nucleosomes

Summary

Summary: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.

Top Publications

  1. ncbi Chromatin modifications and their function
    Tony Kouzarides
    The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB21QN, UK
    Cell 128:693-705. 2007
  2. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
  3. ncbi 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
  4. ncbi A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    Travis N Mavrich
    Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 18:1073-83. 2008
  5. ncbi Nucleosome positioning and gene regulation: advances through genomics
    Cizhong Jiang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 10:161-72. 2009
  6. ncbi The biology of chromatin remodeling complexes
    Cedric R Clapier
    Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Annu Rev Biochem 78:273-304. 2009
  7. ncbi The role of chromatin during transcription
    Bing Li
    Stowers Medical Research Institute, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 128:707-19. 2007
  8. ncbi Histone H4-K16 acetylation controls chromatin structure and protein interactions
    Michael Shogren-Knaak
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 311:844-7. 2006
  9. ncbi Two strategies for gene regulation by promoter nucleosomes
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 18:1084-91. 2008
  10. ncbi Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP
    Daniel R Foltz
    Ludwig Institute for Cancer Research, La Jolla, CA 92093 0670, USA
    Cell 137:472-84. 2009

Research Grants

  1. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    Stephen J Lippard; Fiscal Year: 2010
  2. In vivo imaging of X inactivation
    Matthew Levy; Fiscal Year: 2010
  3. Molecular Architecture of the Regional Kinetochore in Fission Yeast
    Xiangwei He; Fiscal Year: 2010
  4. Immunoglobulin Somatic Mutation
    Ursula Storb; Fiscal Year: 2007
  5. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2004
  6. Molecular Mechanisms of Chromosome Segregation in Yeast
    Jennifer L Gerton; Fiscal Year: 2010
  7. Heterochromatin on the human inactive X chromosome
    Brian P Chadwick; Fiscal Year: 2010
  8. Transcriptional elongation and splicing in human genes in situ
    Richard A Padgett; Fiscal Year: 2010
  9. Elongation of Yeast Pol II Through Nucleosomes
    Michael F Carey; Fiscal Year: 2010
  10. Uracil Damage Recognition by Uracil DNA Glycosylase
    James T Stivers; Fiscal Year: 2010

Detail Information

Publications244 found, 100 shown here

  1. ncbi Chromatin modifications and their function
    Tony Kouzarides
    The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB21QN, UK
    Cell 128:693-705. 2007
    The surface of nucleosomes is studded with a multiplicity of modifications. At least eight different classes have been characterized to date and many different sites have been identified for each class...
  2. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
    ..The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry...
  3. ncbi 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...
  4. ncbi A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    Travis N Mavrich
    Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 18:1073-83. 2008
    Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR)...
  5. ncbi Nucleosome positioning and gene regulation: advances through genomics
    Cizhong Jiang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 10:161-72. 2009
    Knowing the precise locations of nucleosomes in a genome is key to understanding how genes are regulated...
  6. ncbi The biology of chromatin remodeling complexes
    Cedric R Clapier
    Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Annu Rev Biochem 78:273-304. 2009
    The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements...
  7. ncbi The role of chromatin during transcription
    Bing Li
    Stowers Medical Research Institute, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 128:707-19. 2007
    ..In this Review, we highlight advances in our understanding of chromatin regulation and discuss how such regulation affects the binding of transcription factors as well as the initiation and elongation steps of transcription...
  8. ncbi Histone H4-K16 acetylation controls chromatin structure and protein interactions
    Michael Shogren-Knaak
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 311:844-7. 2006
    ....
  9. ncbi Two strategies for gene regulation by promoter nucleosomes
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 18:1084-91. 2008
    ..By analyzing genome-wide data of nucleosome positioning in yeast, we find that the presence of nucleosomes close to the transcription start site is associated with high transcriptional plasticity, while nucleosomes at ..
  10. ncbi Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP
    Daniel R Foltz
    Ludwig Institute for Cancer Research, La Jolla, CA 92093 0670, USA
    Cell 137:472-84. 2009
    ..The proteins responsible for assembly of human CENP-A into centromeric nucleosomes during the G1 phase of the cell cycle are shown here to be distinct from the chromatin assembly factors ..
  11. ncbi Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis
    Hideaki Tagami
    Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
    Cell 116:51-61. 2004
    ..This finding provides new insights into possible mechanisms for maintenance of epigenetic information after chromatin duplication...
  12. ncbi The role of nucleosome positioning in the evolution of gene regulation
    Alexander M Tsankov
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Biol 8:e1000414. 2010
    ..has also substantially diverged in both global quantitative features, such as spacing between adjacent nucleosomes, and in functional groups of genes...
  13. ncbi Biased chromatin signatures around polyadenylation sites and exons
    Noah Spies
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Mol Cell 36:245-54. 2009
    ..Together, these findings provide evidence for extensive functional connections between chromatin structure and RNA processing...
  14. ncbi FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    Paul G Giresi
    Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 17:877-85. 2007
    DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases...
  15. ncbi What controls nucleosome positions?
    Eran Segal
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
    Trends Genet 25:335-43. 2009
    The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins...
  16. ncbi Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
    Alexandra B Lantermann
    Adolf Butenandt Institut, University of Munich, Munich, Germany
    Nat Struct Mol Biol 17:251-7. 2010
    Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes...
  17. ncbi Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4
    Michiel Vermeulen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D 82152 Martinsried, Germany
    Cell 131:58-69. 2007
    ..Our experiments reveal crosstalk between histone modifications and the transcription factor TFIID. This has important implications for regulation of RNA polymerase II-mediated transcription in higher eukaryotes...
  18. ncbi Cse4 is part of an octameric nucleosome in budding yeast
    Raymond Camahort
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 35:794-805. 2009
    The budding yeast CenH3 histone variant Cse4 localizes to centromeric nucleosomes and is required for kinetochore assembly and chromosome segregation...
  19. ncbi Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genome Res 19:1732-41. 2009
    The genomes of higher organisms are packaged in nucleosomes with functional histone modifications...
  20. ncbi Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II
    Olga I Kulaeva
    Department of Pharmacology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
    Nat Struct Mol Biol 16:1272-8. 2009
    ..This coupling is a distinct feature of the Pol II-type mechanism that allows further transcription through the nucleosome, prevents nucleosome translocation and minimizes displacement of H3 and H4 histones from DNA during enzyme passage...
  21. ncbi 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
    ..Closer examination reveals that H3K36me3 is found on well-positioned nucleosomes at exon 5' ends, and that this modification is a global mark of exon expression that also correlates with ..
  22. ncbi Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
    Steven J Petesch
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Cell 134:74-84. 2008
    To efficiently transcribe genes, RNA Polymerase II (Pol II) must overcome barriers imposed by nucleosomes and higher-order chromatin structure...
  23. ncbi HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres
    Muhammad Shuaib
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, The Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, Universite de Strasbourg, Parc d Innovation, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
    Proc Natl Acad Sci U S A 107:1349-54. 2010
    ..Our data identified HJURP as a vertebrate CENP-A chaperone and dissected its mode of interactions with CENP-A...
  24. ncbi Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA
    ShinWu Jeong
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, NOR 8302L, 9181, Los Angeles, CA 90089 9181, USA
    Mol Cell Biol 29:5366-76. 2009
    ..We used sucrose density gradients of nucleosomes prepared by partial and maximum micrococcal nuclease digestion, coupled with Western blot analysis to probe for ..
  25. ncbi H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis
    S Vinod Kumar
    John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
    Cell 140:136-47. 2010
    ..In a forward genetic screen in Arabidopsis, we have found that nucleosomes containing the alternative histone H2A.Z are essential to perceiving ambient temperature correctly...
  26. ncbi Conserved nucleosome positioning defines replication origins
    Matthew L Eaton
    Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Genes Dev 24:748-53. 2010
    ..and nucleosome positioning, we show that yeast origins are characterized by an asymmetric pattern of positioned nucleosomes flanking the ACS...
  27. ncbi A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
    Vladimir R Ramirez-Carrozzi
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
    Cell 138:114-28. 2009
    ..nucleosome occupancy at promoters in this class can be attributed to the assembly of CpG islands into unstable nucleosomes, which may lead to SWI/SNF independence...
  28. ncbi DNA methylation increases nucleosome compaction and rigidity
    John S Choy
    Department of Physics, Bio X Program, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 132:1782-3. 2010
    ..Our studies show that DNA methylation induces a more compact and rigid nucleosome structure, providing a physical basis for how DNA methylation might contribute to regulating chromatin structure...
  29. ncbi Reconstitution of nucleosome core particles from recombinant histones and DNA
    Pamela N Dyer
    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
    Methods Enzymol 375:23-44. 2004
  30. ncbi Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer
    Manu Shubhdarshan Shukla
    Universite Joseph Fourier Grenoble 1, Institut National de la Sante et de la Recherche Medicale, Institut Albert Bonniot, U823, Site Santé BP 170, 38042 Grenoble Cedex 9, France
    Proc Natl Acad Sci U S A 107:1936-41. 2010
    ..remodelers are sophisticated nano-machines that are able to alter histone-DNA interactions and to mobilize nucleosomes. Neither the mechanism of their action nor the conformation of the remodeled nucleosomes are, however, yet well ..
  31. ncbi The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres
    Nikolina Sekulic
    Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104 6059, USA
    Nature 467:347-51. 2010
    ..DNA topological analysis indicates that CENP-A-containing nucleosomes are octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals...
  32. ncbi A high-resolution atlas of nucleosome occupancy in yeast
    William Lee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Nat Genet 39:1235-44. 2007
    ..of nucleosome occupancy across the whole Saccharomyces cerevisiae genome, identifying over 70,000 positioned nucleosomes occupying 81% of the genome...
  33. ncbi The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions
    Andrew J Andrews
    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523 1870, USA
    Mol Cell 37:834-42. 2010
    The organization of the eukaryotic genome into nucleosomes dramatically affects the regulation of gene expression. The delicate balance between transcription and DNA compaction relies heavily on nucleosome dynamics...
  34. ncbi Relationship between nucleosome positioning and DNA methylation
    Ramakrishna K Chodavarapu
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 466:388-92. 2010
    b>Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer...
  35. ncbi From DNA sequence to transcriptional behaviour: a quantitative approach
    Eran Segal
    Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 10:443-56. 2009
    ..been recently gained through quantitative models that describe how molecules such as transcription factors and nucleosomes interact with genomic sequences...
  36. ncbi G+C content dominates intrinsic nucleosome occupancy
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
    BMC Bioinformatics 10:442. 2009
    The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging...
  37. ncbi Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II
    Vladimir A Bondarenko
    Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 675 Hoes Lane, Room 405, Piscataway, New Jersey 08854, USA
    Mol Cell 24:469-79. 2006
    b>Nucleosomes uniquely positioned on high-affinity DNA sequences present a polar barrier to transcription by human and yeast RNA polymerase II (Pol II)...
  38. ncbi The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct atomic force microscopy visualization of variant chromatin
    Fabien Montel
    Universite de Lyon, Laboratoire Joliot Curie, CNRS USR 3010, Ecole Normale Superieure de Lyon, 69364 Lyon Cedex 07, France
    Biophys J 97:544-53. 2009
    ..organization of H1-free nucleosomal arrays is determined mainly by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existence of attractive interactions between nucleosomes to ..
  39. ncbi Phylogenomics of the nucleosome
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nat Struct Biol 10:882-91. 2003
    ..How these diverse functions have evolved from ancestral forms can be addressed by applying phylogenetic tools to increasingly abundant sequence data...
  40. ncbi Chromatin structure analyses identify miRNA promoters
    Fatih Ozsolak
    Department of Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Genes Dev 22:3172-83. 2008
    ..Furthermore, DNA sequences encoding mature miRNAs were found to be preferentially occupied by positioned-nucleosomes, and the 3' end sites of known genes exhibited nucleosome depletion...
  41. ncbi Activator control of nucleosome occupancy in activation and repression of transcription
    Gene O Bryant
    Molecular Biology Program, Sloan Kettering Institute, New York, New York, United States of America
    PLoS Biol 6:2928-39. 2008
    ..The universal transcriptional activator Gal4 removes promoter nucleosomes as it triggers transcription, but how it does so has remained obscure...
  42. ncbi Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 6:365. 2010
    ..Differences in nucleosome positioning propagate to multiple adjacent nucleosomes, supporting the statistical positioning hypothesis, and we provide evidence that nucleosome-free regions, but ..
  43. ncbi Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome
    Sajad Hussain Syed
    Institut National de la Sante et de la Recherche Medicale, Universite Joseph Fourier Grenoble, Grenoble Cedex 9, France
    Proc Natl Acad Sci U S A 107:9620-5. 2010
    ..A molecular model on the basis of these data and coarse-grain DNA mechanics provides novel insights on how the different domains of H1 interact with the nucleosome and predicts a specific H1-mediated stem structure within linker DNA...
  44. ncbi Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly
    Qing Li
    Department of Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
    Cell 134:244-55. 2008
    ..1 (CAF-1) and Rtt106 participate in the deposition of newly synthesized histones onto replicating DNA to form nucleosomes. This process is critical for the maintenance of genome stability and inheritance of functionally specialized ..
  45. ncbi How eukaryotic genes are transcribed
    Bryan J Venters
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Crit Rev Biochem Mol Biol 44:117-41. 2009
    ..This review attempts to integrate the following concepts: (1) a well-defined organization of nucleosomes and modification states at most genes; (2) regulatory networks of sequence-specific transcription factors; (3) ..
  46. ncbi Crystal structures of nucleosome core particles containing the '601' strong positioning sequence
    Dileep Vasudevan
    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
    J Mol Biol 403:1-10. 2010
    ..Our findings indicate that DNA stretching is an intrinsically predisposed site-specific property of the nucleosome and suggest how NCP crystal structures with diverse DNA sequences can be obtained...
  47. ncbi SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes
    Mekonnen Lemma Dechassa
    Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901 4413, USA
    Mol Cell 38:590-602. 2010
    ..mononucleosomes, we demonstrate that remodeling leads to ordered and efficient disassembly of one of the two nucleosomes. An H2A/H2B dimer is first rapidly displaced, and then, in a slower reaction, an entire histone octamer is lost...
  48. ncbi A chromatin landmark and transcription initiation at most promoters in human cells
    Matthew G Guenther
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 130:77-88. 2007
    ..We found that nucleosomes with H3K4me3 and H3K9,14Ac modifications, together with RNA polymerase II, occupy the promoters of most protein-..
  49. ncbi Nucleosome positioning: how is it established, and why does it matter?
    Marta Radman-Livaja
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Dev Biol 339:258-66. 2010
    Packaging of eukaryotic genomes into chromatin affects every process that occurs on DNA. The positioning of nucleosomes on underlying DNA plays a key role in the regulation of these processes, as the nucleosome occludes underlying DNA ..
  50. ncbi Centromeric nucleosomes induce positive DNA supercoils
    Takehito Furuyama
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 138:104-13. 2009
    ..Centromere identity and inheritance require the assembly of nucleosomes containing the CenH3 histone variant in place of canonical H3...
  51. ncbi Mechanism of polymerase II transcription repression by the histone variant macroH2A
    Cécile Marie Doyen
    Institut Albert Bonniot, INSERM U309, 38706 La Tronche Cedex, France
    Mol Cell Biol 26:1156-64. 2006
    ....
  52. ncbi The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure
    Xu Lu
    Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, 1385 Center Avenue, Fort Collins, Colorado 80523 1870, USA
    Nat Struct Mol Biol 15:1122-4. 2008
    ..Here we present crystal structures of nucleosomes reconstituted with methylated histones and investigate the folding behavior of resulting arrays...
  53. ncbi MacroH2A allows ATP-dependent chromatin remodeling by SWI/SNF and ACF complexes but specifically reduces recruitment of SWI/SNF
    Evelyn Y Chang
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Biochemistry 47:13726-32. 2008
    The variant histone macroH2A helps maintain X inactivation and gene silencing. Previous work implied that nucleosomes containing macroH2A cannot be remodeled by ISWI and SWI/SNF chromatin remodeling enzymes...
  54. ncbi Repertoires of the nucleosome-positioning dinucleotides
    Thomas Bettecken
    CAGT Center for Applied Genotyping, Max Planck Institute of Psychiatry, Munich, Germany
    PLoS ONE 4:e7654. 2009
    ..Thus, the selection of the dinucleotides contributing to the chromatin code is species specific, and may differ from region to region, depending on the sequence context...
  55. ncbi A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    Cizhong Jiang
    Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, 456 North Frear Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 10:R109. 2009
    b>Nucleosomes have position-specific functions in controlling gene expression...
  56. ncbi Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription
    Hinrich Boeger
    Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 133:716-26. 2008
    ..based on a small number of simple assumptions, we demonstrate that random removal and reformation of promoter nucleosomes can account for stochastic and kinetic properties of PHO5 expression...
  57. ncbi Architecture of the SWI/SNF-nucleosome complex
    Mekonnen Lemma Dechassa
    Department of Biochemistry and Molecular Biology, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901 4413, USA
    Mol Cell Biol 28:6010-21. 2008
    The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a ..
  58. ncbi FACT facilitates chromatin transcription by RNA polymerases I and III
    Joanna L Birch
    Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, UK
    EMBO J 28:854-65. 2009
    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires ..
  59. ncbi Structural basis for the histone chaperone activity of Asf1
    Christine M English
    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
    Cell 127:495-508. 2006
    ..The Asf1-H3/H4 structure suggests a "strand-capture" mechanism whereby the H4 tail acts as a lever to facilitate chromatin disassembly/assembly that may be used ubiquitously by histone chaperones...
  60. ncbi High nucleosome occupancy is encoded at human regulatory sequences
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    PLoS ONE 5:e9129. 2010
    ..We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells...
  61. ncbi Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
    Raphaël Métivier
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Cell 115:751-63. 2003
    ....
  62. ncbi Chromatin fiber folding: requirement for the histone H4 N-terminal tail
    Benedetta Dorigo
    , Institute for Molecular Biology and Biophysics, , , Switzerland
    J Mol Biol 327:85-96. 2003
    ..Fully compacted chromatin fibers are obtained with any one of the histone tails deleted with the exception of the H4 N terminus. The region of the H4 tail, which mediates compaction, resides in the stretch of amino acids 14-19...
  63. ncbi Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin
    Bing Li
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Science 316:1050-4. 2007
    b>Nucleosomes must be deacetylated behind elongating RNA polymerase II to prevent cryptic initiation of transcription within the coding region...
  64. ncbi Herpes simplex virus type 1 tegument protein VP22 interacts with TAF-I proteins and inhibits nucleosome assembly but not regulation of histone acetylation by INHAT
    Hans van Leeuwen
    Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK
    J Gen Virol 84:2501-10. 2003
    ..Consistent with this possibility was the observation that overexpression of TAF-I in transfected cells interferes with the progression of HSV-1 infection...
  65. ncbi Histone variant nucleosomes: structure, function and implication in disease
    Mathieu Boulard
    Laboratoire Joliot Curie, CNRS UMR 5161 INRA 1237 IFR128 Biosciences Lyon Gerland Ecole Normale Supérieure de Lyon, 46 allee d Italie, 69007 Lyon, France
    Subcell Biochem 41:71-89. 2007
    ..In this article we will discuss the functional significance of histone variants on chromatin function and its link to disease manifestation..
  66. ncbi Transcription. Gene expression needs a break to unwind before carrying on
    Jean Francois Haince
    Health and Environment Unit, Faculty of Medicine, Laval University Medical Research Center, 2705 Boulevard Laurier, Quebec City, QC, G1V 4G2, Canada
    Science 312:1752-3. 2006
  67. ncbi The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control
    David J Dilworth
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Biol 171:955-65. 2005
    ....
  68. ncbi [Transcription on chromatin: overview]
    Kazuhiko Igarashi
    Tanpakushitsu Kakusan Koso 51:2067-8. 2006
  69. ncbi Structure and chromosomal DNA binding of the SWIRM domain
    Chengmin Qian
    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, One Gustave L Levy Place, New York, New York 10029, USA
    Nat Struct Mol Biol 12:1078-85. 2005
    ..These data suggest a functional role of the SWIRM domain in chromatin remodeling...
  70. ncbi Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo
    Thomas G Fazzio
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Mail stop A1 162, P O Box 19024, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Mol Cell Biol 25:9165-74. 2005
    We have previously shown that Saccharomyces cerevisiae Isw2 complex slides nucleosomes to remodel chromatin in vivo...
  71. ncbi SIR2 modifies histone H4-K16 acetylation and affects superhelicity in the ARS region of plasmid chromatin in Saccharomyces cerevisiae
    Francesco Chiani
    Dipartimento di Genetica e Biologia Molecolare, Universita di Roma La Sapienza, Rome, Italy
    Nucleic Acids Res 34:5426-37. 2006
    ..of negative supercoiling when SIR2 is overexpressed, and does not depend on the number or positioning of nucleosomes on plasmids...
  72. ncbi Transcription through chromatin by RNA polymerase II: histone displacement and exchange
    Olga I Kulaeva
    Department of Pharmacology, UMDNJ, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Mutat Res 618:116-29. 2007
    ..Here we propose that critical density of Pol II molecules could be required for displacement of the histone octamer and discuss mechanisms that are most likely involved in the processes of histone exchange...
  73. ncbi Chromatin structure and expression of a gene transcribed by RNA polymerase III are independent of H2A.Z deposition
    Aneeshkumar Gopalakrishnan Arimbasseri
    Centre for Cellular and Molecular Biology, Uppal Road, Tarnaka, Hyderabad 500007, India
    Mol Cell Biol 28:2598-607. 2008
    ..the in vivo chromatin structure of the gene region is characterized by the presence of an array of positioned nucleosomes, with only one of them in the 5' end of the gene having a regulatory role...
  74. ncbi Interplay between chromatin and trans-acting factors on the IME2 promoter upon induction of the gene at the onset of meiosis
    Tomomi Inai
    Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Kagamiyama, Higashi Hiroshima 739 8530, Japan
    Mol Cell Biol 27:1254-63. 2007
    ....
  75. ncbi H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation
    Alastair B Fleming
    Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
    Mol Cell 31:57-66. 2008
    ..We report that H2B ubiquitylation is required for efficient reassembly of nucleosomes during RNA polymerase II (Pol II)-mediated transcription elongation in yeast...
  76. ncbi Transition from a nucleosome-based to a protamine-based chromatin configuration during spermiogenesis in Drosophila
    Christina Rathke
    Philipps Universitat Marburg, Fachbereich Biologie, Entwicklungsbiologie, 35043 Marburg, Germany
    J Cell Sci 120:1689-700. 2007
    ..Finally, we show that histone modifications and removal are independent of protamine synthesis...
  77. ncbi Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock
    Sara J Zanton
    Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genes Dev 20:2250-65. 2006
    ..As expected, assembly of active transcription complexes is coupled to eviction of H2A.Z nucleosomes, and disassembly is coupled to the return of nucleosomes...
  78. ncbi Role of chromatin accessibility in the occupancy and transcription of the insulin gene by the pancreatic and duodenal homeobox factor 1
    Joshua Francis
    Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
    Mol Endocrinol 20:3133-45. 2006
    ....
  79. ncbi Evidence that the localization of the elongation factor Spt16 across transcribed genes is dependent upon histone H3 integrity in Saccharomyces cerevisiae
    Andrea A Duina
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genetics 177:101-12. 2007
    ....
  80. ncbi A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription
    Bong Gun Ju
    Howard Hughes Medical Institute, Department of Medicine, School of Medicine, 9500 Gilman Drive, University of California, San Diego, La Jolla, CA 92093 0648, USA
    Science 312:1798-802. 2006
    ..Our data mechanistically link DNA topoisomerase IIbeta-dependent dsDNA breaks and the components of the DNA damage and repair machinery in regulated gene transcription...
  81. ncbi [Structural biology of transcription on eukaryotic chromatin]
    Yoshifumi Nishimura
    Tanpakushitsu Kakusan Koso 50:1247-63. 2005
  82. ncbi Histone acetylation, chromatin remodelling and nucleotide excision repair: hint from the study on MFA2 in Saccharomyces cerevisiae
    Yachuan Yu
    Department of Pathology, School of Medicine, Cardiff University, Cardiff, UK
    Cell Cycle 4:1043-5. 2005
    ..UV irradiation triggers genome-wide histone hyperacetylation at both histone H3 and H4. However, in nucleosomes at the repressed MFA2 promoter only histone H3, but not histone H4, is hyperacetylated following UV...
  83. ncbi Histone acetylation: facts and questions
    P Loidl
    Department of Microbiology, University of Innsbruck Medical School, Austria
    Chromosoma 103:441-9. 1994
    ..b>Nucleosomes, the structural subunits of chromatin, have long been considered as static structures, incompatible with ..
  84. ncbi The Candida glabrata Amt1 copper-sensing transcription factor requires Swi/Snf and Gcn5 at a critical step in copper detoxification
    K A Koch
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0606, USA
    Mol Microbiol 40:1165-74. 2001
    ..Additionally, these data implicate the involvement of Swi/Snf and Gcn5 at multiple levels of AMT1 gene autoregulation...
  85. ncbi A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin
    Michiel Vermeulen
    NCMLS, Radboud University Nijmegen, Department of Molecular Biology, Geert Grooteplein Zuid 30, Nijmegen, The Netherlands
    Mol Cell Biol 26:5226-36. 2006
    ....
  86. ncbi Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions
    Loredana Verdone
    Fondazione Istituto Pasteur Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c o Dipartimento di Genetica e Biologia Molecolare, Universita La Sapienza, I 00185 Rome, Italy
    EMBO J 21:1101-11. 2002
    ....
  87. ncbi Transcription. Unlocking the gates to gene expression
    Christopher J Fry
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 295:1847-8. 2002
  88. ncbi Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation
    Evi Soutoglou
    Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Post Office Box 1527, 711 10 Herakleion, Crete, Greece
    Science 295:1901-4. 2002
    ..The results suggest that, at this promoter, chromatin reconfiguration is a defining step of the initiation process, acting after the assembly of the Pol II machinery...
  89. ncbi Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors
    Yael Katan-Khaykovich
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 16:743-52. 2002
    ..Our results also indicate that TBP occupancy depends on the presence of the activator, not histone acetylation status...
  90. ncbi Reconstitution of nucleosome positioning, remodeling, histone acetylation, and transcriptional activation on the PHO5 promoter
    Andrea R Terrell
    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
    J Biol Chem 277:31038-47. 2002
    ..Furthermore, we find that DNA binding, nucleosome remodeling, and transcriptional activation are separable steps, facilitating biochemical analysis of the PHO5 regulatory mechanism...
  91. ncbi Chromatin remodeling by RSC involves ATP-dependent DNA translocation
    Anjanabha Saha
    Howard Hughes Medical Institute and the Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
    Genes Dev 16:2120-34. 2002
    ..To test the relative contribution of twist to remodeling, we use nucleosomes containing nicks in precise locations to uncouple twist and translocation...
  92. ncbi Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10
    Chang Hui Shen
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 8028, USA
    Mol Cell Biol 22:6406-16. 2002
    ..Induction of CUP1 with copper resulted in targeted acetylation of both H3 and H4 at the CUP1 promoter. Nucleosomes containing upstream activating sequences and sequences farther upstream were the targets for H3 acetylation...
  93. ncbi Hepatic nuclear factor 1-alpha directs nucleosomal hyperacetylation to its tissue-specific transcriptional targets
    M Parrizas
    Endocrinology and Hormonal Biochemistry Units, Hospital Clinic, Institut d Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain 08036
    Mol Cell Biol 21:3234-43. 2001
    ..However, it is indispensable for hyperacetylation of histones in glut2 and pklr promoter nucleosomes in pancreatic islets but not in liver cells, where glut2 and pklr chromatin remains hyperacetylated in the ..
  94. ncbi Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene
    Y L Chua
    Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
    Plant Cell 13:599-612. 2001
    ..histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified...
  95. ncbi Co-repressor complexes and remodelling chromatin for repression
    A P Wolffe
    Laboratory of Molecular Embryology, National Institute of Child Heath and Human Development, NIH, Building 18T, Room 106, Bethesda, MD 20892 5431, USA
    Biochem Soc Trans 28:379-86. 2000
    ..Remarkably, both of these complexes also contain methyl-CpG-binding proteins. This observation provides a molecular mechanism to integrate DNA methylation fully into gene control in vertebrates...
  96. ncbi Remodeling chromatin structures for transcription: what happens to the histones?
    D J Steger
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802 4500, USA
    Bioessays 18:875-84. 1996
    ..of transcription factors for nucleosomal DNA is determined by the location of recognition sequences within nucleosomes, and by the cooperative interactions of multiple proteins targeting binding sites contained within the same ..
  97. ncbi Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo
    D Kadosh
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell Biol 18:5121-7. 1998
    ..indicate that the domain of histone deacetylation is highly localized, occurring over a range of one to two nucleosomes. Taken together with previous observations, these results define a novel mechanism of transcriptional ..
  98. ncbi Promoter structure and transcriptional activation with chromatin templates assembled in vitro. A single Gal4-VP16 dimer binds to chromatin or to DNA with comparable affinity
    M J Pazin
    Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0347, USA
    J Biol Chem 273:34653-60. 1998
    ..nucleosome positioning and transcriptional activation, we analyzed a series of promoter constructions in which nucleosomes were positioned by Gal4-VP16 at different locations relative to the RNA start site...
  99. ncbi Mutations in both the structured domain and N-terminus of histone H2B bypass the requirement for Swi-Snf in yeast
    J Recht
    Program in Molecular Biology, Sloan Kettering Cancer Center and Cornell University Graduate School of Medical Sciences, New York, NY 10021, USA
    EMBO J 18:229-40. 1999
    ..The phenotypes of double gcn5Deltasnf5Delta mutants suggest that histone acetylation may play both positive and negative roles in the activity of the Swi-Snf-remodeling factor...
  100. ncbi Histone octamer transfer by a chromatin-remodeling complex
    Y Lorch
    Department of Structural Biology, Stanford University School of Medicine, California 94305, USA
    Cell 96:389-92. 1999
    ..The mechanism may entail formation of a duplex displacement loop on the nucleosome, facilitating the entry of exogeneous DNA and the release of the endogenous molecule...
  101. ncbi The regulation of gene activity by histones and the histone deacetylase RPD3
    N Suka
    Department of Biological Chemistry, UCLA School of Medicine 90095, USA
    Cold Spring Harb Symp Quant Biol 63:391-9. 1998

Research Grants100

  1. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    Stephen J Lippard; Fiscal Year: 2010
    ..b>Nucleosomes, the building blocks of chromosomes, will be constructed with site-specific Pt-DNA adducts and structurally ..
  2. In vivo imaging of X inactivation
    Matthew Levy; Fiscal Year: 2010
    ..The project starts with the in vitro generation of histone peptides (and eventually entire reconstituted nucleosomes) with methylation and ubiquitination marks (David Allis and Tom Muir, Rockefeller University) that are then ..
  3. Molecular Architecture of the Regional Kinetochore in Fission Yeast
    Xiangwei He; Fiscal Year: 2010
    ..that the centromeric foundation of a fission yeast kinetochore is composed of an array of well-positioned nucleosomes, among which three contain centromere-specific histone H3 variant Cenp-A (Cnp1p), corresponding to three ..
  4. Immunoglobulin Somatic Mutation
    Ursula Storb; Fiscal Year: 2007
    ..2) How does the position of nucleosomes affect the SHM process? SHM occurs in clusters that suggest involvement of nucleosomes in the targeting of ..
  5. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2004
    ..the two main classes are the histone acetyltransferases and several types of ATPases that disrupt or relocate nucleosomes. Chromatin remodeling by ATPases is regulated by and is essential to the cell cycle, and histone ..
  6. Molecular Mechanisms of Chromosome Segregation in Yeast
    Jennifer L Gerton; Fiscal Year: 2010
    ..This histone variant is incorporated into nucleosomes with centromere sequence which is critical to direct the formation of the kinetochore, a multi-protein ..
  7. Heterochromatin on the human inactive X chromosome
    Brian P Chadwick; Fiscal Year: 2010
    ..small RNAs coincides with the heterochromatic form of DXZ4, and the small RNAs themselves directly align with nucleosomes bearing the heterochromatin modification H3K9me3...
  8. Transcriptional elongation and splicing in human genes in situ
    Richard A Padgett; Fiscal Year: 2010
    ..To support this idea, we have shown that exons are enriched in nucleosomes relative to adjacent intron sequences and that these exonic nucleosomes are also enriched in specific histone ..
  9. Elongation of Yeast Pol II Through Nucleosomes
    Michael F Carey; Fiscal Year: 2010
    ..Aim #3 will examine how histone chaperones, including Spt6, Asf1 and FACT, assemble and disassemble nucleosomes with an emphasis on how covalent modifications affect the process...
  10. Uracil Damage Recognition by Uracil DNA Glycosylase
    James T Stivers; Fiscal Year: 2010
    ..repair enzymes detect damaged DNA bases in the dramatically different contexts of naked duplex DNA as well as nucleosomes and chromatin...
  11. Histone Tail Interactions and Functions in Chromatin
    Jeffrey J Hayes; Fiscal Year: 2010
    ..characterize short-range and long-range inter- nucleosomal interactions of the H3 and H4 tail domains in model nucleosomes and nucleosome arrays, 2) Determine whether linker histone H1, the architectural transcription factor HMGN or a ..
  12. Histone Tail Interactions and Functions in Chromatin
    Jeffrey J Hayes; Fiscal Year: 2011
    ..characterize short-range and long-range inter- nucleosomal interactions of the H3 and H4 tail domains in model nucleosomes and nucleosome arrays, 2) Determine whether linker histone H1, the architectural transcription factor HMGN or a ..
  13. Genetic, Viral and Immunlogic Studies in New Zealand Mice
    SYAMAL DATTA; Fiscal Year: 2009
    ..We have found that autoimmune T and B cells of lupus recognize certain critical histone peptide epitope/s from nucleosomes, which in a low-dose tolerance regimen blocks pathogenesis and progression of lupus by inducing potent ..
  14. Genetic, Viral and Immunlogic Studies in New Zealand Mice
    Syamal K Datta; Fiscal Year: 2010
    ..We have found that autoimmune T and B cells of lupus recognize certain critical histone peptide epitope/s from nucleosomes, which in a low-dose tolerance regimen blocks pathogenesis and progression of lupus by inducing potent ..
  15. Hypoxia Signaling, Chromatin Remodeling and Nickel Carcinogenesis
    Max Costa; Fiscal Year: 2007
    ..and increase the methylation of H3 lysine 9 which is the chromatin mark of gene silencing for the individual nucleosomes. Methylation of H3 lysine 9 leads to DNA methylation and inherited gene silencing...
  16. Hypoxia Signaling, Chromatin Remodeling and Nickel Carcinogenesis
    Max Costa; Fiscal Year: 2007
    ..and increase the methylation of H3 lysine 9 which is the chromatin mark of gene silencing for the individual nucleosomes. Methylation of H3 lysine 9 leads to DNA methylation and inherited gene silencing...
  17. Hypoxia Signaling, Chromatin Remodeling and Nickel Carcinogenesis
    Max Costa; Fiscal Year: 2009
    ..and increase the methylation of H3 lysine 9 which is the chromatin mark of gene silencing for the individual nucleosomes. Methylation of H3 lysine 9 leads to DNA methylation and inherited gene silencing...
  18. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine Wilson; Fiscal Year: 2009
    ..Our supporting results show that BAF interacts with nucleosomes, influences several different histone posttranslational modifications in vivo, and associates in vivo with at ..
  19. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine L Wilson; Fiscal Year: 2010
    ..Our supporting results show that BAF interacts with nucleosomes, influences several different histone posttranslational modifications in vivo, and associates in vivo with at ..
  20. Immunoglobulin Somatic Mutation
    Ursula Storb; Fiscal Year: 2003
    ..2) How does the position of nucleosomes affect the SHM process? SHM occurs in clusters that suggest involvement of nucleosomes in the targeting of ..
  21. Immunoglobulin Somatic Mutation
    Ursula Storb; Fiscal Year: 2006
    ..2) How does the position of nucleosomes affect the SHM process? SHM occurs in clusters that suggest involvement of nucleosomes in the targeting of ..
  22. Mechanisms of Kinetochore Assembly
    Aaron F Straight; Fiscal Year: 2010
    ..dependent proteolysis in the targeting of centromere assembly factors to the chromosome to assemble new CENP-A nucleosomes. Second, using reconstituted biochemical systems we will study how CENP-A nucleosomes are recognized by other ..
  23. Structure of nucleosomes in complex with transcriptional regulators
    Karolin Luger; Fiscal Year: 2009
    ..In specific aim 2, the interaction of the transcription activator FoxA with highly defined nucleosomes will be studied...
  24. Structure of nucleosomes in complex with transcriptional regulators
    Karolin Luger; Fiscal Year: 2007
    ..In specific aim 2, the interaction of the transcription activator FoxA with highly defined nucleosomes will be studied...
  25. Novel nucleosome composition and modifications in protozoal parasite Toxoplasma g
    Sergio Oscar Angel; Fiscal Year: 2010
    ..Thus a major gap in our knowledge is how T. gondii nucleosomes are structured and post-translationally modified in the different stages of the parasite...
  26. Novel nucleosome composition and modifications in protozoal parasite Toxoplasma g
    SERGIO ANGEL; Fiscal Year: 2009
    ..Thus a major gap in our knowledge is how T. gondii nucleosomes are structured and post-translationally modified in the different stages of the parasite...
  27. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2010
    ..The detailed locations of nucleosomes along genomic DNA are critical for proper gene regulation - and therefore for the health and development of ..
  28. Histone Variants and Transcription-linked Deposition
    Kamran Ahmad; Fiscal Year: 2007
    ..b>Nucleosomes are formidable obstacles to proteins that must access DNA...
  29. Spinocerebellar ataxia 7 protein function
    Patrick Grant; Fiscal Year: 2007
    In the eukaryotic cell nucleus, DMA is packaged by histones into nucleosomes, the repeating subunits of chromatin...
  30. DNA LESIONS AND GENE EXPRESSION IN HYPOXIC LUNG DISEASE
    Mark N Gillespie; Fiscal Year: 2010
    ..It is evident that transcriptional activation requires the association between promoter DNA and nucleosomes to be altered such that the steric hindrance to transcription factor binding is removed, but it remains unclear ..
  31. DNA LESIONS AND GENE EXPRESSION IN HYPOXIC LUNG DISEASE
    Mark Gillespie; Fiscal Year: 2009
    ..It is evident that transcriptional activation requires the association between promoter DNA and nucleosomes to be altered such that the steric hindrance to transcription factor binding is removed, but it remains unclear ..
  32. Structure, Function and Evolution of DNA Repair Enzymes
    Susan Wallace; Fiscal Year: 2007
    ..but there is virtually no direct information on how BER enzymes process free radical-induced DNA damage in nucleosomes, which are the fundamental subunit of chromatin...
  33. ATP-dependent Chromatin Remodeling in Neural Development
    Gerald R Crabtree; Fiscal Year: 2010
    ..energy of ATP hydrolysis to control transitions between stable epigenetic states by exchanging or mobilizing nucleosomes thereby altering histone codes...
  34. PROPERTIES AND REGULATION OF P53 IN TUMOR CELLS
    Carol Prives; Fiscal Year: 2010
    ..One particular issue that has not yet been well addressed is how and when p53 locates its site in nucleosomes within chromatin...
  35. ATP-dependent Chromatin Remodeling in Neural Development
    Gerald Crabtree; Fiscal Year: 2009
    ..ATP-dependent chromatin remodeling complexes are thought to regulate the mobility of nucleosomes allowing binding of sequence-specific transcription factors...
  36. Enzymology and Function(s) of Histone Phosphorylation
    CHARLES DAVID ALLIS; Fiscal Year: 2011
    ..How arrays of nucleosomes are folded into higher-order structures, and how the dynamics of such compaction is regulated, are questions ..
  37. Enzymology and Function(s) of Histone Phosphorylation
    CHARLES DAVID ALLIS; Fiscal Year: 2010
    ..How arrays of nucleosomes are folded into higher-order structures, and how the dynamics of such compaction is regulated, are questions ..
  38. COORDINATE GENE REGULATION IN ANIMAL CELLS
    JOHN LIS; Fiscal Year: 2009
    ..In Aim 3, we investigate the mechanisms that bring about rapid large scale loss of nucleosomes over an entire activated locus...
  39. COORDINATE GENE REGULATION IN ANIMAL CELLS
    JOHN LIS; Fiscal Year: 2009
    ..In Aim 3, we investigate the mechanisms that bring about rapid large scale loss of nucleosomes over an entire activated locus...
  40. Core Histone Tall Interactions and Function in Chromatin
    JEFFREY HAYES; Fiscal Year: 2007
    Within the eukaryotic cell nucleus, DNA is associated with core histones to form nucleosomes; which are further assembled with ancillary proteins into a multi-faceted complex known as chromatin...
  41. ROLE OF MACROH2A IN CHROMATIN STRUCTURE AND FUNCTION
    John Pehrson; Fiscal Year: 1993
    ..Recently we discovered a new type of core histone, macroH2A (mH2A), which is present in about 3% of rat liver nucleosomes. It is three times the size of a conventional H2A, and has a novel hybrid structure consisting of a large ..
  42. HISTONE GENE EXPRESSION IN YEAST
    M Smith; Fiscal Year: 2007
    The bulk of eukaryotic nucleosomes are made up of four core histones: H2A, H2B, H3, and H4...
  43. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine Wilson; Fiscal Year: 2006
    ..We further discovered that BAF binds directly to histone H 1 and histone H3, suggesting that BAF interacts with nucleosomes and may either regulate or be influenced by chromatin structure in vivo...
  44. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine Wilson; Fiscal Year: 2007
    ..We further discovered that BAF binds directly to histone H 1 and histone H3, suggesting that BAF interacts with nucleosomes and may either regulate or be influenced by chromatin structure in vivo...
  45. Active Nanofluidics for Analysis of Chromatin and Genomic DNA Structures
    Shuichi Takayama; Fiscal Year: 2010
    ..genomic structures, such as replication forks, and epigenetic structures, as well as the distribution of nucleosomes, and organized chromatin regions...