatly reduced, we found that nerve injury-induced mechanical hypersensitivity, key ..
  98. Biological Functions of Iron Responsive Elements
    Richard S Eisenstein; Fiscal Year: 2013
    ..abstract_text> ..
  99. ATF4 and Osteoclastogenesis
    Guozhi Xiao; Fiscal Year: 2013
    ..Successful completion of this study will provide a molecular basis for the development of new and more specific antiresorptive agents for treating these devastating diseases. ..
  100. Redox regulation in aging and failing heart
    Junichi Sadoshima; Fiscal Year: 2013
    ..sources, such as mitochondrial leakage and NAD(P)H oxidases (Noxs), oxidize signaling molecules and transcription factors. Noxs are major enzymes responsible for production of superoxide (O2-), a component of ROS, at various ..
  101. Renal Angiotensin II Receptor Function in Obesity
    Tahir Hussain; Fiscal Year: 2013
    ..Aim 1 will study the role of p38 MAP kinase and transcription factors IRF-1 and C/EBP2 in increasing AT2 receptor expression by high glucose concentrations in HK-2 cells;renal ..