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. pmc Determinants of nucleosome organization in primary human cells
    Anton Valouev
    Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA
    Nature 474:516-20. 2011
  3. 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
  4. 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
  5. doi 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
  6. 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
  7. doi 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
  8. pmc 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
  9. pmc A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
    Triantaffyllos Gkikopoulos
    Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
    Science 333:1758-60. 2011
  10. 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

Detail Information

Publications284 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. pmc Determinants of nucleosome organization in primary human cells
    Anton Valouev
    Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA
    Nature 474:516-20. 2011
    b>Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation...
  3. 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...
  4. 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...
  5. doi 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...
  6. 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...
  7. doi 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...
  8. pmc 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...
  9. pmc A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
    Triantaffyllos Gkikopoulos
    Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
    Science 333:1758-60. 2011
    The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA...
  10. 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
    ....
  11. pmc The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3
    Pascal Drané
    IGMBC Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch F 67400, France
    Genes Dev 24:1253-65. 2010
    ..3 nucleosomes. These findings establish a new link between the PML bodies and the regulation of pericentric DNA repeat ..
  12. pmc Point centromeres contain more than a single centromere-specific Cse4 (CENP-A) nucleosome
    Josh Lawrimore
    Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
    J Cell Biol 195:573-82. 2011
    ..All approximately five Cse4s may be associated with the CEN nucleosome, but we show that a mean of three Cse4s could be located within flanking nucleosomes at random sites that differ between chromosomes.
  13. pmc 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...
  14. doi Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state
    Peter J Skene
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Mol Cell 37:457-68. 2010
    ..Our data argue that MeCP2 may not act as a gene-specific transcriptional repressor in neurons, but might instead dampen transcriptional noise genome-wide in a DNA methylation-dependent manner...
  15. pmc 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...
  16. ncbi Crystal structure of the human centromeric nucleosome containing CENP-A
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nature 476:232-5. 2011
    ..the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A...
  17. doi Determinants and dynamics of genome accessibility
    Oliver Bell
    Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
    Nat Rev Genet 12:554-64. 2011
    ..advances in genome-scale methods are yielding increasingly detailed profiles of the genomic distribution of nucleosomes, their modifications and their modifiers...
  18. pmc 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). How nucleosomal organization is specified by the genome is less clear...
  19. pmc High-resolution genome-wide mapping of the primary structure of chromatin
    Zhenhai Zhang
    Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Cell 144:175-86. 2011
    ..its regulation mechanisms requires detailed knowledge of chromatin's primary structure-the assembly of nucleosomes throughout the genome...
  20. 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...
  21. doi A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    Zhenhai Zhang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Science 332:977-80. 2011
    Near the 5' end of most eukaryotic genes, nucleosomes form highly regular arrays that begin at canonical distances from the transcriptional start site...
  22. pmc MeCP2 binds cooperatively to its substrate and competes with histone H1 for chromatin binding sites
    Rajarshi P Ghosh
    Program in Molecular and Cellular Biology, University of Massachusetts, 611 N Pleasant Street, Amherst, MA 01003, USA
    Mol Cell Biol 30:4656-70. 2010
    ..This suggests that chromatin binding by MeCP2 and H1 in vivo should be viewed in the context of competitive multifactorial regulation...
  23. pmc Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 322:1845-8. 2008
    ..These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription...
  24. pmc Unstable tandem repeats in promoters confer transcriptional evolvability
    Marcelo D Vinces
    FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
    Science 324:1213-6. 2009
    ..Tandem repeats are variable elements in promoters that may facilitate evolutionary tuning of gene expression by affecting local chromatin structure...
  25. pmc 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...
  26. pmc Chromatin decouples promoter threshold from dynamic range
    Felix H Lam
    Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, 7 Divinity Avenue, Bauer 307, Cambridge, Massachusetts 02138, USA
    Nature 453:246-50. 2008
    ..Here we show that nucleosomes function largely to decouple the threshold of induction from dynamic range...
  27. ncbi Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes
    Raga Krishnakumar
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 319:819-21. 2008
    ..Thus, although H1 and PARP-1 have similar nucleosome-binding properties and effects on chromatin structure in vitro, they have distinct roles in determining gene expression outcomes in vivo...
  28. pmc Assembly of Drosophila centromeric nucleosomes requires CID dimerization
    Weiguo Zhang
    Department of Genome Dynamics, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 45:263-9. 2012
    ..The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue...
  29. pmc Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore
    Jan H Bergmann
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
    EMBO J 30:328-40. 2011
    Kinetochores assemble on distinct 'centrochromatin' containing the histone H3 variant CENP-A and interspersed nucleosomes dimethylated on H3K4 (H3K4me2)...
  30. pmc 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...
  31. pmc Epigenetic centromere propagation and the nature of CENP-a nucleosomes
    Ben E Black
    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA
    Cell 144:471-9. 2011
    ..We present a model for the assembly and deposition of centromeric nucleosomes that couples these processes to the cell cycle...
  32. pmc Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
    Colin R Lickwar
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Nature 484:251-5. 2012
    ..factor binding, and is mediated mainly by control of competition between transcription factors and nucleosomes. Our model predicts a clutch-like mechanism that rapidly engages a treadmilling transcription factor into a ..
  33. pmc 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-..
  34. pmc 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...
  35. 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...
  36. pmc The DNA-encoded nucleosome organization of a eukaryotic genome
    Noam Kaplan
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 458:362-6. 2009
    ..remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves...
  37. pmc 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...
  38. doi Does CTCF mediate between nuclear organization and gene expression?
    Rolf Ohlsson
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
    Bioessays 32:37-50. 2010
    ....
  39. 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...
  40. pmc 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 ..
  41. pmc 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...
  42. pmc 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...
  43. pmc Micrococcal nuclease does not substantially bias nucleosome mapping
    James Allan
    Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    J Mol Biol 417:152-64. 2012
    ..MNase has hitherto been very widely used to map nucleosomes, although concerns have been raised over its potential to introduce bias...
  44. ncbi FACT facilitates transcription-dependent nucleosome alteration
    Rimma Belotserkovskaya
    Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
    Science 301:1090-3. 2003
    The FACT (facilitates chromatin transcription) complex is required for transcript elongation through nucleosomes by RNA polymerase II (Pol II) in vitro...
  45. ncbi Nucleosome structure(s) and stability: variations on a theme
    Andrew J Andrews
    Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523 1870, USA
    Annu Rev Biophys 40:99-117. 2011
    ..The organization of DNA into nucleosomes and higher-order structures has profound implications for DNA accessibility...
  46. 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
  47. pmc Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo
    Minh Bui
    Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Cell 150:317-26. 2012
    ..Unlike exclusively octameric canonical H3 nucleosomes, CENP-A nucleosomes have been shown to exist as octamers, hexamers, and tetramers...
  48. pmc Tripartite organization of centromeric chromatin in budding yeast
    Kristina Krassovsky
    Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 109:243-8. 2012
    ..In most eukaryotes, the centromere consists of highly repetitive DNA sequences that are occupied by nucleosomes containing the CenH3 histone variant, whereas in budding yeast, a ∼120-bp centromere DNA element (CDE) that ..
  49. pmc Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks
    Haico van Attikum
    Division of Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    EMBO J 26:4113-25. 2007
    ..Thus, these two related chromatin remodelers have distinct roles in DSB repair and checkpoint activation...
  50. ncbi Chromatin compaction by a polycomb group protein complex
    Nicole J Francis
    Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    Science 306:1574-7. 2004
    ..Compaction by Polycomb proteins requires nucleosomes but not histone tails. Each Polycomb complex can compact about three nucleosomes...
  51. pmc Nucleosome accessibility governed by the dimer/tetramer interface
    Vera Böhm
    Abteilung Biophysik der Makromolekule, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Nucleic Acids Res 39:3093-102. 2011
    b>Nucleosomes are multi-component macromolecular assemblies which present a formidable obstacle to enzymatic activities that require access to the DNA, e.g. DNA and RNA polymerases...
  52. pmc Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
    Mythily Ganapathi
    Laboratory of Molecular Genetics, New York State Department of Health, Wadsworth Center, Albany, NY 12201 0509, USA
    Nucleic Acids Res 39:2032-44. 2011
    ..These results indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated...
  53. pmc Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions
    Taesoo Kim
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Cell 137:259-72. 2009
    ....
  54. pmc Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
    Noam Kaplan
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Biol 11:140. 2010
    ..We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo...
  55. pmc 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...
  56. pmc The effect of micrococcal nuclease digestion on nucleosome positioning data
    Ho Ryun Chung
    Department of Computational Molecular Biology, MPI für Molekulare Genetik, Berlin, Germany
    PLoS ONE 5:e15754. 2010
    ..More generally, our results show that data generated after MNase digestion of chromatin requires a matched control experiment in order to determine nucleosome positions...
  57. ncbi PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state
    Alejandra Loyola
    CNRS UMR 218, Institut Curie, Paris 75248, France
    Mol Cell 24:309-16. 2006
    ..Although the set of initial modifications present on H3.1 is permissive for further modifications, in H3.3 a subset cannot be K9me3. Thus, initial modifications impact final PTMs within chromatin...
  58. pmc 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...
  59. pmc Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity
    Manolis Papamichos-Chronakis
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Cell 144:200-13. 2011
    ..Z. In the absence of INO80, H2A.Z nucleosomes are mislocalized, and H2A...
  60. pmc 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...
  61. pmc 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 ..
  62. doi 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...
  63. pmc The role of DNA shape in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
    Nature 461:1248-53. 2009
    ....
  64. ncbi Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits
    M L Phelan
    Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
    Mol Cell 3:247-53. 1999
    ..both BRG1 and hBRM, the ATPase subunits of human SWI/SNF complexes, are capable of remodeling mono-nucleosomes and nucleosomal arrays as purified proteins...
  65. pmc 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 ..
  66. ncbi Reconciling the positive and negative roles of histone H2A.Z in gene transcription
    Maud Marques
    Universite de Sherbrooke, Departement de Biologie, Sherbrooke, QC, Canada
    Epigenetics 5:267-72. 2010
    ..Recent experiments have shown that H2A.Z can allow nucleosomes to adopt stable translational positions as compared to H2A, which could influence the accessibility to DNA ..
  67. pmc Toward convergence of experimental studies and theoretical modeling of the chromatin fiber
    Tamar Schlick
    Department of Chemistry, New York University, New York, New York 10003, USA
    J Biol Chem 287:5183-91. 2012
    ..This minireview discusses recent progress and evidence supporting structural heterogeneity in chromatin fibers, reconciling apparently contradictory fiber models...
  68. pmc A map of nucleosome positions in yeast at base-pair resolution
    Kristin Brogaard
    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
    Nature 486:496-501. 2012
    The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function. However, existing methods for mapping nucleosomes do not provide the necessary single-base-pair accuracy to determine these positions...
  69. pmc Cell-cycle-coupled structural oscillation of centromeric nucleosomes in yeast
    Manjunatha Shivaraju
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Cell 150:304-16. 2012
    ..Experimental evidence supports several different models for the structure of centromeric nucleosomes. To investigate Cse4 copy number in live yeast, we developed a method coupling fluorescence correlation ..
  70. pmc 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...
  71. pmc 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...
  72. pmc Discovery and annotation of functional chromatin signatures in the human genome
    Gary Hon
    Bioinformatics Program, University of California at San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000566. 2009
    ..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 ..
  73. pmc 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...
  74. pmc 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 ..
  75. pmc 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...
  76. 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...
  77. pmc 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...
  78. 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...
  79. pmc 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...
  80. pmc 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 ..
  81. 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)...
  82. doi 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...
  83. pmc 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...
  84. pmc 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 ..
  85. pmc 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) ..
  86. pmc 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...
  87. 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...
  88. pmc 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 ..
  89. pmc 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...
  90. pmc 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 ..
  91. pmc 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...
  92. pmc 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...
  93. 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
    ....
  94. pmc 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...
  95. ncbi Chromatin fiber folding: requirement for the histone H4 N-terminal tail
    Benedetta Dorigo
    ETH Zurich, Institute for Molecular Biology and Biophysics, ETH Honggerberg, CH 8093 Zurich, 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...
  96. pmc 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...
  97. pmc 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...
  98. pmc 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...
  99. pmc 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...
  100. pmc 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 ..
  101. pmc 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 ..

Research Grants103 found, 100 shown here

  1. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    STEPHEN LIPPARD; Fiscal Year: 2009
    ..b>Nucleosomes, the building blocks of chromosomes, will be constructed with site-specific Pt-DNA adducts and structurally ..
  2. 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 ..
  3. 2010 Cold Spring Harbor Laboratory Conference on Systems Biology: Global Regulati
    David J Stewart; Fiscal Year: 2010
    ..will focus on five key aspects of gene regulation-cis-regulatory logic, transcriptional regulatory networks, nucleosomes and epigenetics, post-transcriptional regulation, and variation and evolution of regulatory networks...
  4. 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 ..
  5. Molecular Architecture of the Regional Kinetochore in Fission Yeast
    Xiangwei He; Fiscal Year: 2009
    ..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 ..
  6. 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 ..
  7. 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 ..
  8. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2001
    ..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 ..
  9. 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 ..
  10. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2002
    ..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 ..
  11. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2003
    ..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 ..
  12. 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 ..
  13. Molecular Mechanisms of Chromosome Segregation in Yeast
    Jennifer Gerton; Fiscal Year: 2009
    ..This histone variant is incorporated into nucleosomes with centromere sequence which is critical to direct the formation of the kinetochore, a multi-protein ..
  14. Heterochromatin on the human inactive X chromosome
    Brian P Chadwick; Fiscal Year: 2012
    ..small RNAs coincides with the heterochromatic form of DXZ4, and the small RNAs themselves directly align with nucleosomes bearing the heterochromatin modification H3K9me3...
  15. 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...
  16. Heterochromatin on the human inactive X chromosome
    Brian Chadwick; Fiscal Year: 2009
    ..small RNAs coincides with the heterochromatic form of DXZ4, and the small RNAs themselves directly align with nucleosomes bearing the heterochromatin modification H3K9me3...
  17. CHROMATIN HISTONE MODIFICATIONS AND HMG PROTEINS
    EDWIN BRADBURY; Fiscal Year: 1990
    ..To address questions i and ii it is essential to use a well-defined system in which nucleosomes are precisely located on known DNA sequences and are correctly spaced...
  18. 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 ..
  19. The Role of Sex in Self Antigen Generation in SLE
    David Pisetsky; Fiscal Year: 2009
    ..bind to a wide array of nuclear macromolecules (antinuclear antibodies or ANA), although antibodies to nucleosomes and its DNA and histone components are the most characteristic...
  20. The Role of Sex in Self Antigen Generation in SLE
    David Stephen Pisetsky; Fiscal Year: 2010
    ..bind to a wide array of nuclear macromolecules (antinuclear antibodies or ANA), although antibodies to nucleosomes and its DNA and histone components are the most characteristic...
  21. Elongation of Yeast Pol II Through Nucleosomes
    Michael Carey; Fiscal Year: 2009
    ..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...
  22. 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...
  23. MECHANISMS OF DE NOVO METHYLATION IN CANCER
    Peter Jones; Fiscal Year: 2009
    ..To do this, we have developed a custom NimbleGen array allowing for the analyses of nucleosomes, histone modifications and DNA methylation in an integrated way at 1,800 transcription start sites (TSS) in ..
  24. MECHANISMS OF DE NOVO METHYLATION IN CANCER
    Peter A Jones; Fiscal Year: 2010
    ..To do this, we have developed a custom NimbleGen array allowing for the analyses of nucleosomes, histone modifications and DNA methylation in an integrated way at 1,800 transcription start sites (TSS) in ..
  25. Role of Histone H2B Ubiquitylation in DNA Replication
    KELLY MIGUEL TRUJILLO; Fiscal Year: 2011
    ..transcription, the monoubiquitylation of histone H2B (H2Bub1) is important for the efficient reassembly of nucleosomes in the wake of elongating RNA polymerase II (Pol II)...
  26. 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...
  27. Histone Tail Interactions and Functions in Chromatin
    JEFFREY HAYES; Fiscal Year: 2009
    ..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 ..
  28. 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 ..
  29. 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 ..
  30. Histone Tail Interactions and Functions in Chromatin
    JEFFREY HAYES; Fiscal Year: 2009
    ..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 ..
  31. 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 ..
  32. 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 ..
  33. Recombination Repair Complex in Human Cells
    Richard Fishel; Fiscal Year: 2012
    ..Chromosomes are a complex assortment of proteins and DNA (chromatin). Nucleosomes are the fundamental unit of chromatin and contain ~146 bp DNA that surrounds an H2A, H2B, H3, and H4 histone ..
  34. 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...
  35. 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...
  36. 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...
  37. 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 ..
  38. 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 ..
  39. 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 ..
  40. 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 ..
  41. Regulation of nucleosome positions and transcription during CTL differentiation
    MATTHEW EUGENE PIPKIN; Fiscal Year: 2012
    ..b>Nucleosomes are the fundamental repeating subunit of chromatin, and they directly bind DNA, which obscures encoded ..
  42. DNA STRUCTURE AND RECOMBINATIONAL INTERMEDIATES
    Brian Johnston; Fiscal Year: 1990
    ..This will also permit an examination of sites of bending in the DNA wrapped around nucleosomes. Crystal structures indicate that sharp bends occur preferentially at certain positions; if these correlate ..
  43. A Proteomic Interrogation of the Histone Code during HCMV Infection
    Peter A DiMaggio; Fiscal Year: 2010
    ..Code" theory that specific combinatorial post-translational modifications (PTMs) of the histone proteins on nucleosomes modulate these changes in chromatin structure, which in turn subsequently regulate gene transcription...
  44. 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 ..
  45. 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...
  46. 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...
  47. Structure of nucleosomes in complex with transcriptional regulators
    Karolin Luger; Fiscal Year: 2006
    ..In specific aim 2, the interaction of the transcription activator FoxA with highly defined nucleosomes will be studied...
  48. 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...
  49. 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...
  50. Recognition and excision of nucleosomal uracils by human uracil DNA glycosylase
    Mary R Stahley; Fiscal Year: 2010
    ..the excision of uracil from naked DNA substrates, however uracil DNA damage in eukaryotes is also present in nucleosomes. The first aim of this study is to determine the mechanism by which uracil accesses nucleosomal substrates...
  51. 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 ..
  52. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2007
    ..The detailed locations of nucleosomes along genomic DNA are critical for proper gene regulation - and therefore for the health and development of ..
  53. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2005
    ..The detailed locations of nucleosomes along genomic DNA are critical for proper gene regulation - and therefore for the health and development of ..
  54. Mathematical and Statistical Models for Nucleosome...
    Ji Ping Wang; Fiscal Year: 2006
    ..The detailed locations of nucleosomes along genomic DNA are critical for proper gene regulation - and therefore for the health and development of ..
  55. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2009
    ..The detailed locations of nucleosomes along genomic DNA are critical for proper gene regulation - and therefore for the health and development of ..
  56. 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...
  57. Histone Variants and Transcription-linked Deposition
    Kamran Ahmad; Fiscal Year: 2004
    ..b>Nucleosomes are formidable obstacles to proteins that must access DNA...
  58. Spinocerebellar ataxia 7 protein function
    Patrick Grant; Fiscal Year: 2006
    In the eukaryotic cell nucleus, DMA is packaged by histones into nucleosomes, the repeating subunits of chromatin...
  59. Histone Variants and Transcription-linked Deposition
    Kamran Ahmad; Fiscal Year: 2005
    ..b>Nucleosomes are formidable obstacles to proteins that must access DNA...
  60. Histone Variants and Transcription-linked Deposition
    Kamran Ahmad; Fiscal Year: 2007
    ..b>Nucleosomes are formidable obstacles to proteins that must access DNA...
  61. Spinocerebellar ataxia 7 protein function
    Patrick Grant; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): In the eukaryotic cell nucleus, DMA is packaged by histones into nucleosomes, the repeating subunits of chromatin...
  62. Histone Variants and Transcription-linked Deposition
    Kamran Ahmad; Fiscal Year: 2006
    ..b>Nucleosomes are formidable obstacles to proteins that must access DNA...
  63. 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 ..
  64. TRANSCRIPTION FACTOR INTERACTIONS WITH NUCLEOSOMES
    Robert Kingston; Fiscal Year: 2010
    ..The position of nucleosomes on the DNA can be changed, nucleosomes can be evicted, and nucleosomes can contain various histone variants and ..
  65. 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 ..
  66. TRANSCRIPTION FACTOR INTERACTIONS WITH NUCLEOSOMES
    Robert Kingston; Fiscal Year: 2009
    ..The position of nucleosomes on the DNA can be changed, nucleosomes can be evicted, and nucleosomes can contain various histone variants and ..
  67. 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...
  68. ATP-dependent Chromatin Remodeling in Neural Development
    Gerald R Crabtree; Fiscal Year: 2011
    ..energy of ATP hydrolysis to control transitions between stable epigenetic states by exchanging or mobilizing nucleosomes thereby altering histone codes...
  69. ATP-dependent Chromatin Remodeling in Neural Development
    Gerald Crabtree; Fiscal Year: 2009
    ..energy of ATP hydrolysis to control transitions between stable epigenetic states by exchanging or mobilizing nucleosomes thereby altering histone codes...
  70. 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...
  71. 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 ..
  72. 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 ..
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. Core Histone Tall Interactions and Function in Chromatin
    JEFFREY HAYES; Fiscal Year: 2005
    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...
  78. Core Histone Tall Interactions and Function in Chromatin
    JEFFREY HAYES; Fiscal Year: 2006
    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...
  79. 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...
  80. Core Histone Tall Interactions and Function in Chromatin
    JEFFREY HAYES; Fiscal Year: 2004
    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...
  81. CHROMOSOME STRUCTURE AND CONDENSATION MECHANISMS
    William Earnshaw; Fiscal Year: 1990
    The heirarchy of packing interactions in chromatin begins with nucleosomes and culminates in mitotic chromosome bands...
  82. 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 ..
  83. HISTONE GENE EXPRESSION IN YEAST
    M Smith; Fiscal Year: 2005
    The bulk of eukaryotic nucleosomes are made up of four core histones: H2A, H2B, H3, and H4...
  84. FLUORESCENCE STUDIES OF NUCLEOSOME STRUCTURAL CHANGES
    ENOCH SMALL; Fiscal Year: 1990
    Our research objective is to measure and interpret the conformational stability of nucleosomes. This is important if we are to understand the functioning of nucleosomes in vivo during cellular transcription and replication...
  85. HISTONE GENE EXPRESSION IN YEAST
    M Smith; Fiscal Year: 2004
    The bulk of eukaryotic nucleosomes are made up of four core histones: H2A, H2B, H3, and H4...
  86. 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...
  87. HISTONE GENE EXPRESSION IN YEAST
    M Smith; Fiscal Year: 2006
    The bulk of eukaryotic nucleosomes are made up of four core histones: H2A, H2B, H3, and H4...
  88. DNA CONFORMATION AND ENEDIYNE TARGET RECOGNITION
    Peter Dedon; Fiscal Year: 1999
    ..CAL damage was found to be enhanced at a site of sharp DNA bending in nucleosomes reconstituted on 5S rDNA...
  89. Regulation of Chromatin Structure by Heterochromatin Protein 1
    MICHAEL VITALINI; Fiscal Year: 2009
    ..We hypothesize that heterochromatin formation results from linking adjacent nucleosomes by HP1, and that the flexible hinge region of HP1 mediates this linkage...
  90. Modulation of nucleosome dynamics
    ANDREW ANDREWS; Fiscal Year: 2009
    ..the cell regulates chromatin dynamics and thereby DNA accessibility: the incorporation of histone variants into nucleosomes and the role of histone chaperones in DNA accessibility...
  91. Regulation of Chromatin Structure by Heterochromatin Protein 1
    MICHAEL WILLIAM VITALINI; Fiscal Year: 2010
    ..We hypothesize that heterochromatin formation results from linking adjacent nucleosomes by HP1, and that the flexible hinge region of HP1 mediates this linkage...
  92. 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...
  93. 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...
  94. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine Wilson; Fiscal Year: 2003
    ..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...