binding sites

Summary

Summary: The reactive parts of a macromolecule that directly participate in its specific combination with another molecule.

Top Publications

  1. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
  2. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
  3. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
  4. pmc Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    Sven Heinz
    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Mol Cell 38:576-89. 2010
  5. pmc AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    Oleg Trott
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
    J Comput Chem 31:455-61. 2010
  6. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
  7. ncbi Integrins: bidirectional, allosteric signaling machines
    Richard O Hynes
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 110:673-87. 2002
  8. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
  9. ncbi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
  10. 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

Detail Information

Publications311 found, 100 shown here

  1. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains...
  2. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  3. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
    ..Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease...
  4. pmc Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    Sven Heinz
    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Mol Cell 38:576-89. 2010
    ..1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions. PU...
  5. pmc AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    Oleg Trott
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
    J Comput Chem 31:455-61. 2010
    ..Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user...
  6. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
    ..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...
  7. ncbi Integrins: bidirectional, allosteric signaling machines
    Richard O Hynes
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 110:673-87. 2002
    ..Long-range conformational changes couple these functions via allosteric equilibria...
  8. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
  9. ncbi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    ..Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.
  10. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various ..
  11. pmc Histone modifications at human enhancers reflect global cell-type-specific gene expression
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 459:108-12. 2009
    ..Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression...
  12. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs...
  13. pmc The microRNA.org resource: targets and expression
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
    Nucleic Acids Res 36:D149-53. 2008
    ..The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation...
  14. ncbi In vivo activation of the p53 pathway by small-molecule antagonists of MDM2
    Lyubomir T Vassilev
    Department of Discovery Oncology, Roche Research Center, Hoffmann La Roche, Inc, Nutley, NJ 07110, USA
    Science 303:844-8. 2004
    ..These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice...
  15. pmc Identification of functional elements and regulatory circuits by Drosophila modENCODE
    Sushmita Roy
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 330:1787-97. 2010
    ..Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation...
  16. ncbi miRWalk--database: prediction of possible miRNA binding sites by "walking" the genes of three genomes
    Harsh Dweep
    Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, D 68167 Mannheim, Germany
    J Biomed Inform 44:839-47. 2011
    ..we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat...
  17. ncbi Hfq and its constellation of RNA
    Jörg Vogel
    Institute for Molecular Infection Biology, University of Wurzburg, Joseph Schneider Strasse, Wurzburg, Germany
    Nat Rev Microbiol 9:578-89. 2011
    ..In this Review, we describe the salient structural and functional features of Hfq and discuss possible mechanisms by which this protein can promote RNA interactions to catalyse specific and rapid regulatory responses in vivo...
  18. 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...
  19. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
    ..Glide is also found to be more accurate than the recently described Surflex method...
  20. ncbi Identification of c-MYC as a target of the APC pathway
    T C He
    Howard Hughes Medical Institute and Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
    Science 281:1509-12. 1998
    ..to be repressed by wild-type APC and activated by beta-catenin, and these effects were mediated through Tcf-4 binding sites in the c-MYC promoter...
  21. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy...
  22. pmc FIMO: scanning for occurrences of a given motif
    Charles E Grant
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Bioinformatics 27:1017-8. 2011
    ..Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix...
  23. ncbi Transcriptional control of human p53-regulated genes
    Todd Riley
    The Institute for Advanced Study, Princeton, New Jersey, USA
    Nat Rev Mol Cell Biol 9:402-12. 2008
    ..In addition, we present the most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation.
  24. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
    ..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...
  25. ncbi A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    Kevin C Miranda
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, P O Box 218, NY 10598, USA
    Cell 126:1203-17. 2006
    We present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes...
  26. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    ..different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of ..
  27. pmc High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor
    Vadim Cherezov
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 318:1258-65. 2007
    ....
  28. pmc Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    Jie Wang
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 22:1798-812. 2012
    ..The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion...
  29. pmc An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
    ..Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin ..
  30. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
    ..JASPAR is available at http://jaspar.genereg.net...
  31. pmc Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    Lingyun Song
    Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Genome Res 21:1757-67. 2011
    ..to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start ..
  32. pmc RNAhybrid: microRNA target prediction easy, fast and flexible
    Jan Krüger
    Center for Biotechnology, CeBiTec, Universitat Bielefeld, 33594 Bielefeld, Germany
    Nucleic Acids Res 34:W451-4. 2006
    ..RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid...
  33. 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...
  34. pmc Structure of a nanobody-stabilized active state of the β(2) adrenoceptor
    Søren G F Rasmussen
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
    Nature 469:175-80. 2011
    ..This structure provides insights into the process of agonist binding and activation...
  35. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
    ..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
  36. pmc A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution
    Sreeram V Ramagopalan
    Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
    Genome Res 20:1352-60. 2010
    ..VDR binding sites were significantly enriched near autoimmune and cancer associated genes identified from genome-wide ..
  37. ncbi Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    J Med Chem 49:6177-96. 2006
    ..Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives...
  38. pmc Targeting DNA double-strand breaks with TAL effector nucleases
    Michelle Christian
    Department of Plant Pathology, Iowa State University, Ames, Iowa 50011, USA
    Genetics 186:757-61. 2010
    ..Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites...
  39. pmc Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist
    Ellen Y T Chien
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 330:1091-5. 2010
    ..This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications...
  40. 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...
  41. ncbi Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    James A Wells
    Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street 503A, San Francisco, California 94156, USA
    Nature 450:1001-9. 2007
    ..Some of these small molecules are now making their way through clinical trials, so this high-hanging fruit might not be far out of reach...
  42. pmc The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist
    Veli Pekka Jaakola
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
    Science 322:1211-7. 2008
    ....
  43. pmc miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements
    Ashish Lal
    Immune Disease Institute, Children s Hospital Boston, Department of Pediatrics, Harvard Medical School, MA 02115, USA
    Mol Cell 35:610-25. 2009
    ..The E2F2 3'UTR lacks a predicted miR-24 recognition element. In fact, miR-24 regulates expression of E2F2, MYC, AURKB, CCNA2, CDC2, CDK4, and FEN1 by recognizing seedless but highly complementary sequences...
  44. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
    ..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
  45. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..The first pass identifies putative binding sites and compensates for genomic variation in the 'mappability' of sequences...
  46. pmc RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
    Socorro Gama-Castro
    Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, AP 565 A, Cuernavaca, Morelos 62100, Mexico
    Nucleic Acids Res 39:D98-105. 2011
    ..RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated...
  47. pmc Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31
    Amy C Groth
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genetics 166:1775-82. 2004
    ..These experiments demonstrate the potential for precise genetic engineering of the Drosophila genome with the phiC31 integrase system and will likely benefit research in Drosophila and other insects...
  48. 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
    Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin ..
  49. pmc The cyclin D1 gene is a target of the beta-catenin/LEF-1 pathway
    M Shtutman
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 96:5522-7. 1999
    ..Increased beta-catenin levels may thus promote neoplastic conversion by triggering cyclin D1 gene expression and, consequently, uncontrolled progression into the cell cycle...
  50. pmc The crystal structure of TAL effector PthXo1 bound to its DNA target
    Amanda Nga Sze Mak
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3 025 Seattle, WA 98019, USA
    Science 335:716-9. 2012
    ..Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition...
  51. pmc Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
    Stephen G Aller
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, CB105, La Jolla, CA 92037, USA
    Science 323:1718-22. 2009
    ..Two additional P-gp structures with cyclic peptide inhibitors demonstrate distinct drug-binding sites in the internal cavity capable of stereoselectivity that is based on hydrophobic and aromatic interactions...
  52. ncbi A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
    Alex Clop
    Unit of Animal Genomics, Department of Animal Production, Faculty of Veterinary Medicine and Centre for Biomedical Integrative Genoproteomics, University of Liège B43, 20 Boulevard de Colonster, 4000 Liege, Belgium
    Nat Genet 38:813-8. 2006
    ..Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation...
  53. pmc Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    Dominic Schmidt
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Science 328:1036-40. 2010
    ..Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution...
  54. pmc Crystal structure of the µ-opioid receptor bound to a morphinan antagonist
    Aashish Manglik
    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nature 485:321-6. 2012
    ..These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction...
  55. ncbi Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    Michael Weber
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
    Nat Genet 39:457-66. 2007
    ..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
  56. ncbi Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Mol Cell 15:185-97. 2004
    ..The specific role of Ago2 in guiding target RNA cleavage was confirmed independently by siRNA-based depletion of individual Ago members in combination with a sensitive positive-readout reporter assay...
  57. pmc Design and analysis of ChIP-seq experiments for DNA-binding proteins
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA
    Nat Biotechnol 26:1351-9. 2008
    ..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.
  58. ncbi A quantitative analysis of kinase inhibitor selectivity
    Mazen W Karaman
    Ambit Biosciences, 4215 Sorrento Valley Blvd, San Diego, California 92121, USA
    Nat Biotechnol 26:127-32. 2008
    ..We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity...
  59. pmc Automated design of synthetic ribosome binding sites to control protein expression
    Howard M Salis
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Biotechnol 27:946-50. 2009
    ..the need for trial and error optimization, we developed a predictive method for designing synthetic ribosome binding sites, enabling a rational control over the protein expression level...
  60. ncbi Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    Thomas A Halgren
    Schrodinger, L L C, 120 W 45th Street, New York, New York 10036, USA
    J Med Chem 47:1750-9. 2004
    ..Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01...
  61. pmc Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
    Neelanjan Mukherjee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell 43:327-39. 2011
    ..The number of binding sites per transcript, degree of HuR association, and degree of HuR-dependent RNA stabilization were positively ..
  62. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  63. pmc beta-catenin is a target for the ubiquitin-proteasome pathway
    H Aberle
    Max Planck Institute for Immunobiology, Department of Molecular Embryology, Freiburg, Germany
    EMBO J 16:3797-804. 1997
    ..We show that ubiquitination of beta-catenin is greatly reduced in Wnt-expressing cells, providing the first evidence that the ubiquitin-proteasome degradation pathway may act downstream of GSK3beta in the regulation of beta-catenin...
  64. pmc The role of dynamic conformational ensembles in biomolecular recognition
    David D Boehr
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
    Nat Chem Biol 5:789-96. 2009
    ....
  65. pmc Carbohydrate-binding modules: fine-tuning polysaccharide recognition
    Alisdair B Boraston
    Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6
    Biochem J 382:769-81. 2004
    ..The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands...
  66. ncbi The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
    Alexander G Baltz
    Max Delbruck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
    Mol Cell 46:674-90. 2012
    ..and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms...
  67. ncbi The SR protein family of splicing factors: master regulators of gene expression
    Jennifer C Long
    Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH42XU, UK
    Biochem J 417:15-27. 2009
    ..Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression...
  68. pmc An alternative mode of microRNA target recognition
    Sung Wook Chi
    Laboratory of Neuro Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York, USA
    Nat Struct Mol Biol 19:321-7. 2012
    ..We call position 6 the 'pivot' nucleotide and suggest a model in which a transitional 'nucleation bulge' leads to functional bulge mRNA-miRNA interactions, expanding the number of potential miRNA regulatory sites...
  69. pmc UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
    Daniel E Newburger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School and Harvard MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 37:D77-82. 2009
    ..assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. The UniPROBE database is available at http://thebrain.bwh.harvard...
  70. pmc Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2
    Scott B Hansen
    Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA
    Nature 477:495-8. 2011
    ....
  71. pmc Structure of the human histamine H1 receptor complex with doxepin
    Tatsuro Shimamura
    Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Kyoto 606 8501, Japan
    Nature 475:65-70. 2011
    ..Our study sheds light on the molecular basis of H(1)R antagonist specificity against H(1)R...
  72. pmc Structure of the human κ-opioid receptor in complex with JDTic
    Huixian Wu
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 485:327-32. 2012
    ....
  73. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011
    ..Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites corresponding to 239 position weight matrices ..
  74. pmc ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
    Willem Jan Welboren
    Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
    EMBO J 28:1418-28. 2009
    We used ChIP-Seq to map ERalpha-binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant...
  75. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
    ..Applications include the discovery of new transcription factor binding sites and protein domains...
  76. pmc Inferring direct DNA binding from ChIP-seq
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Nucleic Acids Res 40:e128. 2012
    ..motif enrichment analysis' (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ..
  77. pmc Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
    Nucleic Acids Res 37:W247-52. 2009
    ..expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g...
  78. pmc Structure of a beta1-adrenergic G-protein-coupled receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 454:486-91. 2008
    ....
  79. pmc Structural basis for RNA 3'-end recognition by Hfq
    Evelyn Sauer
    Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 108:13065-70. 2011
    ..The capacity of Hfq to occupy and sequester the RNA 3' end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation...
  80. pmc A map of open chromatin in human pancreatic islets
    Kyle J Gaulton
    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    Nat Genet 42:255-9. 2010
    ..These findings illuminate the tissue-specific organization of cis-regulatory elements and show that FAIRE-seq can guide the identification of regulatory variants underlying disease susceptibility...
  81. ncbi Transposable elements have rewired the core regulatory network of human embryonic stem cells
    Galih Kunarso
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
    Nat Genet 42:631-4. 2010
    ..These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells...
  82. pmc Heritable individual-specific and allele-specific chromatin signatures in humans
    Ryan McDaniell
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
    Science 328:235-9. 2010
    ..Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans...
  83. ncbi Refined structure of alpha beta-tubulin at 3.5 A resolution
    J Lowe
    MRC Laboratory of Molecular Biology, Cambridge, UK
    J Mol Biol 313:1045-57. 2001
    ..In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues.
  84. pmc Principles of activation and permeation in an anion-selective Cys-loop receptor
    Ryan E Hibbs
    Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
    Nature 474:54-60. 2011
    ..GluCl provides a framework for understanding mechanisms of fast inhibitory neurotransmission and allosteric modulation of Cys-loop receptors...
  85. pmc Structure of a V3-containing HIV-1 gp120 core
    Chih Chin Huang
    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
    Science 310:1025-8. 2005
    ..The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization...
  86. pmc Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming
    Yi Cao
    Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Dev Cell 18:662-74. 2010
    ..Therefore, in addition to regulating muscle gene expression, MyoD binds genome wide and has the ability to broadly alter the epigenome in myoblasts and myotubes...
  87. pmc Structure of an agonist-bound human A2A adenosine receptor
    Fei Xu
    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 332:322-7. 2011
    ..The results define the molecule UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration...
  88. pmc RNAstructure: software for RNA secondary structure prediction and analysis
    Jessica S Reuter
    Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
    BMC Bioinformatics 11:129. 2010
    ..RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence...
  89. ncbi RNA recognition motifs: boring? Not quite
    Antoine Cléry
    Institute for Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
    Curr Opin Struct Biol 18:290-8. 2008
    ..The extreme structural versatility of the RRM interactions explains why RRM-containing proteins have so diverse biological functions...
  90. pmc Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
    Stewart MacArthur
    Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
    Genome Biol 10:R80. 2009
    ....
  91. pmc Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    Robert K Bradley
    Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Biol 8:e1000343. 2010
    ....
  92. pmc A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
    Teemu D Laajala
    Turku Centre for Biotechnology, FI 20521 Turku, Finland
    BMC Genomics 10:618. 2009
    ..While numerous algorithms have recently been proposed for analysing the large ChIP-seq datasets, their relative merits and potential limitations remain unclear in practical applications...
  93. pmc Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
    Kimberly R Blahnik
    Department of Computer Science, University of California Davis, Davis, CA 95616, USA
    Nucleic Acids Res 38:e13. 2010
    Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome...
  94. pmc Principles of microRNA-target recognition
    Julius Brennecke
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e85. 2005
    ....
  95. pmc Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
    Gong Hong Wei
    Public Health Genomics Unit, National Institute for Health and Welfare THL and Genome Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
    EMBO J 29:2147-60. 2010
    ..The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo...
  96. 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...
  97. ncbi Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
    Cell 127:635-48. 2006
    ..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...
  98. pmc Benchmarking sets for molecular docking
    Niu Huang
    Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143 2550, USA
    J Med Chem 49:6789-801. 2006
    ..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
  99. pmc Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
    Benjamin A Shoemaker
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D518-24. 2010
    ..This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins...
  100. pmc Frequent gain and loss of functional transcription factor binding sites
    Scott W Doniger
    Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Comput Biol 3:e99. 2007
    ..We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs)...
  101. ncbi Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand
    Jian Ping Xiong
    Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
    Science 296:151-5. 2002
    ..Ligand binding induces small changes in the orientation of alphaV relative to beta3...

Research Grants73

  1. Computational Design of Small Molecule Drugs Inhibiting the Zinc Finger Transcrip
    David Sherris; Fiscal Year: 2010
    ..Using a homology model of VEZF1 and an active lead compound, M1012, potential binding sites on the VEZF1/DNA binding surface will be identified...
  2. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..TREs are the binding sites where the thyroid hormone receptor (TR) binds/acts as a transcription factor...
  3. Structure and function of urea transporters
    Ming Zhou; Fiscal Year: 2013
    ..if dvUT is a functional urea transporter, and if so, we will then use X-ray crystallography to identify urea binding sites. Although many functional studies suggest that UT operates by a channel-like mechanism, the transporter ..
  4. Mechanisms of action of ghrelin in muscle and adipose tissue in cancer-related ca
    Jose M Garcia; Fiscal Year: 2013
    ..to express luciferase and green fluorescent protein under control of a promoter that contains NF:B consensus binding sites. The role of NF:B will be confirmed by using NF:B antagonists...
  5. INSULIN RECEPTORS AND THE GLUCOSE TRANSPORT SYSTEM
    JERROLD MICHAEL OLEFSKY; Fiscal Year: 2013
    ..propose a number of new studies to explore this finding by using Chip sequencing to define the global promoter binding sites (cistrome) of both FOX01 and PPAR3...
  6. Interdisciplinary Research Training in Reproduction for Indian Fellows
    John C Herr; Fiscal Year: 2010
    ..by faculty expertise in X-ray crystallography of reproductive proteins, mathematical modeling of ligand binding sites and organic synthesis of new small molecule inhibitors and the testing of their contraceptive action...
  7. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..In addition, immunoprecipitates will shipped to GenPathway (San Diego, CA) to determine the RpoS binding sites in the V. cholerae genome...
  8. Present Homologous and Heterologous Antigen with Hepatitis E Virus
    R Holland Cheng; Fiscal Year: 2012
    ..to lower the reactivity of VLP to antibody- induced neutralization by structural alteration at antibody-binding sites, a mechanism that viruses have evolved to mediate their escape from host immune surveillance...
  9. Human Beta-Defensin-1 in HSV-1 Innate Immunity
    LISA KATHLEEN RYAN; Fiscal Year: 2010
    ..We will examine TLR 2, 7 and 9 signaling, induction of interferon regulatory factors and identification of binding sites of transcription factors in the hBD-1 promoter region...
  10. Bioflavonoid Effects on EGF Signaling and Cell Cycle Pathways in Prostate Cancer
    BARRY MATTHEW MARKAVERICH; Fiscal Year: 2013
    ..luteolin (L or LUT), and two synthetic ligands (BMHPC and ZN-2) interact with type II [3H]estradiol binding sites with high affinity (Kd" 5nM) and inhibit normal and malignant prostate cell proliferation in vivo and in vitro...
  11. Inhibition of bone formation by Prx1
    Mark S Nanes; Fiscal Year: 2013
    ..the mechanism of action of Prx1on the Osx promoter: Determine if Prx1 interacts with RUNX2 at their continuous binding sites on the Osx promoter. Pull down experiments will be used to study protein-protein interaction. 1C...
  12. MOLECULAR BIOLOGY OF HUMAN COAGULATION FACTOR V
    Thomas Ortel; Fiscal Year: 2010
    ..The specific aims of the present proposal are to define the PS specificity pocket(s) and membrane binding sites within the factor V C1 and C2 domains and to determine their contribution to prothrombinase assembly on both ..
  13. Pax8-PPARgamma regulation of transcription and metabolism in thyroid cancer
    RONALD JAY KOENIG; Fiscal Year: 2013
    ..first Specific Aim, chromatin immunoprecipitation - deep sequencing (ChIP-Seq) will be used to identify PPFP binding sites on a genome wide level...
  14. Regulation of apoptosis by PI 3-kinase/Akt signaling
    Geoffrey M Cooper; Fiscal Year: 2012
    ..period, global expression profiling combined with computational/experimental analysis of transcription factor binding sites has been used to characterize gene regulation by PI 3-kinase/Akt/GSK-3 signaling, both following growth factor ..
  15. Neuropeptide modulation of biogenic amine function and aggression in a crustacean
    Maria A Sosa; Fiscal Year: 2013
    ..actions of CNS biogenic amines will help to dramatically expand the inventory of potential target molecules, binding sites, messenger systems and genes for controlling or regulating various forms of interactive behaviors and will ..
  16. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
    ..Such genome-wide analyses are now capable of routinely identifying thousands of transcription factor binding sites in a single experiment...
  17. DlaT as a transcriptional regulator in non-replicating Mycobacterium tuberculosis
    Ruslana Bryk; Fiscal Year: 2012
    ..DlaT binding sites on Mtb's DNA will be located by ChIP-Seq and confirmed through secondary assays including in vitro ..
  18. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..Given our observation that SATB1 is down- regulated in LIC of AML patients, binding of SATB1 to low affinity binding sites may be abrogated and cause expression changes of genes involved in the formation or maintenance of LIC...
  19. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..next generation DNA sequencing (ChIP-Seq) and functional genomic methods to identify and characterize EBNA1 binding sites in the human genome...
  20. Regulation of insulator function and globin gene expression by USF and associated
    Suming Huang; Fiscal Year: 2013
    ..HS2 is perhaps the most powerful regulatory element in the LCR. It consists of several binding sites for hematopoietic and ubiquitously expressed transcription factors...
  21. MECHANISMS OF DENDRITE MORPHOGENESIS BY THE ANAPHASE-PROMOTING COMPLEX
    ALBERT HONG JAE KIM; Fiscal Year: 2013
    ..gene targets of cohesion in post-mitotic neurons will be identified through a genome-wide search for cohesion binding sites through chromatin immunoprecipitation coupled with next generation sequencing and correlated cohesion- ..
  22. Regulation of Rhox5 Transcriptional Elongation
    Marcy E Richardson; Fiscal Year: 2013
    ..A strong candidate to control AR recruitment is DNA methylation, as many of the AR- binding sites in the Pp are methylated in tissues and developmental stages that exhibit the elongation block...
  23. MUCOSAL DEFENSE MECHANISMS IN SUBSTANCE ABUSE
    David R Brown; Fiscal Year: 2010
    ..we will characterize changes in the ligand affinity and G protein coupling coupling of specific opioid binding sites in neural membranes from inflamed and uninflamed Peyer's patches by radioligand binding techniques...
  24. A Cis-regulatory Model for Neural Border Induction
    Daniel Meulemans Medeiros; Fiscal Year: 2013
    ..inducible, activated forms of these factors, and mutagenesis of evolutionarily conserved TCF/LEF and SMAD binding sites and, 2) Test for direct binding of the TCF/LEF-ss-catenin complex and SMAD1/5/8 to CREs using ChIP...
  25. REGULATION OF CXC CHEMOKINE EXPRESSION BY H. PYLORI
    Yoshio Yamaoka; Fiscal Year: 2013
    ..b>Binding sites for the transcription factors nuclear factor-:B (NF-:B), activator protein 1 (AP-1), interferon-stimulated ..
  26. Genome-wide measurement of bacterial transcriptional regulatory states
    Peter L Freddolino; Fiscal Year: 2013
    ..In the process of these development and validation experiments, follow-ups will target TF binding sites and specificities inferred from IPODHR data but not yet characterized in detail, further expanding our ..
  27. Molecular Determinants of DNA Sliding and Hopping by a DNA Repair Glycosylase
    MENG MENG ROWLAND; Fiscal Year: 2013
    ..transfer can occur (even in the absence of an energy- providing cofactor) if thermodynamically stable binding sites are inserted between the two uracil target sites...
  28. Biosynthetic Protein Models of Heme-copper Oxidases and Nitric Oxide Reductases
    Yi Lu; Fiscal Year: 2013
    ..expressed protein ligation (EPL) will be employed to introduce natural or unnatural amino acids into the metal-binding sites. Studies of the model proteins will be carried out using spectroscopy as well as X-ray crystallography...
  29. Thrombospondin 4 A1
    JOHN W LAWLER; Fiscal Year: 2010
    ..In Aim 1, we will identify the integrin, collagen and GAG binding sites in the COMP molecule...
  30. STRUCTURE AND FUNCTION OF HEPARIN COFACTOR II
    Douglas M Tollefsen; Fiscal Year: 2010
    ..2) Obtain evidence for activation of HCII upon binding to DS in the vessel wall, and identify HCII-binding sites in other tissues...
  31. Pbx Homeodomain Proteins in Skeletal Muscle Differentiation
    LISA A MAVES; Fiscal Year: 2011
    ..Pbx proteins bind broadly to, or specifically to only a subset of, muscle gene promoters, genome-wide Pbx binding sites will be determined using a global chromatin immunoprecipitation approach...
  32. EICOSANOID SYNTHESIS AND FUNCTION IN CORONARY VESSELS
    WILLIAM BRYSON CAMPBELL; Fiscal Year: 2010
    ..We will determine if the EETs have specific binding sites/receptors on membranes from coronary arteries, ECs and smooth muscle cells using agonist analogs that ..
  33. Humanized Transgenic Mice Reproduce the Disease Evolution in Severe RA
    Grete Sonderstrup; Fiscal Year: 2010
    ..HLA- DR*0401 gene and a luciferase transgene (controlled by a minimal Drosophila promoter activated by 3 NF:B binding sites), which will facilitate continuous in vivo monitoring of the disease process...
  34. Lipocalin 2 in Inflammation and Metabolic Control
    Xiaoli Chen; Fiscal Year: 2012
    ..LCN2 promoter possesses NF-(B and C/EBP binding sites and glucocorticoid response element;and LCN2 secretion is highly regulated by LPS and TNF(...
  35. DEVELOPMENT OF SPLIT DAMID AS AN ALTERNATIVE METHODOLOGY TO CHROMATIN IMMUNOPRECI
    Raphael Kopan; Fiscal Year: 2010
    ..when fused to interacting transcription factors, the halves will reconstitute enzymatic activity only at the binding sites where these transcription factors interact...
  36. Translating human PPARy binding regions to gene regulation and metabolic disease
    RAYMOND EDWARD SOCCIO; Fiscal Year: 2013
    ..used chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) to identify the genome-wide binding sites, or cistrome, for PPAR in cultured human adipocytes...
  37. Epigenetic Changes in the Glucocorticoid Receptor Gene Due to Arsenic Exposure
    Andrea M Allan; Fiscal Year: 2013
    ..Methylation specific DNA sequencing of the GR promoter showed greater methylation at one of the transcription binding sites in the prenatal arsenic offspring...
  38. Live cell imaging of IgH and c-Myc gene loci and the role of nuclear organization
    Mark T Groudine; Fiscal Year: 2010
    ..compartments and specific loci (via fluorescently tagged LacI and TetR binding to arrays of LacO and TetO binding sites). LacO and TetO arrays will be integrated at the c-Myc and IgH loci, respectively to label those genes...
  39. High-throughput multiplex microsphere screening for toxin protease inhibitors
    Steven W Graves; Fiscal Year: 2012
    ..that will enable the discovery of inhibitor compounds that target protease interactions with substrate binding sites distal to the active site...
  40. Molecular mechanisms of bacterial homologs of neurotransmitter:sodium symporters
    Jonathan A Javitch; Fiscal Year: 2013
    ..vestibule was identified during the previous project period;binding and flux experiments showed that the two binding sites can be occupied simultaneously...
  41. Genome-Wide Analysis of RXR-alpha Binding In Mouse Liver Chromatin with ChIP-SEQ
    SAUL JOSEPH KARPEN; Fiscal Year: 2010
    ..specifically those regulated by RXR(-containing heterodimer pairs, yet we only know a small fraction of RXR( binding sites in the genome...
  42. Biophysics of Drug Interactions with Viral Episomes
    James K Bashkin; Fiscal Year: 2013
    ..Aim 2 Footprint the HPV18 genome in vitro with antiviral PAs. Identify related binding sites for both HPV16 and 18...
  43. PAX2 gene targets, binding sites and function
    Patrick D Brophy; Fiscal Year: 2010
    ..As such, it may provide novel insight into the mechanisms controlling the normal differentiation and proliferation of epithelium as well as those involved in both congenital and acquired human disease processes. ..
  44. Roles of Hox genes in skin and hair follicle development
    Alexander Awgulewitsch; Fiscal Year: 2010
    ..We will test functionality of putative Foxql and Hoxc13 binding sites in the promoter region of Dsc2 as a paradigm in vitro, and determine whether these mediate potential ..
  45. C MYC--TRANSCRIPTION AND APOPTOSIS
    Chi V Dang; Fiscal Year: 2011
    ..Our genome-wide chromatin immunoprecipitation study of Myc binding sites in neoplastic human P493 B cell model with inducible MYC and our recent genome wide measure of nuclear run-on ..
  46. Striated Muscle Gene Transcription and Regulatory Gene Cassettes for Gene Therapy
    STEPHEN DENISON HAUSCHKA; Fiscal Year: 2012
    ..dimerization depends on drug concentration, the transcription rate of therapeutic cDNAs linked to unique DNA- binding sites for the ATF can then be regulated by manipulating drug dosage. PUBLIC HEALTH RELEVANCE...
  47. TRANSGENIC ANALYSIS OF PLATELET RECEPTOR EXPRESSION
    Jerry Ware; Fiscal Year: 2012
    ..the hypothesis that Pt-vWD mimics GP Ib-IX blockade and presents neoepitopes, analogous to the ligand-induced binding sites characterized for platelet integrin receptors (Aim 2)...
  48. A cell-specific inducible model of hearing loss
    Albert S Edge; Fiscal Year: 2011
    ..In this construct the human caspase-3 gene is fused with FK506 binding sites, adding a further layer of control. Activity of the transgene will be tested in vitro and in vivo in Aim 1a...
  49. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..Target gene expression will be monitored using a Renilla luciferase reporter with three miR-122 binding sites from the cationic amino acid transporter 1 (CAT-1) mRNA, qPCR for five endogenous target mRNAs, and by Western ..
  50. Alternative regulation of ISGs in WNV-infected cells
    Margo A Brinton; Fiscal Year: 2013
    ..Under Aim 1, we will map the critical transcription factor binding sites (TFBSs) involved in interferon-independent up-regulation of ISGs in the promoters of model ISGs that are ..
  51. Mechanisms of vascular-specific gene regulation by estrogen
    Gavin R Schnitzler; Fiscal Year: 2013
    ..ChIP-seq and bioinformatic studies also indicate that only a small fraction of the genomewide ER[unreadable] binding sites in mouse aorta overlap with ER[unreadable] binding sites in mouse liver, and that consensus sequences for ..
  52. Identification of the transcriptional regulators of chondrocyte hypertrophy
    ANDREW BRUCE LASSAR; Fiscal Year: 2013
    ..established: (1) that FoxA factors are specifically expressed in differentiated chondrocytes, (2) that FoxA binding sites are conserved in both avian and mammalian collagen X enhancers, (3) that mutation of FoxA binding sites in the ..
  53. Integration of Signaling Pathways Regulating Chondrocyte Differentiation
    Sherrill L Adams; Fiscal Year: 2010
    ..T3, RA and BMP signaling pathways converge on a small distal region of the chick Col10 promoter that contains binding sites for multiple transcription factors, including RA receptors, Runx2, an Ets family member and two DNA-bending ..
  54. Nuclear Function of Abl in DNA Damage Response
    Jean Y J Wang; Fiscal Year: 2012
    ..several thousand genes using a fiber-optic bead array-based technology;(3) identify DNA damage-induced genomic binding sites for Abl using the human genome tiling arrays, because we have found that doxorubicin causes an enhanced ..
  55. Dietary HDAC Inhibitors in Colon Cancer Prevention
    Roderick H Dashwood; Fiscal Year: 2012
    ..de- repress'epigenetically silenced genes, such as P21/WAF1, through Sp1/Sp3 transcription factor binding sites in the corresponding gene promoters, causing growth arrest/apoptosis in cancer cells...
  56. Phosphoprotein CDP138 regulates glucose metabolism
    ZHEN YUE JIANG; Fiscal Year: 2013
    ..Second, we wil identify lipid-binding sites in the C2 domain and test their role in GLUT4 translocation and GLUT4 vesicle - PM fusion in live cels...
  57. microRNA and Down Syndrome
    Karl H Obrietan; Fiscal Year: 2010
    ..all of the Hsa21-derived miRNA/mRNA pairs were re-analyzed for the presence of multiple Hsa21-derived miRNA binding sites. This list of candidate targets was subsequently prioritized with respect to the potential clinical relevance ..
  58. Regulation of guanylyl cyclase A and B by hormones, ATP and phosphorylation
    Lincoln Ross Potter; Fiscal Year: 2013
    ..first aim will measure the effects of structurally unique and reactive purines on the kinetic properties and binding sites of GC-A and GC-B...
  59. Microbial regulation of intestinal gene expression through microRNA
    Sushila Dalal; Fiscal Year: 2012
    ..I will also use quantitative PCR to determine whether miRNAs with predicted binding sites on Hsp70 have altered expression in stool- transplanted germ-free mice or mouse stool exposed YAMC cells...
  60. Regulators of Cancer-Specific DNA Hypermethylation.
    Jean Pierre J Issa; Fiscal Year: 2013
    ..in myeloid leukemia and colorectal carcinomas) and (b) to identify the genomic (transcription factor binding sites, retrotransposons, short direct repeats) and epigenomic (histone modifications in normal cells) factors that ..
  61. Estrogen and TMJ Pain
    Phillip R Kramer; Fiscal Year: 2013
    ..A homology search for estrogen receptor [unreadable] and [unreadable] (ER [unreadable] and ER[unreadable]) binding sites 10kb of the transcriptional start site for these three genes showed that at least one potential binding site ..
  62. Analysis of the Human c-myc Gene Replication Origin
    Michael Leffak; Fiscal Year: 2012
    ..Aim 1 will use deletion analysis to identify protein binding sites in the c-myc replicator by quantitative chromatin immunoprecipitation (ChIP), define the minimal c-myc ..
  63. Point-of Care System for Determination of Bilirubin Capacity in Neonates
    GLEN D RAMSAY; Fiscal Year: 2010
    ..Despite considerable work indicating that the level of bilirubin in the blood relative to the level of albumin binding sites is a key factor in assessing risk for bilirubin associated brain damage, management of neonatal jaundice ..
  64. DOSAGE COMPENSATION IN DROSOPHILA
    Bruce Baker; Fiscal Year: 1999
    ..Baker has developed FISH based method to finally provide the technical means of deletion mapping the binding sites. The first specific aim is to determine how the MSL-2 gene is regulated...
  65. ANESTHETIC MECHANISMS AND GABA-A RECEPTOR STRUCTURE
    MYLES AKABAS; Fiscal Year: 2001
    ..Progress has been made towards identifying the binding sites for these drugs...
  66. Monovalent metal ion binding sites in nucleic acids
    SCOTT STROBEL; Fiscal Year: 2004
    The overall objective of this proposal is to identify and characterize specific monovalent metal ion binding sites within RNA tertiary structures. Metal ions act as essential cofactors in the folding of RNAs...
  67. PROMYELOCYTIC ZINC FINGER GENE
    Jennifer Morris; Fiscal Year: 1999
    ..the nine C2H2 zinc fingers will be used to affinity select (by gel shift assays or chromatography) DNA binding sites from a degenerate oligonucleotide library and a genomic DNA fragment library...
  68. Cardiolipin Function in Mitochondrial Electron-Transfer Complexes
    Neal C Robinson; Fiscal Year: 2011
    ..Cardiolipin binding to cytochrome c oxidase is well defined and the binding sites have been localized within the enzyme...
  69. NEUROCHEMICAL CORRELATES OF CEREBELLAR DEVELOPMENT
    Andrej Rotter; Fiscal Year: 1992
    ..GABA/BZ receptor binding sites will be autoradiographically localized with the receptor specific ligands, [3H]muscimol and [3H]flunitrazepam; ..
  70. PAF AND PRE-IMPLANTATION/IMPLANTATION PHENOMENA
    Michael Harper; Fiscal Year: 1991
    This proposal will investigate the physiological role of binding sites for platelet-activating factor (PAF), a glycerophospholipid, with potent smooth-muscle stimulating and vascular permeability inducing properties...
  71. Novel lead molecule optimization targeting nicotinic receptor subtypes
    DENNIS BRIAN contact MCKAY; Fiscal Year: 2010
    ..3) most drug discovery programs in this area targeting orthosteric sites [endogenous agonist (acetylcholine) binding sites], and 4) few drugs that are selectively targeting specific subtypes of nAChRs being identified, new approaches ..
  72. MOLECULAR MARKER FOR INVASIVE CANDIDA ALBICANS
    MARGARET HOSTETTER; Fiscal Year: 2001
    ..alpha INT1 gene product contains a ligand binding site for iC3b and fibrinogen, two EF-hand divalent cation binding sites, a hydrophobic transmembrane domain, and a tyrosine residue in the cytoplasmic tail...
  73. RADIOLIGANDS FOR CENTRAL NORADRENERGIC UPTAKE SITES
    Shanaz Tejani Butt; Fiscal Year: 1992
    ..A major advance in recent years has been the identification of high affinity binding sites for tricyclic antidepressants, in particular, sites in the brain to which labelled imipramine binds...