dna binding proteins

Summary

Summary: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.

Top Publications

  1. 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
  2. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
  3. ncbi Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis
    Manuela Neumann
    Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Science 314:130-3. 2006
  4. ncbi ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    Shuhei Matsuoka
    Department of Genetics and Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 316:1160-6. 2007
  5. 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
  6. ncbi Foxp3 programs the development and function of CD4+CD25+ regulatory T cells
    Jason D Fontenot
    Howard Hughes Medical Institute, Department of Immunology, University of Washington, Box 357370, Seattle, WA 98195, USA
    Nat Immunol 4:330-6. 2003
  7. 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
  8. ncbi A Toll-like receptor recognizes bacterial DNA
    H Hemmi
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Suita
    Nature 408:740-5. 2000
  9. ncbi TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis
    Jemeen Sreedharan
    Department of Clinical Neuroscience, King s College London, Medical Research Council MRC Centre for Neurodegeneration Research, and Institute of Psychiatry, London, SE5 8AF, UK
    Science 319:1668-72. 2008
  10. 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

Research Grants

  1. Epithelial differentiation in cornea
    Bogi Andersen; Fiscal Year: 2012
  2. Hepatitis B virus replication and DDB1
    Betty L Slagle; Fiscal Year: 2013
  3. Role of poly (ADP-ribose) polymerase 1 (PARP-1) in experimental colitis
    Claire Larmonier; Fiscal Year: 2013
  4. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
  5. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
  6. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
  7. GENETICS OF DELAYED PUBERTY
    Lawrence C Layman; Fiscal Year: 2013
  8. Genome-wide measurement of bacterial transcriptional regulatory states
    Peter L Freddolino; Fiscal Year: 2013
  9. Regulation of Odorant Receptor Gene Expression
    Paul Feinstein; Fiscal Year: 2013
  10. Molecular Determinants of DNA Sliding and Hopping by a DNA Repair Glycosylase
    MENG MENG ROWLAND; Fiscal Year: 2013

Detail Information

Publications347 found, 100 shown here

  1. 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...
  2. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency...
  3. ncbi Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis
    Manuela Neumann
    Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Science 314:130-3. 2006
    ..TDP-43 represents the common pathologic substrate linking these neurodegenerative disorders...
  4. ncbi ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    Shuhei Matsuoka
    Department of Genetics and Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 316:1160-6. 2007
    ..This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals...
  5. 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...
  6. ncbi Foxp3 programs the development and function of CD4+CD25+ regulatory T cells
    Jason D Fontenot
    Howard Hughes Medical Institute, Department of Immunology, University of Washington, Box 357370, Seattle, WA 98195, USA
    Nat Immunol 4:330-6. 2003
    ..Furthermore, ectopic expression of Foxp3 confers suppressor function on peripheral CD4+CD25- T cells. Thus, Foxp3 is a critical regulator of CD4+CD25+ regulatory T cell development and function...
  7. 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
    ..These findings establish a central role for Nanog in the transcription factor hierarchy that defines ES cell identity...
  8. ncbi A Toll-like receptor recognizes bacterial DNA
    H Hemmi
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Suita
    Nature 408:740-5. 2000
    ..The in vivo CpG-DNA-mediated T-helper type-1 response was also abolished in TLR9-/- mice. Thus, vertebrate immune systems appear to have evolved a specific Toll-like receptor that distinguishes bacterial DNA from self-DNA...
  9. ncbi TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis
    Jemeen Sreedharan
    Department of Clinical Neuroscience, King s College London, Medical Research Council MRC Centre for Neurodegeneration Research, and Institute of Psychiatry, London, SE5 8AF, UK
    Science 319:1668-72. 2008
    ..Mutant forms of TDP-43 fragmented in vitro more readily than wild type and, in vivo, caused neural apoptosis and developmental delay in the chick embryo. Our evidence suggests a pathophysiological link between TDP-43 and ALS...
  10. 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...
  11. 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...
  12. 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
    ..Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell...
  13. ncbi Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2
    R E Amir
    Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Genet 23:185-8. 1999
    ..This suggests that the mother is a germline mosaic for this mutation. Our study reports the first disease-causing mutations in RTT and points to abnormal epigenetic regulation as the mechanism underlying the pathogenesis of RTT...
  14. ncbi DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation
    Christopher J Bakkenist
    Department of Hematology Oncology, St Jude Children s Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105, USA
    Nature 421:499-506. 2003
    ....
  15. ncbi A DNA damage checkpoint response in telomere-initiated senescence
    Fabrizio d'Adda di Fagagna
    1 The Wellcome Trust Cancer Research UK Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge CB2 1QR, UK 2 Present address IFOM FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
    Nature 426:194-8. 2003
    ..Thus, we propose that telomere-initiated senescence reflects a DNA damage checkpoint response that is activated with a direct contribution from dysfunctional telomeres...
  16. ncbi The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells
    Kaoru Mitsui
    Laboratory of Animal Molecular Technology, Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Nara 630 0192, Japan
    Cell 113:631-42. 2003
    ..nanog-deficient ES cells lost pluripotency and differentiated into extraembryonic endoderm lineage. These data demonstrate that Nanog is a critical factor underlying pluripotency in both ICM and ES cells...
  17. ncbi Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes
    Lee Zou
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Science 300:1542-8. 2003
    ..Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling...
  18. ncbi TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis
    Edor Kabashi
    Center of Excellence in Neuromics, Centre Hospitalier de l Universite de Montreal, and Department of Medicine, University of Montreal, Montreal, Quebec H2L4MI, Canada
    Nat Genet 40:572-4. 2008
    ..These findings further corroborate that TDP-43 is involved in ALS pathogenesis...
  19. 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...
  20. 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
    ..Further, our observations suggest the existence of additional, as-yet-unknown, key regulators of the UPR...
  21. 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
    ..Within the nucleus, FKHRL1 triggers apoptosis most likely by inducing the expression of genes that are critical for cell death, such as the Fas ligand gene...
  22. ncbi TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis
    Tetsuaki Arai
    Department of Psychogeriatrics, Tokyo Institute of Psychiatry, Setagaya Ku, Tokyo 156 8585, Japan
    Biochem Biophys Res Commun 351:602-11. 2006
    ....
  23. pmc Multipotent cell lineages in early mouse development depend on SOX2 function
    Ariel A Avilion
    Division of Developmental Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Genes Dev 17:126-40. 2003
    ..5 days postcoitum. Our data suggest that maternal components could be involved in establishing early cell fate decisions and that a combinatorial code, requiring SOX2 and OCT4, specifies the first three lineages present at implantation...
  24. 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...
  25. pmc Human CtIP promotes DNA end resection
    Alessandro A Sartori
    The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nature 450:509-14. 2007
    ..These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination...
  26. ncbi Stats: transcriptional control and biological impact
    David E Levy
    Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
    Nat Rev Mol Cell Biol 3:651-62. 2002
    ..In addition to several roles in normal cell decisions, dysregulation of STAT function contributes to human disease, making the study of these proteins an important topic of current research...
  27. ncbi Control of regulatory T cell development by the transcription factor Foxp3
    Shohei Hori
    Laboratory of Immunopathology, Research Center for Allergy and Immunology, Institute for Physical and Chemical Research, Yokohama 230 0045, Japan
    Science 299:1057-61. 2003
    ..Thus, Foxp3 is a key regulatory gene for the development of regulatory T cells...
  28. ncbi Extension of life-span by introduction of telomerase into normal human cells
    A G Bodnar
    Geron Corporation, Menlo Park, CA 94025, USA
    Science 279:349-52. 1998
    ..The ability to maintain normal human cells in a phenotypically youthful state could have important applications in research and medicine...
  29. ncbi DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis
    Jirina Bartkova
    Institute of Cancer Biology and Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, DK 2100 Copenhagen, Denmark
    Nature 434:864-70. 2005
    ..Mutations compromising this checkpoint, including defects in the ATM-Chk2-p53 pathway, might allow cell proliferation, survival, increased genomic instability and tumour progression...
  30. ncbi DNA double-strand breaks: signaling, repair and the cancer connection
    K K Khanna
    The Queensland Institute of Medical Research, and Department of Pathology, University of Queensland, PO Royal Brisbane Hospital, Brisbane, Queensland, Australia
    Nat Genet 27:247-54. 2001
    ..Moreover, we discuss how tumor suppressor proteins such as p53, ATM, Brca1 and Brca2 have been linked to such pathways, and how accumulating evidence is connecting deficiencies in cellular responses to DNA DSBs with tumorigenesis...
  31. ncbi Functional interaction of beta-catenin with the transcription factor LEF-1
    J Behrens
    Max Delbruck Centre for Molecular Medicine, Berlin, Germany
    Nature 382:638-42. 1996
    ..Thus beta-catenin regulates gene expression by direct interaction with transcription factors such as LEF-1, providing a molecular mechanism for the transmission of signals, from cell-adhesion components or wnt protein to the nucleus...
  32. ncbi TGF-beta signal transduction
    J Massague
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Annu Rev Biochem 67:753-91. 1998
    ..Mutations in these pathways are the cause of various forms of human cancer and developmental disorders...
  33. ncbi The transcription factor snail is a repressor of E-cadherin gene expression in epithelial tumour cells
    E Batlle
    Unitat de Biologia Cel lular i Molecular, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Spain
    Nat Cell Biol 2:84-9. 2000
    ..Inhibition of Snail function in epithelial cancer cell lines lacking E-cadherin protein restores the expression of the E-cadherin gene...
  34. pmc Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions
    Adrian P Bracken
    Biotech Research and Innovation Centre BRIC, 2100 Copenhagen Ø, Denmark
    Genes Dev 20:1123-36. 2006
    ....
  35. ncbi A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage
    T T Paull
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0540, USA
    Curr Biol 10:886-95. 2000
    ..Recently it has been reported that a member of the histone H2A family, H2AX, becomes extensively phosphorylated within 1-3 minutes of DNA damage and forms foci at break sites...
  36. ncbi TGF-beta signalling from cell membrane to nucleus through SMAD proteins
    C H Heldin
    Ludwig Institute for Cancer Research, Biomedical Centre, Uppsala, Sweden
    Nature 390:465-71. 1997
    ..Inhibitory SMADs have been identified that block the activation of these pathway-restricted SMADs...
  37. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
    ..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
  38. ncbi Stat3 as an oncogene
    J F Bromberg
    Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021 6399, USA
    Cell 98:295-303. 1999
    ..Thus, the activated Stat3 molecule by itself can mediate cellular transformation and the experiments focus attention on the importance of constitutive Stat3 activation in human tumors...
  39. ncbi LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1
    S Hacein-Bey-Abina
    INSERM Unit 429, Cedex 15, France
    Science 302:415-9. 2003
    ..Thus, retrovirus vector insertion can trigger deregulated premalignant cell proliferation with unexpected frequency, most likely driven by retrovirus enhancer activity on the LMO2 gene promoter...
  40. ncbi Active genes are tri-methylated at K4 of histone H3
    Helena Santos-Rosa
    Wellcome Trust Cancer Research UK Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QR, UK
    Nature 419:407-11. 2002
    ..These findings establish the concept of methyl status as a determinant for gene activity and thus extend considerably the complexity of histone modifications...
  41. pmc EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells
    Celina G Kleer
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 100:11606-11. 2003
    ..This study provides compelling evidence for a functional link between dysregulated cellular memory, transcriptional repression, and neoplastic transformation...
  42. ncbi ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin
    Aaron A Goodarzi
    Genome Damage and Stability Centre, University of Sussex, East Sussex BN1 9RQ, UK
    Mol Cell 31:167-77. 2008
    ..These data suggest that the importance of ATM signaling for DSB repair increases as the heterochromatic component of a genome expands...
  43. ncbi STATs and gene regulation
    J E Darnell
    Laboratory of Molecular Cell Biology, Rockefeller University, New York, NY 10021, USA
    Science 277:1630-5. 1997
    ..The discovery of a STAT in Drosophila, and most recently in Dictyostelium discoideum, implies an ancient evolutionary origin for this dual-function set of proteins...
  44. ncbi Role of histone H2A ubiquitination in Polycomb silencing
    Hengbin Wang
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7295, USA
    Nature 431:873-8. 2004
    ..Thus, our studies identify the H2A ubiquitin ligase, and link H2A ubiquitination to Polycomb silencing...
  45. ncbi Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer
    Martin F Lavin
    Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
    Nat Rev Mol Cell Biol 9:759-69. 2008
    ....
  46. 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...
  47. ncbi The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Yuin Han Loh
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Nat Genet 38:431-40. 2006
    ..The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination...
  48. ncbi SOX2 functions to maintain neural progenitor identity
    Victoria Graham
    Neuroscience Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
    Neuron 39:749-65. 2003
    ..Taken together, these data indicate that SOXB1 signaling is both necessary and sufficient to maintain panneural properties of neural progenitor cells...
  49. pmc PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways
    Minli Wang
    University of Duisburg Essen, Medical School, Institute of Medical Radiation Biology, Hufeland Street 55, 45122 Essen, Germany
    Nucleic Acids Res 34:6170-82. 2006
    ..This form of DSB repair is sensitive to PARP-1 inhibitors. The results define the function of PARP-1 in DSB repair and characterize a candidate pathway responsible for joining errors causing genomic instability and cancer...
  50. ncbi DNA repair by ERCC1 in non-small-cell lung cancer and cisplatin-based adjuvant chemotherapy
    Ken A Olaussen
    Laboratory of Radiobiology and Oncology, Commissariat a l Energie Atomique, Fontenay aux Roses, University of Paris 11, Paris, France
    N Engl J Med 355:983-91. 2006
    ..Adjuvant cisplatin-based chemotherapy improves survival among patients with completely resected non-small-cell lung cancer, but there is no validated clinical or biologic predictor of the benefit of chemotherapy...
  51. pmc Conversion of peripheral CD4+CD25- naive T cells to CD4+CD25+ regulatory T cells by TGF-beta induction of transcription factor Foxp3
    Wanjun Chen
    Cellular Immunology Section, Oral Infection and Immunity Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
    J Exp Med 198:1875-86. 2003
    ..Finally, in a murine asthma model, coadministration of these TGF-beta-induced suppressor T cells prevented house dust mite-induced allergic pathogenesis in lungs...
  52. ncbi Protection of telomeres through independent control of ATM and ATR by TRF2 and POT1
    Eros Lazzerini Denchi
    Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 448:1068-71. 2007
    ..The results reveal how mammalian telomeres use multiple mechanisms to avoid DNA damage surveillance and provide an explanation for the induction of replicative senescence and genome instability by shortened telomeres...
  53. 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
    ..These results have implications in the development of carcinomas and the molecular diagnosis and treatment of prostate cancer...
  54. 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
    ....
  55. ncbi Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls
    R J Kaufman
    Department of Biological Chemistry and Howard Hughes Medical Institute, The University of Michigan Medical Center, Ann Arbor, Michigan 48109 0650 USA
    Genes Dev 13:1211-33. 1999
  56. ncbi Histone methyltransferase activity of a Drosophila Polycomb group repressor complex
    Jurg Muller
    EMBL, Gene Expression Programme, Meyerhofstr 1, 69117 Heidelberg, Germany
    Cell 111:197-208. 2002
    ..These results identify E(Z) as a PcG protein with enzymatic activity and implicate histone methylation in PcG-mediated silencing...
  57. ncbi Mechanisms of TGF-beta signaling from cell membrane to the nucleus
    Yigong Shi
    Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
    Cell 113:685-700. 2003
    ..This article reviews these latest advances and presents our current understanding on the mechanisms of TGF-beta signaling from cell membrane to the nucleus...
  58. pmc PRDM16 controls a brown fat/skeletal muscle switch
    Patrick Seale
    Dana Farber Cancer Institute and the Department of Cell Biology, Harvard Medical School, 1 Jimmy Fund Way, Boston, Massachusetts 02115, USA
    Nature 454:961-7. 2008
    ..Taken together, these data indicate that PRDM16 specifies the brown fat lineage from a progenitor that expresses myoblast markers and is not involved in white adipogenesis...
  59. ncbi ATM and related protein kinases: safeguarding genome integrity
    Yosef Shiloh
    The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Nat Rev Cancer 3:155-68. 2003
    ..Understanding ATM's mode of action provides new insights into the association between defective responses to DNA damage and cancer, and brings us closer to resolving the issue of cancer predisposition in some A-T carriers...
  60. pmc Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability
    Asad Umar
    Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    J Natl Cancer Inst 96:261-8. 2004
    ....
  61. ncbi Regulation of DNA double-strand break repair pathway choice
    Meena Shrivastav
    Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine and Cancer Center, Albuquerque, NM 87131, USA
    Cell Res 18:134-47. 2008
    ....
  62. pmc Rethinking ALS: the FUS about TDP-43
    Clotilde Lagier-Tourenne
    Department of Cellular and Molecular Medicine, University of California San Diego, Ludwig Institute for Cancer Research, La Jolla, CA 92093 0670, USA
    Cell 136:1001-4. 2009
    ..TDP-43 and FUS/TLS have striking structural and functional similarities, implicating alterations in RNA processing as a key event in ALS pathogenesis...
  63. ncbi Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice
    R Z Chen
    The Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 27:327-31. 2001
    ..Mecp2 deficiency in these neurons is sufficient to cause neuronal dysfunction with symptomatic manifestation similar to Rett syndrome...
  64. ncbi ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs
    J Ye
    Department of Molecular Genetics, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
    Mol Cell 6:1355-64. 2000
    ..ATF6 processing did not require SCAP, which is essential for SREBP processing. We conclude that S1P and S2P are required for the ER stress response as well as for lipid synthesis...
  65. ncbi DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression
    D K Bishop
    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
    Cell 69:439-56. 1992
    ..DMC1 is homologous to yeast's RAD51 gene, supporting the view that mitotic DSB repair has been recruited for use in meiotic chromosome metabolism...
  66. pmc SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins
    David C Schultz
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 16:919-32. 2002
    ..Thus, KAP-1 is a molecular scaffold that is targeted by KRAB-ZFPs to specific loci and coordinates both histone methylation and the deposition of HP1 proteins to silence gene expression...
  67. ncbi Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
    X Nan
    Institute of Cell and Molecular Biology, University of Edinburgh, UK
    Nature 393:386-9. 1998
    ..The data suggest that two global mechanisms of gene regulation, DNA methylation and histone deacetylation, can be linked by MeCP2...
  68. pmc XRCC3 promotes homology-directed repair of DNA damage in mammalian cells
    A J Pierce
    Cell Biology Program, Memorial Sloan Kettering Cancer Center and Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
    Genes Dev 13:2633-8. 1999
    ..These results establish that XRCC3-mediated homologous recombination can reverse DNA damage that would otherwise be mutagenic or lethal...
  69. 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
    ....
  70. pmc Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress
    K Haze
    HSP Research Institute, Kyoto Research Park, Shimogyo ku, Kyoto 600 8813, Japan
    Mol Biol Cell 10:3787-99. 1999
    ..Unlike yeast UPR, mammalian UPR appears to use a system similar to that reported for cholesterol homeostasis...
  71. ncbi How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
    Sean D Taverna
    Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
    Nat Struct Mol Biol 14:1025-40. 2007
    ..Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer...
  72. ncbi Cancer susceptibility and the functions of BRCA1 and BRCA2
    Ashok R Venkitaraman
    University of Cambridge, CRC Department of Oncology, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
    Cell 108:171-82. 2002
    ..Here, I examine what is known about the biological functions of the BRCA proteins and ask how their disruption can induce susceptibility to specific types of cancer...
  73. ncbi STATs in oncogenesis
    T Bowman
    Molecular Oncology Program, H Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida, FL 33612, USA
    Oncogene 19:2474-88. 2000
    ..This review presents the evidence for critical roles of STATs in oncogenesis and discusses the potential for development of novel cancer therapies based on mechanistic understanding of STAT signaling. Oncogene (2000)...
  74. pmc The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6
    Haruhiko Akiyama
    Department of Molecular Genetics, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Genes Dev 16:2813-28. 2002
    ..We conclude that Sox9 is required during sequential steps of the chondrocyte differentiation pathway...
  75. ncbi Human DNA repair genes
    R D Wood
    Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
    Science 291:1284-9. 2001
    ..Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process...
  76. ncbi A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome
    J Guy
    Wellcome Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, The King s Buildings, Edinburgh, UK
    Nat Genet 27:322-6. 2001
    ....
  77. ncbi Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair
    J R Walker
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 412:607-14. 2001
    ..These features seem well designed to structurally support broken DNA ends and to bring the DNA helix into phase across the junction during end processing and ligation...
  78. pmc Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element
    M Ohme-Takagi
    Plant Molecular Biology Laboratory, National Institute of Bioscience and Human Technology, Ibaraki, Japan
    Plant Cell 7:173-82. 1995
    ..Four different cDNAs encoding DNA binding proteins specific for the GCC box sequence were isolated, and their products were designated ethylene-responsive ..
  79. pmc Orchestrating the unfolded protein response in health and disease
    Randal J Kaufman
    Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan Medical Center, Ann Arbor 48109 0650, USA
    J Clin Invest 110:1389-98. 2002
  80. pmc XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease
    Arthur Kaser
    Division of Gastroenterology, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
    Cell 134:743-56. 2008
    ..Hence, intestinal inflammation can originate solely from XBP1 abnormalities in IECs, thus linking cell-specific ER stress to the induction of organ-specific inflammation...
  81. ncbi Interleukin 17-producing CD4+ effector T cells develop via a lineage distinct from the T helper type 1 and 2 lineages
    Laurie E Harrington
    Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Nat Immunol 6:1123-32. 2005
    ..These findings provide a basis for understanding how inhibition of IFN-gamma signaling enhances development of pathogenic T(H)-17 effector cells that can exacerbate autoimmunity...
  82. ncbi IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway
    Katherine A Fitzgerald
    Division of Infectious Disease and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nat Immunol 4:491-6. 2003
    ..Thus, IKKepsilon and TBK1 have a pivotal role in coordinating the activation of IRF3 and NF-kappaB in the innate immune response...
  83. ncbi Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis
    T J Kwiatkowski
    Department of Neurology, Massachusetts General Hospital, 114 16th Street, Charlestown, MA 02129, USA
    Science 323:1205-8. 2009
    ..Neuronal cytoplasmic protein aggregation and defective RNA metabolism thus appear to be common pathogenic mechanisms involved in ALS and possibly in other neurodegenerative disorders...
  84. ncbi Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6
    Caroline Vance
    Department of Clinical Neuroscience, King s College London, Medical Research Council MRC Centre for Neurodegeneration Research, Institute of Psychiatry, London SE5 8AF, UK
    Science 323:1208-11. 2009
    ..FUS is involved in the regulation of transcription and RNA splicing and transport, and it has functional homology to another ALS gene, TARDBP, which suggests that a common mechanism may underlie motor neuron degeneration...
  85. 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
    ....
  86. ncbi Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway
    Masahiro Yamamoto
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3 1 Yamada oka, Suita Osaka 565 0871, Japan
    Science 301:640-3. 2003
    ..These findings demonstrate that TRIF is essential for TLR3- and TLR4-mediated signaling pathways facilitating mammalian antiviral host defense...
  87. ncbi Activation of the ATM kinase by ionizing radiation and phosphorylation of p53
    C E Canman
    The Johns Hopkins School of Medicine, Oncology Center, Baltimore, MD 21205, USA
    Science 281:1677-9. 1998
    ..These observations, along with the fact that phosphorylation of p53 on serine-15 in response to ionizing radiation is reduced in ataxia telangiectasia cells, suggest that ATM is a protein kinase that phosphorylates p53 in vivo...
  88. ncbi Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription
    P L Jones
    Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institute of Health, Bethesda, Maryland 20892 5431, USA
    Nat Genet 19:187-91. 1998
    ..These results establish a direct causal relationship between DNA methylation-dependent transcriptional silencing and the modification of chromatin...
  89. ncbi Enhanced phosphorylation of p53 by ATM in response to DNA damage
    S Banin
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Science 281:1674-7. 1998
    ..Various damage-induced responses may be activated by enhancement of the protein kinase activity of ATM...
  90. ncbi RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement
    Y Shinkai
    Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, New York 10032
    Cell 68:855-67. 1992
    ..Because the SCID phenotype was the only obvious abnormality detected in RAG-2 mutant mice, RAG-2 function and V(D)J recombinase activity, per se, are not required for development of cells other than lymphocytes...
  91. ncbi Plasma cell differentiation requires the transcription factor XBP-1
    A M Reimold
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Nature 412:300-7. 2001
    ..XBP-1 is the only transcription factor known to be selectively and specifically required for the terminal differentiation of B lymphocytes to plasma cells...
  92. ncbi XBP1, downstream of Blimp-1, expands the secretory apparatus and other organelles, and increases protein synthesis in plasma cell differentiation
    A L Shaffer
    Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Immunity 21:81-93. 2004
    ..Thus, XBP1 coordinates diverse changes in cellular structure and function resulting in the characteristic phenotype of professional secretory cells...
  93. 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
    ..Snail may thus be considered as a marker for malignancy, opening up new avenues for the design of specific anti-invasive drugs...
  94. ncbi Mechanism of eukaryotic homologous recombination
    Joseph San Filippo
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Annu Rev Biochem 77:229-57. 2008
    ..Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here...
  95. ncbi The NF-kappa B and I kappa B proteins: new discoveries and insights
    A S Baldwin
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill 27599, USA
    Annu Rev Immunol 14:649-83. 1996
    ....
  96. ncbi Double chromodomains cooperate to recognize the methylated histone H3 tail
    John F Flanagan
    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
    Nature 438:1181-5. 2005
    ..Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction...
  97. ncbi Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
    A C Bell
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0540, USA
    Nature 405:482-5. 2000
    ..Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary...
  98. ncbi Signalling downstream of activated mammalian Notch
    S Jarriault
    Unité de Biologie Moléculaire de l Expression Génique, URA 1149 CNRS, Institut Pasteur, Paris, France
    Nature 377:355-8. 1995
    ..Here we show that activated forms of mNotch associate with the human analogue of Su(H), KBF2/RBP-J kappa (refs 8,9) and act as transcriptional activators through the KBF2-binding sites of the HES-1 promoter...
  99. ncbi Genomic DNA methylation: the mark and its mediators
    Robert J Klose
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
    Trends Biochem Sci 31:89-97. 2006
    ..Recent studies have illuminated the role of DNA methylation in controlling gene expression and have strengthened its links with histone modification and chromatin remodelling...
  100. ncbi UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex
    Kaoru Sugasawa
    Cellular Physiology Laboratory, RIKEN Discovery Research Institute, Japan Science and Technology Agency, Wako, Saitama 351 0198, Japan
    Cell 121:387-400. 2005
    ..Our results strongly suggest that ubiquitylation plays a critical role in the transfer of the UV-induced lesion from UV-DDB to XPC...
  101. ncbi A road map for those who don't know JAK-STAT
    David S Aaronson
    Department of Pharmacology and Biological Chemistry, Immunobiology Center, Mount Sinai School of Medicine, New York, NY 10029 USA
    Science 296:1653-5. 2002
    ..In addition, the JAK-STAT signaling pathways are regulated by a vast array of intrinsic and environmental stimuli, which can add plasticity to the response of a cell or tissue...

Research Grants70

  1. Epithelial differentiation in cornea
    Bogi Andersen; Fiscal Year: 2012
    ....
  2. Hepatitis B virus replication and DDB1
    Betty L Slagle; Fiscal Year: 2013
    ..This important new knowledge will reveal virus-induced changes at the post-translational level, and is predicted to provide mechanistic insight into new strategies through which to treat chronic HBV infection and prevent liver disease. ..
  3. Role of poly (ADP-ribose) polymerase 1 (PARP-1) in experimental colitis
    Claire Larmonier; Fiscal Year: 2013
    ..Those specific aims will help address the following hypothesis: PARP1 contributes to aggravated mucosal immune response via modulation of inflammatory signaling pathways within the cells of the innate immune system. ..
  4. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
    ..These small molecules achieve affinities and specificities of DNA binding proteins, inhibit DNA binding of a broad range of transcription factors, localize to the cell nucleus, bind to ..
  5. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..More detailed understanding of EBNA1 is further justified by its potential value as a target for therapeutic intervention in diseases and cancers associated with EBV latent infection. ..
  6. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
    ....
  7. GENETICS OF DELAYED PUBERTY
    Lawrence C Layman; Fiscal Year: 2013
    ..We hope to understand how mutations in two genes (CHD7 and NELF) disrupt puberty and cause infertility in humans. These human studies will be complemented by experiments in relevant cell types and an animal model. ..
  8. Genome-wide measurement of bacterial transcriptional regulatory states
    Peter L Freddolino; Fiscal Year: 2013
    ..throughout the genome, is then split during data processing into contributions from different TFs and other DNA binding proteins, using a computational method that is currently under development...
  9. Regulation of Odorant Receptor Gene Expression
    Paul Feinstein; Fiscal Year: 2013
    ..The identification of more candidate DNA binding proteins and their interactions is necessary to understand the "singular choice" process...
  10. Molecular Determinants of DNA Sliding and Hopping by a DNA Repair Glycosylase
    MENG MENG ROWLAND; Fiscal Year: 2013
    ..These peptides will be derived from several DNA binding proteins (p53, HOXD9, H3), and are chosen because they represent various sizes and overall charge, and are known to ..
  11. Astrocyte Development and Reactive Gliosis
    Teri L Belecky-Adams; Fiscal Year: 2012
    ....
  12. ALS therapies and genomics for mutant TDP-43 and TLS/FUS
    Don W Cleveland; Fiscal Year: 2010
    ..New, very high through put DNA/RNA sequencing methods will be used to identify genes whose expression is altered by the mutations, thereby identifying new targets and approaches for devising a successful therapy for ALS. ..
  13. Epigenetic mechanisms of TDP43-mediated neurodegeneration
    Amit Berson; Fiscal Year: 2013
    ....
  14. Transcriptional Regulation by a Deacetylase, CobB, in a Periodontopathogen
    DAVID J KOLODRUBETZ; Fiscal Year: 2013
    ..Importantly, since CobB is an NAD+-dependent deacetylase, our results would also suggest that there is a possible new connection between physiology (NAD levels) and transcriptional regulation (acetylation) in bacteria. ..
  15. Novel immunotherapeutics for the management of otitis media due to H. influenzae
    Steven D Goodman; Fiscal Year: 2013
    ..e. hearing loss due to OM), a goal of Strategic Plan Priority Area I. ..
  16. Transcriptional regulation of enteroendocrine cell differentiation by NeuroD
    Andrew B Leiter; Fiscal Year: 2013
    ..activation by NeuroD is not well characterized but preliminary results indicate interactions with other DNA binding proteins, CtBP, and the histone modifying enzyme, lysine specific demethylase 1 (LSD1) are involved...
  17. Transcriptional Networks Regulating Luminal Environment in the Epididymis
    Ann Harris; Fiscal Year: 2013
    ..Through modulation of this environment we may also be able to inhibit normal sperm maturation and thereby develop novel methods of birth control. ..
  18. GENETIC ASPECTS OF DNA METHYLATION
    Eric U Selker; Fiscal Year: 2012
    ..Finally, we will follow up our observations suggesting that histone demethylases influence DNA methylation. ..
  19. Small Molecule Probes for TAR DNA Binding Protein 43_TDP-43
    Allen B Reitz; Fiscal Year: 2012
    ....
  20. Targeted epigenetic silencing of oncogenic Transcription Factors (PQ18)
    Pilar Blancafort; Fiscal Year: 2013
    ..Thus, this work will be of vital importance to develop stable, inherited, oncogenic silencing methods, to suppress oncogenic expression in tumor cells. ..
  21. Regulators of Cancer-Specific DNA Hypermethylation.
    Jean Pierre J Issa; Fiscal Year: 2013
    ..difference is that an interplay between local sequence features (repeat elements, recognition sites for DNA binding proteins) and baseline chromatin states (histone modifications) related to developmental transcription programs ..
  22. Multilevel Targeted Therapeutics Using Surface Functionalized Nanoparticles encap
    JILL STEINBACH; Fiscal Year: 2012
    ..I expect this approach will improve current HSV-2 therapy and can be extended to multiple STD combinations, including elusive viruses such as HIV. ..
  23. Development of Novel Agents Targeting Genome Stability and Maintenance for Treati
    John J Turchi; Fiscal Year: 2013
    ..Successful completion of these studies will support a phase II STTR application to pursue Investigational New Drug (IND)-enabling studies, including expanded safety, toxicity, and efficacy studies. ..
  24. Role of the developmental regulator Gon4-like in B lymphopoiesis
    JOHN D COLGAN; Fiscal Year: 2011
    ..Further, the knowledge gained will provide new insights regarding the fundamental processes that contribute to immune dysfunction or the development of lymphoid cancers. ..
  25. DETERMINATION OF NEURONAL FATES IN VISUAL CORTEX
    Susan K McConnell; Fiscal Year: 2013
    ..The goals of our research are to identify the genes that regulate neurogenesis in the visual cortex and to understand how they affect the formation of cortical circuitry. ..
  26. STRUCTURAL STUDIES OF NUCLEOPROTEIN COMPLEXES
    Edward H Egelman; Fiscal Year: 2012
    ..II) Determination of the structure of the filaments formed by viral single-stranded DNA binding proteins. The initial focus will be on Herpes Simplex Type 1 Virus (HSV-1) ICP8, but will then be extended to ..
  27. Inhibition of Stat3 and inflammatory cytokine production
    Lionel B Ivashkiv; Fiscal Year: 2013
    ..We anticipate that these studies will yield insights about specific regulation of subsets of TLR-inducible cytokines and genes that will be useful in developing therapeutic approaches to modulate specific innate immune functions. ..
  28. Analysis of intestinal genes regulated by the transcription factor CDX2
    Ramesh A Shivdasani; Fiscal Year: 2013
    ..Investigation of its regulatory functions will improve understanding and, ultimately, treatment of many common GI diseases. ..
  29. Amphetamine-Induced Transcriptional Plasticity in Striatal GABAergic Interneurons
    ANNE ELIZABETH WEST; Fiscal Year: 2013
    ..abstract_text> ..
  30. Assay Development for Inhibitors of KSHV
    Paul M Lieberman; Fiscal Year: 2010
    ..Finally, this research may provide therapeutic strategies for related tumor viruses, especially EBV and human papillomavirus (HPV), which possess LANA-like orthologues. ..
  31. Regulatory Mechanisms Controlling Expression of P. gingivalis Surface Structures
    MARY ELLEN DAVEY; Fiscal Year: 2013
    ..gingivalis. These mechanisms are in essence an "Achilles heel" that can be used as a target to stop the injury caused by this bacterium. ..
  32. Regulation of Nucleotide Excision Repair by Proteolysis
    Pengbo Zhou; Fiscal Year: 2013
    ..4A (CUL-4A) ubiquitin ligase has recently emerged as a key regulator of two DNA damage sensors: the damaged DNA binding proteins (DDBs, heterodimers of DDB1 and DDB2) and xeroderma pigmentosum complementation group C (XPC) protein...
  33. A Conserved G-rich Region within Human TH Promoter Regulates Its Activity
    Soumitra Basu; Fiscal Year: 2011
    ....
  34. Illumina Sequencer to Facilitate Functional Genomics at Berkeley
    John W Taylor; Fiscal Year: 2010
    ..investigators have developed new sequencing-based techniques to characterize the in vitro affinity of DNA binding proteins to their targets, and to rationally evolve proteins to have desired functions...
  35. Hepatoma derived growth factor and vascular smooth muscle cell proliferation
    Allen D Everett; Fiscal Year: 2010
    ..We propose here to determine the mechanism regulating the activity of this protein to provide the basis for the future design of new drugs to treat cardiovascular disease. ..
  36. HMGB1 and neutrophil efferocytosis.
    JAROSLAW WALDEMAR ZMIJEWSKI; Fiscal Year: 2012
    ....
  37. Regulation of Cocaine Reward and Reinforcement by MeCP2
    ANNE ELIZABETH WEST; Fiscal Year: 2013
    ..These studies promise to yield significant new insights into the neurobiological mechanisms that impact susceptibility to cocaine addiction. ..
  38. Tumor-cell-specific targets for combined hyperthermia and radiation effects
    Tej K Pandita; Fiscal Year: 2013
    ..If the proposed research is successfully carried out, the novel information generated from the proposed studies will be useful in designing tumor specific therapies. ..
  39. Using Microfluidic Affinity Analysis to Probe Transcriptional Regulation
    POLLY MORRELL FORDYCE; Fiscal Year: 2013
    ..interactions between transcription factors and target sequences to the nucleation of assemblies of DNA binding proteins at regulatory loci...
  40. New players in immune function: identification through RNAi and micro-RNA screens
    Anjana Rao; Fiscal Year: 2010
    ..This important resource would be broadly available to the general scientific community. ..
  41. RovA regulon and virulence of Yersinia enterocolitica
    Virginia L Miller; Fiscal Year: 2012
    ..This will expand our understanding and ability to intervene therapeutically not only with Yersinia but with many other gastrointestinal pathogens as well. ..
  42. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..We expect our research to ultimately catalyze numerous studies by us and other laboratories leading to a better understanding of E. coli biology at a molecular level and provide a framework for similar studies in other organisms. ..
  43. Histone Deacetylases and Kidney Development
    Samir S El Dahr; Fiscal Year: 2010
    ..Thus, understanding the epigenetic regulation of kidney development may open new avenues to the treatment or prevention of kidney and urinary tract malformations and kidney failure. ..
  44. Function of MTG16/ETO2 in acute leukemia
    SCOTT HIEBERT; Fiscal Year: 2010
    ..members are nuclear proteins that appear to function as transcriptional co-repressors that link regulatory DNA binding proteins to histone modifying enzymes to repress and/or silence gene expression...
  45. TOX, a Novel Regulator of Thymocyte Selection
    JONATHAN G KAYE; Fiscal Year: 2013
    ....
  46. Tumor Progression of Nuclear EGFR in Breast Cancer
    Mien Chie Hung; Fiscal Year: 2013
    ....
  47. Development of a protein-driven gene targeting technology
    Francesca Storici; Fiscal Year: 2010
    ....
  48. Defining Mechanisms of TDP-43 Ubiquitination for Quality Control and Aggregation
    ERIC BERNARD DAMMER; Fiscal Year: 2012
    ....
  49. TDP-43 acetylation as a pathogenic modification in ALS &related proteinopathies
    TODD JONATHAN COHEN; Fiscal Year: 2013
    ..These innovative studies will highlight TDP-43 acetylation as a critical modification linked to the progression of ALS and related TDP-43 proteinopathies. ..
  50. Genetic Analysis of Snail Superfamily Genes in Mice
    THOMAS HOOKER GRIDLEY; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Snail superfamily genes encode zinc finger-containing DNA binding proteins that act as transcriptional repressors...
  51. SOLID STATE RADIATION CHEMISTRY OF DNA
    Jeffrey J Hayes; Fiscal Year: 2012
    ..by which these DNA lesions are formed, and (iii) evaluate how molecules such as histones and other DNA binding proteins modulate the yield and distribution of these DNA lesions...
  52. Targeting stromal reaction in pancreatic cancer to overcome chemo-resistance
    Hidayatullah G Munshi; Fiscal Year: 2013
    ..abstract_text> ..
  53. Genetic Analysis of T Cell Leukemogenesis
    Stephen J Brandt; Fiscal Year: 2013
    ..abstract_text> ..
  54. In Vivo Gene-Specific Regulation Using Engineered ZFPs in Drug Abuse
    Elizabeth Heller; Fiscal Year: 2013
    ..The research proposed here will shed new light on the mechanisms of transcriptional regulation by drugs of abuse, as well as demonstrate the use of ZFPs as novel tools in the study of the neurobiology of drug addiction. ..
  55. Progranulin, TDP-43 and Cell Death
    Leonard Petrucelli; Fiscal Year: 2013
    ..Our hypothesis is that loss of functional PGRN leads to loss of functional TDP-43, which leads to cell death. ..
  56. Mechanisms of HbF Activation by Non-deletional HPFH
    Kenneth R Peterson; Fiscal Year: 2013
    ....
  57. CELLULAR AND MOLECULAR MICROBIOLOGY TRAINING PROGRAM
    JACK J HAWIGER; Fiscal Year: 2010
    ..Transduction and Gene Transcription Evoked by Pathogens;(vii) Nuclear Import and Export;(viii) RNA and DNA Binding Proteins in Pathogen-Host Interaction;(ix) ER and Golgi Pathways for Microbial Peptides, Glycolipids, and ..
  58. POTENTIATED STATE OF THE HSP70 HEAT SHOCK GENE
    DAVID SCOTT GILMOUR; Fiscal Year: 2013
    ..DSIF and P-TEFb both contribute to transcription of the HIV provirus, and an inhibitor of P-TEFb is in phase 2 clinical trials for cancer therapy. ..
  59. Mechanisms of Polycomb Silencing
    Yi Zhang; Fiscal Year: 2010
    ..Our results suggest a hierarchical model by which the PRC2 is recruited to PRE through interactions with DNA binding proteins. PRC2-mediated H3K27 methylation then facilitates recruitment of PRC1, which mediates H2A ubiquitylation ..
  60. Structure and Function of the SAGA Deubiquitinating Module
    Cynthia Wolberger; Fiscal Year: 2013
    ....
  61. Silencing and Counter-Silencing of Salmonella Virulence Genes
    Ferric C Fang; Fiscal Year: 2013
    ..silencing by NAPs that bind DNA with relatively low specificity is countered by the actions of other DNA binding proteins. The latter are comprised of classical transcriptional activators, repressors, and alternative sigma ..
  62. Mechanism of the Transcriptional Response to Transition Metals
    MICHAEL THOMAS MARR; Fiscal Year: 2013
    ..The long-term objective of our studies is to understand how a cell, in response to a diverse set of metals, differentially regulates the appropriate metal responsive genes to control metal homeostasis. ..
  63. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    ....
  64. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2007
    ..The results we would obtain during this Phase I study will help determine if pWGA has less bias when small quantities of template DNA is used. [unreadable] [unreadable] [unreadable]..
  65. SUBUNIT INTERACTIONS IN DNA BINDING PROTEINS
    Catherine Royer; Fiscal Year: 1992
    ..While the binding of a number of DNA binding proteins to their specific recognition sequences has been well characterized, the aggregation state of these ..
  66. STRUCTURE/FUNCTION OF TWO DNA BINDING PROTEINS
    WILHELMUS HOL; Fiscal Year: 2004
    ..tuberculosis), and (iii) the most devastating eukaryotic parasite (P. falciparum) known. The latter two account for roughly five million deaths per year worldwide. ..
  67. HEX EXPRESSION AND REGULATION IN DEVELOPING LUNG
    CLIFFORD BOGUE; Fiscal Year: 2000
    ..Homeobox genes, which encode proteins which function as sequence-specific DNA binding proteins, are expressed in specific temporo-spatial patterns in the developing mouse and have been shown to direct ..
  68. ACTIVATION OF RNA POLYMERASE BY SSDNA BINDING PROTEIN
    LUCIA ROTHMAN DENES; Fiscal Year: 1999
    ..6) Initiate structural studies of N4SSB. We expect that the proposed studies will provide new insights into the mechanism of transcription activation in prokaryotes as well as eukaryotes. ..
  69. DAMAGED DNA AND REPAIR
    Chulhee Kang; Fiscal Year: 1999
    ..We have crystallized the native protein and we prepare to crystallize protein-single stranded DNA complex. ..
  70. Molecular Basis of mu-Opioid Receptor Gene Regulation
    Jane Ko; Fiscal Year: 2009
    ..roles of single-stranded (ss) DNA binding protein and its functional interaction with double-stranded (ds) DNA binding proteins in MOR gene regulation...