nucleic acid regulatory sequences


Summary: Nucleic acid sequences involved in regulating the expression of genes.

Top Publications

  1. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
  2. 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
  3. pmc VISTA: computational tools for comparative genomics
    Kelly A Frazer
    Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Nucleic Acids Res 32:W273-9. 2004
  4. ncbi The evolutionary significance of cis-regulatory mutations
    Gregory A Wray
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Nat Rev Genet 8:206-16. 2007
  5. pmc Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Genet 40:158-60. 2008
  6. ncbi Genetic dissection of transcriptional regulation in budding yeast
    Rachel B Brem
    Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, D4 100, Seattle, WA 98109, USA and Howard Hughes Medical Institute
    Science 296:752-5. 2002
  7. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
  8. 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
  9. ncbi CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    A T Hark
    Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, New Jersey 08544, USA
    Nature 405:486-9. 2000
  10. ncbi Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans
    Adam S Wenick
    Department of Biochemistry and Molecular Biophysics, Center for Neurobiology and Behavior, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA
    Dev Cell 6:757-70. 2004

Detail Information

Publications321 found, 100 shown here

  1. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
    ..This report summarizes the present status of this database and available tools...
  2. 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 here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under
  3. pmc VISTA: computational tools for comparative genomics
    Kelly A Frazer
    Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Nucleic Acids Res 32:W273-9. 2004
    ..We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein...
  4. ncbi The evolutionary significance of cis-regulatory mutations
    Gregory A Wray
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Nat Rev Genet 8:206-16. 2007
    ..Cases in which parallel mutations have produced parallel trait modifications in particular suggest that some phenotypic changes are more likely to result from cis-regulatory mutations than from coding mutations...
  5. pmc Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Genet 40:158-60. 2008
    ..Developmental enhancers were equally prevalent in both populations, suggesting instead that ultraconservation identifies a small, functionally indistinct subset of similarly constrained cis-regulatory elements...
  6. ncbi Genetic dissection of transcriptional regulation in budding yeast
    Rachel B Brem
    Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, D4 100, Seattle, WA 98109, USA and Howard Hughes Medical Institute
    Science 296:752-5. 2002
    ..We found eight such trans-acting loci, each affecting the expression of a group of 7 to 94 genes of related function...
  7. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at
  8. 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...
  9. ncbi CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    A T Hark
    Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, New Jersey 08544, USA
    Nature 405:486-9. 2000
    ..Consistent with our model, CTCF binding is abolished by DNA methylation. This is the first example, to our knowledge, of a regulated chromatin boundary in vertebrates...
  10. ncbi Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans
    Adam S Wenick
    Department of Biochemistry and Molecular Biophysics, Center for Neurobiology and Behavior, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA
    Dev Cell 6:757-70. 2004
    ..The identity of these homeodomain targets provides novel insights into the biology of the AIY interneuron...
  11. pmc Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors
    Alona Sosinsky
    Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, USA
    Nucleic Acids Res 31:3589-92. 2003
    ..It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at
  12. pmc Regulatory sequence analysis tools
    Jacques van Helden
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 31:3593-6. 2003
    ..RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank...
  13. ncbi A genomic regulatory network for development
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 295:1669-78. 2002
    ..Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time...
  14. pmc Highly conserved non-coding sequences are associated with vertebrate development
    Adam Woolfe
    Medical Research Council Rosalind Franklin Centre for Genomics Research Hinxton, Cambridge, United Kingdom
    PLoS Biol 3:e7. 2005
    ..These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development...
  15. pmc ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    Ivan Ovcharenko
    Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W280-6. 2004
    ..The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes...
  16. ncbi Sequencing and comparison of yeast species to identify genes and regulatory elements
    Manolis Kellis
    Whitehead MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 423:241-54. 2003
    ..We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human...
  17. pmc Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    Jason Gertz
    Center for Genome Sciences, Department of Genetics, Washington University in Saint Louis School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 457:215-8. 2009
    ..Quantitative analyses of synthetic promoter libraries will be an important tool in unravelling the rules underlying combinatorial cis-regulation...
  18. ncbi RNA recognition and translational regulation by a homeodomain protein
    J Dubnau
    Howard Hughes Medical Research Institute, Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
    Nature 379:694-9. 1996
    ..RNA binding by bcd seems to involve direct interactions between the bcd homeodomain and discrete target sequences within the 3' untranslated region of the cad messenger RNA and to block the initiation of cad translation...
  19. pmc MATCH: A tool for searching transcription factor binding sites in DNA sequences
    A E Kel
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:3576-9. 2003 The same program with a different web interface can be found at An advanced version of the tool called Match Professional is available at
  20. pmc SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D
    Massimo Caputi
    Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratory, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    EMBO J 21:845-55. 2002
    ..hnRNP H is required for interaction of U1 snRNP with the enhancer, independent of the point mutation. We propose that SC35 binding to the point mutation region may convert the hnRNP H-U1 snRNP complex into a splicing enhancer...
  21. pmc Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening
    Barbara D'haene
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    PLoS Genet 5:e1000522. 2009
    ..4 kb deleted fragment. Overall, this study revealed the smallest distant deletion causing monogenic disease and impacts upon the concept of mutation screening in human disease and developmental disorders in particular...
  22. ncbi Preferential activation of an IL-2 regulatory sequence transgene in TCR gamma delta and NKT cells: subset-specific differences in IL-2 regulation
    Mary A Yui
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    J Immunol 172:4691-9. 2004
  23. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    ..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
  24. pmc Prediction of rho-independent transcriptional terminators in Escherichia coli
    E A Lesnik
    Ibis Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
    Nucleic Acids Res 29:3583-94. 2001
  25. pmc The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins
    I A Wadman
    MRC Laboratory of Molecular Biology, Cambridge, UK
    EMBO J 16:3145-57. 1997
    ..These data demonstrate one function for the LIM-binding protein Ldb1 and establish a function for the LIM-only protein Lmo2 as an obligatory component of an oligomeric, DNA-binding complex which may play a role in haematopoiesis...
  26. pmc Key features of heat shock regulatory elements
    J Amin
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Florida 33101
    Mol Cell Biol 8:3761-9. 1988
    ..Second, the nucleotides at the two positions immediately upstream from GAA segments played an important role in defining the competence of regulatory elements...
  27. pmc High-resolution DNA-binding specificity analysis of yeast transcription factors
    Cong Zhu
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:556-66. 2009
    ..These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes...
  28. ncbi HLA-G and IL-10 in serum in relation to HLA-G genotype and polymorphisms
    Thomas Vauvert F Hviid
    Department of Clinical Biochemistry, Copenhagen University Hospital, Rigshospitalet, Denmark
    Immunogenetics 56:135-41. 2004
    ..In conclusion, this study indicates that polymorphisms in the 3'UTR and the 5'URR of the HLA-G gene may influence the expression of sHLA-G of possible importance in pathological pregnancies and also in organ transplantation...
  29. ncbi Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
    Gael Yvert
    Howard Hughes Medical Institute and Division of Human Biology, Fred Hutchinson Cancer Research Center, Mailstop D4 100, 1100 Fairview Avenue North, Seattle, Washington 98103 USA
    Nat Genet 35:57-64. 2003
    ..Notably, transcription factors showed no enrichment, and trans-regulatory variation seems to be broadly dispersed across classes of genes with different molecular functions...
  30. pmc Suppression of ribosomal reinitiation at upstream open reading frames in amino acid-starved cells forms the basis for GCN4 translational control
    J P Abastado
    Section on Molecular Genetics of Lower Eukaryotes, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
    Mol Cell Biol 11:486-96. 1991
    ..Under nonstarvation conditions, ribosomes would recover more rapidly from uORF1 translation, causing them all to reinitiate at uORF4 rather than at GCN4...
  31. pmc Detection of functional DNA motifs via statistical over-representation
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:1372-81. 2004
    ..It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription...
  32. pmc Regulatory divergence modifies limb length between mammals
    Chris J Cretekos
    Department of Molecular Genetics, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Genes Dev 22:141-51. 2008
  33. pmc The cis-regulatory logic of the mammalian photoreceptor transcriptional network
    Timothy H C Hsiau
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 2:e643. 2007
    ..This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation...
  34. pmc Control of stochastic gene expression by host factors at the HIV promoter
    John C Burnett
    Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California, United States of America
    PLoS Pathog 5:e1000260. 2009
    ..These results may have biomedical implications for the treatment of HIV latency...
  35. pmc The molecular genetics of the bithorax complex of Drosophila: cis-regulation in the Abdominal-B domain
    S E Celniker
    Division of Biology, California Institute of Technology, Pasadena 91125
    EMBO J 9:4277-86. 1990
    ..Such sharing is proposed as a factor that tends to keep gene complexes intact during evolution...
  36. pmc Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells
    Anthony A Philippakis
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    PLoS Comput Biol 2:e53. 2006
    ..We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells...
  37. ncbi Evidence for nucleosome depletion at active regulatory regions genome-wide
    Cheol Koo Lee
    Department of Biology, CB 3280, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Nat Genet 36:900-5. 2004
    ..Given the conservation of sequence and function among components of both chromatin and the transcriptional machinery, nucleosome depletion at promoters may be a fundamental feature of eukaryotic transcriptional regulation...
  38. pmc An integrated approach to identifying cis-regulatory modules in the human genome
    Kyoung Jae Won
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 4:e5501. 2009
    ..Incorporating histone signature information successfully penalized false prediction and improved the whole performance. The dataset we used and the software are available at
  39. ncbi Conservation of RET regulatory function from human to zebrafish without sequence similarity
    Shannon Fisher
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Science 312:276-9. 2006
    ..The majority of human RET noncoding sequences also directed ret-specific expression in zebrafish. Thus, vast amounts of functional sequence information may exist that would not be detected by sequence similarity approaches...
  40. pmc Discovery and annotation of functional chromatin signatures in the human genome
    Gary Hon
    Bioinformatics Program, University of California at San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000566. 2009
    ..Together, these results highlight the rich information embedded in the human epigenome and underscore its value in studying gene regulation...
  41. ncbi Transcriptional regulation of the mosquito vitellogenin gene via a blood meal-triggered cascade
    V A Kokoza
    Department of Entomology and Program in Genetics, Michigan State University, East Lansing, MI 48824, USA
    Gene 274:47-65. 2001
    ..The present work elucidates the molecular basis of blood meal-dependent expression of this mosquito gene, laying the foundation for mosquito-specific expression cassettes with predictable stage and tissue specificity...
  42. ncbi Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
    Y d'Aubenton Carafa
    C N R S Centre de Génétique Moleculaire, Laboratoire associé à l Université Pierre et Marie Curie, Gif sur Yvette, France
    J Mol Biol 216:835-58. 1990
    ..It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators...
  43. ncbi Identification and characterization of a conserved erythroid-specific enhancer located in intron 8 of the human 5-aminolevulinate synthase 2 gene
    K H Surinya
    Department of Biochemistry, University of Adelaide, Adelaide, South Australia, Australia 5005
    J Biol Chem 273:16798-809. 1998
  44. pmc A multicassette Gateway vector set for high throughput and comparative analyses in ciona and vertebrate embryos
    Agnes Roure
    Institut de Biologie du Developpement de Marseille Luminy, UMR 6216 CNRS Université de la Méditerranée, Marseille, France
    PLoS ONE 2:e916. 2007
    ..Large scale cross-species comparisons of protein function and cis-regulatory sequences may help to understand the emergence of specific traits during evolution...
  45. pmc UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs
    G Pesole
    Dipartimento di Biologia, D B A F, Universita della Basilicata, via Anzio 10, 85100 Potenza, Italy
    Nucleic Acids Res 27:188-91. 1999
    ..Furthermore, UTRdb entries have been annotated for the presence of repetitive elements...
  46. pmc Prediction of regulatory elements in mammalian genomes using chromatin signatures
    Kyoung Jae Won
    Dept of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0359, USA
    BMC Bioinformatics 9:547. 2008
  47. ncbi Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
    Benjamin Prud'homme
    University of Wisconsin and Howard Hughes Medical Institute, Bock Laboratories, 1525 Linden Drive, Madison, Wisconsin 53706, USA
    Nature 440:1050-3. 2006
    ..These results demonstrate how the functional diversification of the modular CREs of pleiotropic genes contributes to evolutionary novelty and the independent evolution of morphological similarities...
  48. ncbi Characterization of the transvection mediating region of the abdominal-B locus in Drosophila
    J Zhou
    Dept Mol Cell Biol, Division of Genetics, University of California, Berkeley, CA 94720, USA
    Development 126:3057-65. 1999
    ..We discuss the significance of these findings with regard to Abd-B transvection and long-range enhancer-promoter interactions in mammalian globin loci...
  49. ncbi Structurally similar but functionally distinct factors, IRF-1 and IRF-2, bind to the same regulatory elements of IFN and IFN-inducible genes
    H Harada
    Institute for Molecular and Cellular Biology, Osaka University, Japan
    Cell 58:729-39. 1989
    ..Our results suggest that transcription of the IFN and IFN-inducible genes is regulated by two similar trans-acting factors that apparently compete for the same cis-acting recognition sequences, but which have opposite effects...
  50. 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...
  51. pmc High incidence of SHOX anomalies in individuals with short stature
    C Huber
    Department of Medical Genetics and INSERM U781, Hopital Necker Enfants Malades, 149 rue de Sévres 75015 Paris, France
    J Med Genet 43:735-9. 2006
    ..To study the SHOX gene and the PAR1 region in individuals with short stature...
  52. ncbi Male development of chromosomally female mice transgenic for Sry
    P Koopman
    Laboratory of Eukaryotic Molecular Genetics, MRC National Institute for Medical Research, Mill Hill, London, UK
    Nature 351:117-21. 1991
    ..It is now shown that Sry on a 14-kilobase genomic DNA fragment is sufficient to induce testis differentiation and subsequent male development when introduced into chromosomally female mouse embryos...
  53. ncbi Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit
    H Xiao
    Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853
    Cell 64:585-93. 1991
    ..This cooperativity is particularly important in binding HSF at 37 degrees C, and could account for the requirement for multiple binding sites in vivo and, in part, for the differential expression of heat shock genes...
  54. ncbi Genome-scale identification of nucleosome positions in S. cerevisiae
    Guo Cheng Yuan
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    Science 309:626-30. 2005
    ..Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access...
  55. ncbi Anatomy of Escherichia coli ribosome binding sites
    R K Shultzaberger
    University of Maryland, College Park, 20742, USA
    J Mol Biol 313:215-28. 2001
    ..Such models should be useful for refining gene-start predictions of any sequenced bacterial genome...
  56. ncbi Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
    O Johansson
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 19:i169-76. 2003
    ..However, utility of module detection methods has been severely limited by insufficient training data. For only a few tissues can one obtain sufficient numbers of literature-derived regulatory modules...
  57. ncbi B lymphocyte-induced maturation protein (Blimp)-1, IFN regulatory factor (IRF)-1, and IRF-2 can bind to the same regulatory sites
    Tracy C Kuo
    Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
    J Immunol 173:5556-63. 2004
    ..Thus, our data suggest that Blimp-1 competes in vivo with a subset of IRF proteins and help predict the sites and IRF family members that may be affected...
  58. ncbi Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly
    Laura A Lettice
    MRC Human Genetics Unit, Western General Hospital, Crewe Rd, Edinburgh EH4 2XU, UK
    Hum Mol Genet 17:978-85. 2008
    ..The polydactyly mutations define a new genetic mechanism that results in human congenital abnormalities and identifies a pathogenetic mechanism that may underlie other congenital diseases...
  59. pmc Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
    Gregory E Crawford
    Genome Technology Branch and National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 101:992-7. 2004
  60. ncbi Evolution of transcriptional regulation
    D Tautz
    Department of Genetics, University of Koeln, Weyertal 121, 50931, Koeln, Germany
    Curr Opin Genet Dev 10:575-9. 2000
    ..Evidence is accumulating for the involvement of regulatory evolution in morphological changes between closely related species, as well as in major changes of body plans...
  61. pmc Xce haplotypes show modified methylation in a region of the active X chromosome lying 3' to Xist
    B Courtier
    Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
    Proc Natl Acad Sci U S A 92:3531-5. 1995
    ..We propose that such a region could be involved in the initial stages of the inactivation process and in particular in the choice of which of the two X chromosomes present in a female cell will be inactivated...
  62. pmc Downstream sequence elements with different affinities for the hnRNP H/H' protein influence the processing efficiency of mammalian polyadenylation signals
    George K Arhin
    Department of Microbiology and Molecular Genetics, UMDNJ New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
    Nucleic Acids Res 30:1842-50. 2002
    ..Sequences capable of binding hnRNP H protein with varying affinities may play a role in determining the processing efficiency of a significant number of mammalian polyadenylation signals...
  63. ncbi Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3
    Lynda J Kieffer
    Department of Laboratory Medicine and Department of Genetics and Section of Immunobiology, Yale University, New Haven, CT 06520, USA
    J Immunol 168:3915-22. 2002
    ..This clustering of DNase HS sites and MARs capable of binding SATB1 and GATA-3 at the 3' end of the CD8B gene suggests that this region is an epigenetic regulator of CD8 expression...
  64. pmc Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis
    Ming Yu
    Department of Pediatric Hematology Oncology, Children s Hospital Boston and Dana Farber Cancer Institute, Harvard Medical School, MA 02115, USA
    Mol Cell 36:682-95. 2009
    ..These data provide insights into GATA-1-mediated gene regulation in vivo...
  65. ncbi Disruption of imprinting caused by deletion of the H19 gene region in mice
    P A Leighton
    Howard Hughes Medical Institute, Princeton University, New Jersey 08544, USA
    Nature 375:34-9. 1995
    ..The somatic overgrowth of heterozygotes for the maternal deletion is attributed to a gain of function of insulin-like growth factor 2, rather than a loss of function of H19...
  66. ncbi Internal ribosome entry site biology and its use in expression vectors
    E Martinez-Salas
    Centro de Biología Molecular Severo Ochoa Consejo Superior de Investigaciones Cientificas Universidad Autónoma de Madrid Cantoblanco, 28049, Madrid, Spain
    Curr Opin Biotechnol 10:458-64. 1999
    ..Additionally, the progress made in the understanding of the parameters that influence start codon selection will be instrumental in establishing the rational design of bicistronic expression vectors...
  67. pmc Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters
    Huiquan Wang
    UC Davis Genome Center, University of California, Davis, California 95616, USA
    Genome Res 14:1575-84. 2004
    ..We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes...
  68. ncbi Germline transformation used to define key features of heat-shock response elements
    H Xiao
    Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853
    Science 239:1139-42. 1988
    ..These and additional analyses indicate that the heat-shock regulatory element includes sequences beyond the 14-base pair HSE and may be better described as a dimer of a 10-base pair sequence, NTTCNNGAAN...
  69. pmc Variation in alternative splicing across human tissues
    Gene Yeo
    Department of Biology, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
    Genome Biol 5:R74. 2004
    ..To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues...
  70. doi Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages
    Serena Ghisletti
    Department of Experimental Oncology, European Institute of Oncology IEO, IFOM IEO Campus, Via Adamello 16, Milan, Italy
    Immunity 32:317-28. 2010
    ..We suggest that this may represent a general paradigm in tissue-restricted and stimulus-responsive gene regulation...
  71. ncbi R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres
    Roger Revilla-i-Domingo
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 274:438-51. 2004
    ..In addition, we introduce new methodological tools for quantitative measurement of the output of expression constructs that promise to be of general value for cis-regulatory analysis in sea urchin embryos...
  72. pmc Negative regulation of phosphate starvation-induced genes
    U T Mukatira
    Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 1165, USA
    Plant Physiol 127:1854-62. 2001
    ..Interestingly, the DNA binding activity disappeared during Pi starvation, leading to the hypothesis that Pi starvation-induced genes may be under negative regulation...
  73. ncbi Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
  74. pmc Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    Duncan T Odom
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:730-2. 2007
    ..When the same protein binds the promoters of orthologous genes, approximately two-thirds of the binding sites do not align...
  75. pmc Bipartite pattern discovery by entropy minimization-based multiple local alignment
    Chengpeng Bi
    Laboratory of Human Molecular Genetics, Children s Mercy Hospital and Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
    Nucleic Acids Res 32:4979-91. 2004
    ..Finally, a new bipartite information weight matrix for vitamin D3 receptor/retinoid X receptor alpha (VDR/RXRalpha) binding sites was derived that comprehensively models the natural variability inherent in these sequence elements...
  76. ncbi Transcriptional regulation by the phosphorylation-dependent factor CREB
    B Mayr
    Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Rev Mol Cell Biol 2:599-609. 2001
    ..CREB is phosphorylated in response to various signals, but how is specificity achieved in these signalling pathways?..
  77. pmc Functional analysis of Arabidopsis WRKY25 transcription factor in plant defense against Pseudomonas syringae
    Zuyu Zheng
    Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 2054, USA
    BMC Plant Biol 7:2. 2007
    ..However, there is only limited information about the roles of specific WRKY DNA-binding transcription factors in plant defense...
  78. pmc Genome-wide discovery of human heart enhancers
    Leelavati Narlikar
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health NIH, Bethesda, Maryland 20894, USA
    Genome Res 20:381-92. 2010
    ..These results support the existence of underlying cis-regulatory codes dictating tissue-specific transcription in mammalian genomes and validate our enhancer classifier strategy as a method to uncover these regulatory codes...
  79. pmc Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells
    Maria Shnyreva
    Department of Immunology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 101:12622-7. 2004
    ..Like IFN-gamma expression, these histone modifications were T-bet-dependent in CD4+ cells, but not CD8+ T cells. These findings define two distal regulatory elements associated with T cell subset-specific IFN-gamma expression...
  80. pmc rVISTA 2.0: evolutionary analysis of transcription factor binding sites
    Gabriela G Loots
    Genome Biology Division and EEBI Computing Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W217-21. 2004
    ..The rVISTA tool is publicly available at
  81. pmc ConSite: web-based prediction of regulatory elements using cross-species comparison
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:W249-52. 2004
    ..Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/
  82. ncbi Predictive identification of exonic splicing enhancers in human genes
    William G Fairbrother
    Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 297:1007-13. 2002
    ..The motifs identified enable prediction of the splicing phenotypes of exonic mutations in human genes...
  83. ncbi Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
    Peter J Sabo
    Department of Genome Sciences, University of Washington, 1705 NE Pacific St, Box 357730, Seattle, Washington 98195, USA
    Nat Methods 3:511-8. 2006
    ..DNase-array is a powerful and straightforward approach for systematic exposition of the cis-regulatory architecture of complex genomes...
  84. ncbi Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    Nadav Ahituv
    Genomics Division, Lawrence Berkeley National Laboratory, CA 94720, USA
    Hum Mol Genet 14:3057-63. 2005
    ..Our results provide an extensive data set characterizing the regulatory domains of genes and the conserved regulatory elements within them...
  85. ncbi Evolutionary analyses of the human genome
    W H Li
    Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Nature 409:847-9. 2001
    ..Here we present some first glimpses of these features...
  86. pmc WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
    Giulio Pavesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
    BMC Bioinformatics 8:46. 2007
  87. pmc Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    David M McGaughey
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 18:252-60. 2008
    ..Collectively, these data demonstrate that the noncoding functional component of vertebrate genomes may far exceed estimates predicated on evolutionary constraint...
  88. ncbi Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated
    N Olivares-Zavaleta
    Department of Molecular Microbiology, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, 62271 Morelos, Mexico
    Genomics 87:329-37. 2006
    ..All our results point toward a more widespread role of curved DNA in gene transcription, a fact that has previously been underestimated...
  89. pmc Conversion of a dorsal-dependent silencer into an enhancer: evidence for dorsal corepressors
    J Jiang
    Department of Biology, UCSD, La Jolla 92093 0322
    EMBO J 12:3201-9. 1993
    ..These results suggest that dl is intrinsically an activator, but is converted into a potent silencer when it interacts with neighboring corepressors...
  90. pmc fREDUCE: detection of degenerate regulatory elements using correlation with expression
    Randy Z Wu
    Department of Biochemistry and Biophysics, UCSF, 1700 4th Street, San Francisco, CA 94143 2542, USA
    BMC Bioinformatics 8:399. 2007
    ..A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs...
  91. ncbi Nongenic transcription, gene regulation and action at a distance
    Peter R Cook
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    J Cell Sci 116:4483-91. 2003
  92. pmc Mcp and Fab-7: molecular analysis of putative boundaries of cis-regulatory domains in the bithorax complex of Drosophila melanogaster
    F Karch
    Department of Zoology and Animal Biology, University of Geneva, Switzerland
    Nucleic Acids Res 22:3138-46. 1994
    ..3 kb nuclease hypersensitive region in chromatin. We also show that sequences contributing to the Fab-7 boundary appear to be spread over a larger stretch of DNA, but like Mcp have an unusual chromatin structure...
  93. pmc Limitations and potentials of current motif discovery algorithms
    Jianjun Hu
    Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN 47907, USA
    Nucleic Acids Res 33:4899-913. 2005
    ..Since the sequence-based algorithms are the baseline of most of the modern motif discovery algorithms, this paper suggests substantial improvements would be possible for them...
  94. ncbi Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    Albertha J M Walhout
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 16:1445-54. 2006
  95. ncbi Divergence of transcription factor binding sites across related yeast species
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Science 317:815-9. 2007
    ..Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species...
  96. ncbi Evolution of alternative transcriptional circuits with identical logic
    Annie E Tsong
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143 2200, USA
    Nature 443:415-20. 2006
    ..These changes indicate specific mechanisms by which fitness barriers were traversed during the transition...
  97. ncbi A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview
    Jian Min Chen
    INSERM, U613, 29220, Brest, France
    Hum Genet 120:1-21. 2006
  98. ncbi Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover
    Emmanouil T Dermitzakis
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
    Mol Biol Evol 19:1114-21. 2002
    ..These results have important implications for the efficacy of phylogenetic footprinting and the interpretation of the pattern of evolution in regulatory sequences...
  99. ncbi Oxygen-dependent and tissue-specific regulation of erythropoietin gene expression
    Joachim Fandrey
    Institut fur Physiologie, Universitat Duisburg Essen, Hufelandstr 55, D 45147 Essen, Germany
    Am J Physiol Regul Integr Comp Physiol 286:R977-88. 2004
    ..Understanding oxygen and tissue-specific regulation of EPO production is of high relevance for physiology. Moreover, this knowledge might be useful for new therapies to treat human diseases...
  100. ncbi Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen
    W Driever
    Max Planck Institut fur Entwicklungsbiologie, Abteilung Genetik, Tubingen, FRG
    Nature 340:363-7. 1989
  101. pmc DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Building 31, Room 4B09, Bethesda, Maryland 20892, USA
    Nat Methods 3:503-9. 2006
    ..This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome...

Research Grants74

  1. 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. ..
    Lisa M Salati; Fiscal Year: 2012
    ..This project will provide important new data on the ways in which dietary fat can regulate intracellular metabolism. ..
  3. Exome re-sequencing candidate loci for familial essential tremor
    Barry E Kosofsky; Fiscal Year: 2012
    ..Studying the untoward effects of mutant ET genes will increase our knowledge of ET and other movement disorders such as Parkinson disease. ..
  4. Molecular Epidemiology of DNA Repair in Head and Neck Cancer
    Qingyi Wei; Fiscal Year: 2012
    ..The long- term goal of this study is to identify effective biomarkers that can be used to identify at-risk individuals who will be targeted for primary prevention and early detection of SCCHN in the general population. ..
  5. Regulation of apoptosis by PI 3-kinase/Akt signaling
    Geoffrey M Cooper; Fiscal Year: 2012
    ..The present proposal seeks to further understand the mechanism by which this pathway regulates cell survival. Discoveries of novel targets of PI 3-kinase signaling may provide new targets for cancer treatment. ..
  6. Regulated Accessibility of a cytokine gene locus.
    Anjana Rao; Fiscal Year: 2013
    ..In this proposal we plan to investigate the role of TET proteins in T cells, a major class of cells in the immune system that protect the organism from attack by bacteria, viruses and other pathogens including cancer cells. ..
  7. Regulation of Odorant Receptor Gene Expression
    Paul Feinstein; Fiscal Year: 2013
    ..Studying odorant receptor gene expression will give insights into how the olfactory system is put together and maintained throughout adulthood. ..
  8. Function and Structure Adaptations in Forebrain Development
    PAT R LEVITT; Fiscal Year: 2013
    ..This project includes basic and clinical translational studies that will provide insight into gene- gene and gene-environment interactions that may underlie atypical brain functions in ASD. ..
  9. Translating human PPARy binding regions to gene regulation and metabolic disease
    RAYMOND EDWARD SOCCIO; Fiscal Year: 2013
    ..Soccio from the mentored to the independent phase of this 5 year career development award. These studies of the human PPAR cistrome have potentially great translational relevance to the epidemics of diabetes and obesity. . ..
  10. Genome-wide Identification of Immediate Early Genes in Insects
    Anandasankar Ray; Fiscal Year: 2012
    Terri H Beaty; Fiscal Year: 2013
  12. Functionally Significant Polymorphisms in Serotonin Pathway Genes
    Beverly H Koller; Fiscal Year: 2010
    ..These mice can be used to study the impact of this polymorphism on gene expression, protein function, development, and on the behavioral tests/models known to be sensitive to alterations in this specific pathway in rodents. ..
  13. Identifying the Atoh1 targetome in hair cells with deep sequencing
    Andrew K Groves; Fiscal Year: 2013
    ..We now propose to apply these same methods to identify the Atoh1 targetome in hair cells. ..
  14. Persistent microRNA changes in serum of cancer-free breast cancer patients
    Harikrishna Nakshatri; Fiscal Year: 2012
    ..The circulating microRNAs may be the invisible long-arm of cancer that reaches distant organs as circulating microRNAs can fuse with heterotypic cells and influence gene expression. ..
  15. De novo establishment of Polycomb-group-mediated repression
    Richard S Jones; Fiscal Year: 2010
  16. Functional characterization of ATP1A1 and DEspR variants associated with essentia
    Nelson Ruiz Opazo; Fiscal Year: 2010
  17. Tsetse Fecundity Reduction for Trypanosomiasis Control
    Serap Aksoy; Fiscal Year: 2013
    ..These elements stand to provide targets for tsetse specific vector control strategies for use in the prevention of trypanosomiasis. ..
  18. Control of developmental timing and body size in Drosophila
    MICHAEL BRENDAN O'CONNOR; Fiscal Year: 2013
  19. Nuclear Receptor Networks in Human Disease
    Frances M Sladek; Fiscal Year: 2010
    ..Our work will help bring us closer to an era of personalized medicine in which prevention, diagnosis and treatment are tailored to the individual patient, making them more effective and less costly. ..
  20. Sex-specific gene regulation of neuronal chloride co-transporter, kcc2
    WOLFGANG B LIEDTKE; Fiscal Year: 2010
    Pamela L Mellon; Fiscal Year: 2013
    ..This multifaceted approach should yield a comprehensive understanding of the program of GnRH neuronal migration and cell fate in vivo and in vitro and provide insight into the genetics of hypogonadotropic hypogonadism. ..
  22. Role of LHX3 Protein Isoforms in Pituitary Development
    SIMON JAMES RHODES; Fiscal Year: 2012
    ..Further, clinical collaborations will continue to provide information that enhances our understanding of the basic mechanisms of pituitary development, thereby allowing the formulation of new research hypotheses. ..
  23. Sox10 Alleles for Functional Analysis of Glial Lineages
    E Michelle Southard-Smith; Fiscal Year: 2013
    Jeffrey C Murray; Fiscal Year: 2013
    ..We hope we have established an environment in which students can explore paths to careers in dental/craniofacial research. ..
  25. Structural Basis for Synergistic Gene Expression by Runx1 and Ets1 Proteins
    Tahir H Tahirov; Fiscal Year: 2012
    ..Success with the proposed structural studies ultimately will lead to the discovery of novel therapies for the prevention and treatment of leukemia and other cancers. ..
  26. Critical roles of GA binding protein in HSC maintenance and ageing
    Hai Hui Xue; Fiscal Year: 2013
    Donata Vercelli; Fiscal Year: 2013
    ..Our studies will be the first to explore human Th2 cytokine regulation in vivo and will identify novel rational targets for effective treatments of allergic disease. ..
    VAINORIOUS E; Fiscal Year: 2009
  29. Role of Cyclin A's in mammalian gametogenesis
    Debra J Wolgemuth; Fiscal Year: 2013
  30. Insulin and IGF-1 regulation of the GnR H neuron
    Sara A DiVall; Fiscal Year: 2012
    ..These studies will provide insight into how the brain's control of reproduction is affected by the nutrition dependent hormones insulin and insulin-like growth factor-1. ..
  31. Behavioral and Molecular Effects of Antenatal SSRI Exposure
    Lawrence S Quang; Fiscal Year: 2013
    ..Together, they will test the Principal Investigator's hypothesis that antenatal SSRI exposure will lead to behavioral pathogenesis from perturbations in the regulatory programs that govern 5-HT neuron development. ..
    Michael L Cunningham; Fiscal Year: 2013
    ..There is an incomplete understanding of the causes of craniosynostosis and we lack experimental models. The development of these resources will improve clinical care, design biologically based therapies, and pursue primary prevention. ..
  33. Sexual conflict and relocation of genes by duplication
    ESTHER BETRAN; Fiscal Year: 2013
    ..Whole genome polymorphism data from D. melanogaster and comparative genomics will be exploited using the most current bioinformatics tools and molecular evolution software to achieve these objectives. ..
  34. Regulated Retrotransposon Elements in Neuroendocrine System
    Janusz Puc; Fiscal Year: 2009
  35. Fliz1 regulation of GATA-3 in breast cancer
    Janice E Knepper; Fiscal Year: 2013
    ..If Fliz1 expression contributes to the loss of GATA-3 expression seen in invasive human breast cancer, a potent therapeutic target is presented which could increase tumor sensitivity to hormone therapy and decrease metastatic potential. ..
  36. Transcriptional Control of Liver Development
    Joshua Friedman; Fiscal Year: 2009
    ..The information which will be obtained from this and future investigations will improve our understanding of liver development and may enhance the diagnosis, treatment, and prevention of liver disease in humans. ..
  37. Defining the thyroid hormone receptor Cistrome in vivo
    Anthony N Hollenberg; Fiscal Year: 2012
    ..Together, completion of these Aims will provide a new platform for understanding TR action in vivo and allow for greater insight into how TH regulates key transcriptional pathways in vivo. ..
  38. Mechanism/Regulation of Intestinal Thiamin Uptake
    Hamid M Said; Fiscal Year: 2013
    ..abstract_text> ..
    Mark Lim; Fiscal Year: 2010
    ..We will also maintain a close contact during Phase II with two leading diagnostic companies, LabCorp and Genzyme Genetics, who have expressed an interest in the ultimate commercialization of the DRAMA-ACD approach. ..
  40. A Haplotype Map for Multiple Sclerosis
    Stephen L Hauser; Fiscal Year: 2013
    ..This information may translate into clinically useful genetic biomarkers and reveal novel targets for therapy. ..
    Peter Hornsby; Fiscal Year: 2009
    ..Cell transplantation offers the possibility of future testing of molecular mechanisms of zonation under controlled in vivo conditions. ..
  42. Disparities in cervical cancer precursors and deregulation of imprinted genes
    Susan Kay Murphy; Fiscal Year: 2013
    ..We will then test the performance of these markers to identify CIN2+ cases from among 500 ASCUS cases. Data from the proposed study will improve triage decisions and reduce disparities in ICC morbidity and mortality. ..
  43. Obesity and deregulation of imprinted genes in early life
    Susan Kay Murphy; Fiscal Year: 2013
    ..Understanding the role of epigenetics in the genesis of childhood obesity will ulti- mately lead to new ways of preventing obesity and associated human diseases. ..
  44. The transcriptional basis of tumor promotion
    Joseph D Locker; Fiscal Year: 2013
    ..Experiments will also determine the alternative pathways by which liver regeneration and T3-induced hyperplasia activate Cyclin D1 transcription. ..
  45. Neurobiological studies of gammahydroxybutyrate
    Thomas S Kilduff; Fiscal Year: 2012
    ..We will exploit a mouse model of narcolepsy in which the Hcrt neurons degenerate postnatally as they do in human narcoleptics to understand how GHB is beneficial in human narcolepsy. ..
  46. Establishment of a phenotypical model of adverse outcomes associated with ART
    KEVIN DALE WELLS; Fiscal Year: 2011
    ..The proposed model will enable the long-term goal of elucidating the mechanisms by which assisted reproductive technologies can induce loss-of-imprinting syndromes, and most importantly, induce the resulting phenotypes. ..
  47. Structures of Lipid-DNA Nonviral Gene Delivery Systems 4
    Cyrus R Safinya; Fiscal Year: 2013
  48. Genetic and Developmental Mechanisms of Evolutionary Innovations
    Artyom Kopp; Fiscal Year: 2012
  49. A Novel Approach to Decoding Vertebrate Gene Regulation
    ..In addition, it will pave the way for gene therapy by genetically engineering regulatory elements that drive compounds to specific tissues at different time points. ..
  50. High-Throughput Low Cost Production of Chromatin-Immunoprecipitation-Grade Antib
    KEITH ELLIOTT KROPP; Fiscal Year: 2010
    ..The goal of this project is to develop a system to generate low cost, high performance antibody substitutes to enable larger scale mapping studies with chromatin immunoprecipitation. ..
  51. Genome Wide Identification of PTF1-J Targets in Dorsal Neural Tube
    Jane E Johnson; Fiscal Year: 2010
    ..This is a unique opportunity to combine multiple technical advances to begin to tackle the challenging goal of defining the molecular rationale controlling the generation of neuronal diversity. ..
  52. Identification of XX DSD Mutations by RNA-seq and Comparative Genomics
    Vicki N Meyers-Wallen; Fiscal Year: 2013
  53. Dynamics of nucleosome positioning and the role of chromatin in myogenesis
    DUSTIN EDWARD SCHONES; Fiscal Year: 2013
    ..These studies will lead to a greater understanding of the mechanisms responsible for the organization of nucleosomes across the genome and further elucidate the role of chromatin in the regulation of transcription. ..
  54. Interactive effects of ethanol and estrogen on brain vasopressin during puberty
    Toni R Pak; Fiscal Year: 2010
  55. Molecular mechanism of cytochrome P4501A1 expression.
    Bhagavatula Moorthy; Fiscal Year: 2013
  56. Effects of early-life experience:role of CRH
    Tallie Z Baram; Fiscal Year: 2013
    ..The resulting information would enable us to use the same mechanisms as a basis for therapy in people who have not had the same type of optimal childhood experience. ..
  57. Molecular mechanisms of Axenfeld-Rieger syndrome
    Elena V Semina; Fiscal Year: 2013
  58. Redox-Control of MMP-1 and Senescence
    JUAN ANDRES MELENDEZ; Fiscal Year: 2012
  59. Gene Expression in Myeloma Cells
    Laurel A Eckhardt; Fiscal Year: 2010
    ..An understanding of the latter will contribute to models relating allelic exclusion to protection from autoimmunity. ..
  60. The Role of Myc in ChREBP-dependent, Glucose-stimulated Gene Expression
    Donald K Scott; Fiscal Year: 2010
    ..Understanding how they interact to regulate metabolism will provide crucial information for informed therapies for the treatment of diabetes and cancer. ..
  61. Identification and functional characterization of a novel positive cis-control el
  62. Intestinal Biotin Absorption: Physiological, Cellular and Molecular Aspects
    Hamid M Said; Fiscal Year: 2013
    ..This should ultimately assist us in the designing of effective strategies to optimize biotin body homeostasis, especially in conditions associated with biotin deficiency and sub-optimal levels. ..
    Anath Das; Fiscal Year: 1991
    ..thaliana genes by similar procedures. Induction of flowering is a critical process in angiosperm lifecycle. Understanding how photoperiod control this process will greatly broaden our knowledge on developmental processes in plants...
  64. DNA Methylation Profiling of Chronic Pain
    Andreas S Beutler; Fiscal Year: 2010
    ..Research outcomes of Aims 1 and 2 will be confirmed in an independent set of animals. If conducted now, the proposed study would be the first to investigate DNA cytosine methylation in pain. ..
    Sunil Ahuja; Fiscal Year: 1999
  66. Human Neurotropic JC Virus and CNS Diseases
    Kamel Khalili; Fiscal Year: 2006
    ..abstract_text> ..
    Gregory Brent; Fiscal Year: 1999
    ..This in vitro system will complement the in vivo studies and provide a model to study tissue specific gene regulation under more defined conditions. ..
    Ronald Cohen; Fiscal Year: 2002
    ..This will provide an ideal environment to complete this project, and will provide a basis for Dr. Cohen's transition to an independent investigator. ..
  69. Structure and mechanism of the AMP-activated protein kinase
    Lawrence Shapiro; Fiscal Year: 2010
    ..Our preliminary results and the further work proposed will provide high-resolution structural information on AMPK, and should directly enable the rational design of AMPK-directed therapeutics. ..
    Steven Ackerman; Fiscal Year: 2006
    Edward Newman; Fiscal Year: 2001
    ..The overall goal of this proposal is to understand the actions of MT'ase inhibitors and to use this understanding to develop more effective methods of modulating DNA methylation in human diseases. ..
  72. Molecular mechanisms underlying parallel Agouti adaptation in Peromyscus
    CATHERINE LINNEN; Fiscal Year: 2009
    ..Relevance: This research is of direct relevance to the mission of NIH because it will identify and molecularly characterize Agouti mutations, which will inform current models of mammalian pigmentation and human obesity. ..
  73. C elegans:a model to study intestinal water-soluble vitamins transport in vivo
    HAMID SAID; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
    GOKUL DAS; Fiscal Year: 1991
    ..The possibility of sequence-directed or protein-induced bending of the regulatory region will be tested...