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. 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
  4. 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
  5. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
  6. 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
  7. 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
  8. 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
  9. pmc Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres
    Peter W Lewis
    Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, 1230 York Ave, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 107:14075-80. 2010
  10. pmc Genome-wide nucleosome specificity and directionality of chromatin remodelers
    Kuangyu Yen
    Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
    Cell 149:1461-73. 2012

Research Grants

Detail Information

Publications314 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. 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
    ....
  4. 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...
  5. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
    ....
  6. 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...
  7. 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...
  8. 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...
  9. pmc Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres
    Peter W Lewis
    Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, 1230 York Ave, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 107:14075-80. 2010
    ..H3.3-containing nucleosomes are assembled in a replication-independent manner by means of dedicated chaperone proteins...
  10. pmc Genome-wide nucleosome specificity and directionality of chromatin remodelers
    Kuangyu Yen
    Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
    Cell 149:1461-73. 2012
    How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known...
  11. 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
    ....
  12. 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...
  13. 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...
  14. pmc A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Mol Cell 32:878-87. 2008
    ....
  15. 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...
  16. 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
    ....
  17. ncbi 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...
  18. 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 ..
  19. ncbi Functions of site-specific histone acetylation and deacetylation
    Mona D Shahbazian
    Department of Biological Chemistry, Geffen School of Medicine and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
    Annu Rev Biochem 76:75-100. 2007
    ..For example, the acetylation pattern on newly synthesized histones is important for their assembly into nucleosomes by histone chaperones...
  20. 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.
  21. 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...
  22. ncbi Dynamics of replication-independent histone turnover in budding yeast
    Michael F Dion
    Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Science 315:1405-8. 2007
    ..We find that nucleosomes at promoters are replaced more rapidly than at coding regions and that replacement rates over coding regions ..
  23. pmc Nascent transcript sequencing visualizes transcription at nucleotide resolution
    L Stirling Churchman
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, USA
    Nature 469:368-73. 2011
    ..Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements...
  24. 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 ..
  25. 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...
  26. 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...
  27. 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...
  28. pmc A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern
    Amanda L Hughes
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 48:5-15. 2012
    ..We suggest a three-step model in which nucleosome remodelers, general transcription factors, and the transcriptional elongation machinery are primarily involved in generating the nucleosome positioning pattern in vivo...
  29. pmc Nucleosome dynamics define transcriptional enhancers
    Housheng Hansen He
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Genet 42:343-7. 2010
    ..We performed genome-wide mapping of epigenetically marked nucleosomes to determine their position both near transcription start sites and at distal regulatory elements, including ..
  30. 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...
  31. 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...
  32. pmc Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
    Roger B Deal
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Science 328:1161-4. 2010
    ..b>Nucleosomes turn over faster at sites for trithorax-group than polycomb-group protein binding, suggesting that nucleosome ..
  33. pmc Asymmetrically modified nucleosomes
    Philipp Voigt
    Howard Hughes Medical Institute, New York University School of Medicine, Department of Biochemistry, New York, NY 10016, USA
    Cell 151:181-93. 2012
    ..We demonstrate that nucleosomes in embryonic stem cells, fibroblasts, and cancer cells exist in both symmetrically and asymmetrically modified ..
  34. pmc Nucleosome-interacting proteins regulated by DNA and histone methylation
    Till Bartke
    The Gurdon Institute, Department of Pathology, Cambridge, UK
    Cell 143:470-84. 2010
    Modifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify "..
  35. ncbi 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...
  36. pmc Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Cell 143:540-51. 2010
    ..whose sequences inherently disfavor nucleosome formation within the gene but favor occlusion of the promoter by nucleosomes. In contrast, housekeeping genes that lack pronounced Pol II pausing show higher nucleosome occupancy ..
  37. pmc Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes
    Karen E Gascoigne
    Whitehead Institute for Biomedical Research, Department of Biology, Nine Cambridge Center, MA 02142, USA
    Cell 145:410-22. 2011
    ..We additionally find that CENP-T phosphorylation regulates the mitotic assembly of both endogenous and ectopic kinetochores. Thus, CENP-C and CENP-T form a critical regulated platform for vertebrate kinetochore assembly...
  38. 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...
  39. 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...
  40. ncbi Dynamics of histone H3 deposition in vivo reveal a nucleosome gap-filling mechanism for H3.3 to maintain chromatin integrity
    Dominique Ray-Gallet
    Centre de Recherche, Institut Curie, 75248 Paris, France
    Mol Cell 44:928-41. 2011
    ..3, and HIRA association with Pol II ensures local H3.3 enrichment at specific sites. We discuss the importance of this H3.3 deposition as a salvage pathway to maintain chromatin integrity...
  41. ncbi Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes
    Xiaoshu Chen
    State Key Laboratory of Bio Control, College of Life Sciences, Sun Yat Sen University, Guangzhou 510275, China
    Science 335:1235-8. 2012
    ..Furthermore, the rates of G→T and A→T mutations were also about twofold suppressed by nucleosomes. On the basis of these results, we conclude that nucleosome-dependent mutation spectra affect eukaryotic genome ..
  42. ncbi 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...
  43. pmc HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
    Gary P Wang
    University of Pennsylvania, School of Medicine, Department of Microbiology, Philadelphia, PA 19104 6076, USA
    Genome Res 17:1186-94. 2007
    ..The pyrosequencing and bioinformatic methods described here should be useful for investigating many aspects of retroviral DNA integration...
  44. pmc High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
    Assaf Weiner
    School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
    Genome Res 20:90-100. 2010
    Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression, and has led to mechanistic hypotheses regarding the rules by which chromatin structure is ..
  45. pmc In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae
    Andrea J Gossett
    Department of Biology, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Genet 8:e1002771. 2012
    ..To probe the mechanism of this transcriptional de-repression, we depleted nucleosomes in vivo by conditional repression of histone H3 transcription...
  46. 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...
  47. pmc The mechanics behind DNA sequence-dependent properties of the nucleosome
    Eugene Y D Chua
    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
    Nucleic Acids Res 40:6338-52. 2012
    ..This provides a basis for improved prediction of nucleosomal properties and the design of tailored DNA constructs for chromatin investigations...
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. pmc Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    Courtney Hodges
    Jason L Choy Laboratory of Single Molecule Biophysics and Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    Science 325:626-8. 2009
    RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA...
  54. 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
  55. 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...
  56. 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...
  57. 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-..
  58. pmc Chromatin higher-order structures and gene regulation
    Guohong Li
    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People s Republic of China
    Curr Opin Genet Dev 21:175-86. 2011
    ..Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order ..
  59. pmc Acetylation of histones and transcription-related factors
    D E Sterner
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Microbiol Mol Biol Rev 64:435-59. 2000
    ..Thus, we also detail these known factor acetyltransferase (FAT) substrates and the demonstrated or potential roles of their acetylation in transcriptional processes...
  60. pmc Genome-wide "re"-modeling of nucleosome positions
    Ronen Sadeh
    Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
    Cell 147:263-6. 2011
    Two recent studies mapped nucleosomes across the yeast and human genomes, teasing apart the relative contributions of DNA sequence and chromatin remodelers to nucleosome organization...
  61. 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...
  62. pmc Overcoming the nucleosome barrier during transcript elongation
    Steven J Petesch
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Trends Genet 28:285-94. 2012
    ..Our review highlights mechanisms that Pol II utilizes to transcribe through nucleosomes, including the roles of chromatin remodelers, histone chaperones, post-translational modifications of histones, ..
  63. pmc Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner
    Yuri M Moshkin
    Department of Biochemistry and Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
    Mol Cell Biol 32:675-88. 2012
    ..We conclude that the cellular nucleosome landscape is the result of the balance between DNA sequence-driven nucleosome placement and active nucleosome repositioning by remodelers and the transcription machinery...
  64. pmc The unconventional structure of centromeric nucleosomes
    Steven Henikoff
    Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Chromosoma 121:341-52. 2012
    ..but traditional nucleosome assembly protocols have generally yielded partially unwrapped left-handed octameric nucleosomes. In budding yeast, topology analysis and high-resolution mapping has revealed that a single right-handed cenH3 ..
  65. 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 ..
  66. 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...
  67. 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)...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. ncbi Enhanced histone acetylation and transcription: a dynamic perspective
    Alison L Clayton
    Nuclear Signalling Laboratory, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
    Mol Cell 23:289-96. 2006
    ..quot;special cases," restricted to specific genes and specific types of histone modifications, or could the entire panoply of histone modifications associated with transcription now be revisited with a much more dynamic perspective?..
  74. ncbi Regulation of replication fork progression through histone supply and demand
    Anja Groth
    Laboratory of Nuclear Dynamics and Genome Plasticity, UMR218 CNRS Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    Science 318:1928-31. 2007
    ....
  75. ncbi Rapid spontaneous accessibility of nucleosomal DNA
    Gu Li
    Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208 3500, USA
    Nat Struct Mol Biol 12:46-53. 2005
    DNA wrapped in nucleosomes is sterically occluded, creating obstacles for proteins that must bind it. How proteins gain access to DNA buried inside nucleosomes is not known...
  76. 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...
  77. ncbi 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
    ....
  78. 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 ..
  79. 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...
  80. 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...
  81. 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...
  82. 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...
  83. 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...
  84. 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...
  85. 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 ..
  86. 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...
  87. 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...
  88. 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...
  89. 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
    ....
  90. 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...
  91. 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...
  92. 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...
  93. 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...
  94. 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 ..
  95. 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...
  96. 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...
  97. 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...
  98. 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 ..
  99. 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...
  100. 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 ..
  101. 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...

Research Grants76

  1. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..control of RNA translocation, DNA synthesis, and cell cycle progression via modulating effects on chromatin and nucleosomes. RCC1 is partially degraded in lytic infection but induced in neuronal cells by T3/TR upon infection (C.12, Fig...
  2. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    Stephen J Lippard; Fiscal Year: 2013
    ..b>Nucleosomes, the building blocks of chromosomes, will be constructed with site-specific Pt-DNA adducts and structurally ..
  3. DNA REPAIR IN A HORMONE RESPONSIVE GENE
    Michael J Smerdon; Fiscal Year: 2013
    ..The bracketed GRE sequence containing G::U mismatches will be packaged into nucleosomes containing unmodified or specifically modified histones for comparisons with naked DNA...
  4. The molecular mechanism of Aire: partnering with DNA-PK
    Diane J Mathis; Fiscal Year: 2013
    ..of a complex (including DNA-PK, PARP1, TOP2, FACT, H2AX) responsible for disassembling and re-assembling nucleosomes as the transcriptional machinery progresses along DNA...
  5. 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...
  6. REGULATION OF NUCLEAR ENVELOPE ASSEMBLY AND DISASSEMBLY
    Katherine L Wilson; Fiscal Year: 2012
    ..Our supporting results show that BAF interacts with nucleosomes, influences several different histone posttranslational modifications in vivo, and associates in vivo with at ..
  7. Assembly and Maintenance of Centromeres in Filamentous Fungi
    Michael Freitag; Fiscal Year: 2013
    ..major hypotheses are that maintenance of Neurospora centromeres relies on interactions of centromere-specific nucleosomes with heterochromatic histone modifications, and that incorporation of CenH3 during meiosis is controlled by a ..
  8. Genetic and Molecular Studies of Drosophila Chromatin Remodeling Factors
    John W Tamkun; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Nucleosomes and other components of chromatin can repress transcription by blocking the access of transcription factors and other regulatory proteins to DNA...
  9. Long-Range Genetic and Epigenetic Control of Igh Gene Assembly
    Eugene M Oltz; Fiscal Year: 2010
    ..forms between distant promoter and enhancer elements to recruit proteins that covalently modify and remodel nucleosomes, thus generating recombinase accessible chromatin...
  10. MECHANISMS OF AUTOIMMUNITY IN SLE
    David Stephen Pisetsky; Fiscal Year: 2013
    ..While antibodies to nucleosomes and its DNA and histone components are the most characteristic of SLE, antibodies to RNA and RNA binding ..
  11. Recombination Repair Complex in Human Cells
    Richard Fishel; Fiscal Year: 2013
    ..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 ..
  12. The Role of BAF53b Mediated Nucleosome Remodeling in Long-Term Memory Formation
    ANNIE THERESE VOGEL-CIERNIA; Fiscal Year: 2013
    ..enzymatic complexes, which use the energy of ATP hydrolysis to disrupt nucleosome-DNA contacts, move nucleosomes along DNA, and remove or exchange nucleosomes...
  13. DNA LESIONS AND GENE EXPRESSION IN HYPOXIC LUNG DISEASE
    Mark N Gillespie; Fiscal Year: 2013
    ..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 ..
  14. Biochemical and Genetic Analysis of yFACT, A Novel Nucleosome Reorganizing Factor
    TIMOTHY G FORMOSA; Fiscal Year: 2013
    ..b>Nucleosomes are the fundamental subunit of chromatin, which is the DNA packaging in eukaryotes...
  15. 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...
  16. Coupling of Transcription with Pre-mRNA Metabolism
    DAVID LEONARD BENTLEY; Fiscal Year: 2013
    ..The template that is transcribed is made of chromatin: DNA wrapped around histone proteins in assemblies called nucleosomes. Transcription and pre- mRNA processing are not independent events;they are integrated with one another in a ..
  17. Structural and Mechanistic Characterization of the Histone Chaperone FACT
    Duane David Winkler; Fiscal Year: 2012
    ..reorganization and changes in chromatin architecture can result from a direct interaction between FACT and nucleosomes, the mechanistic details of this process are poorly understood...
  18. HIV-1 Inhibition using Tat Peptide Derivatives
    Fatah Kashanchi; Fiscal Year: 2013
    ..the functional consequence of SWI/SNF phosphorylation by cdk2/E in relation to HIV-1 chromatin remodeling of nucleosomes. Finally, we will examine the effect of cdk9 phosphorylation by cdk2/E in presence of chromatinized HIV-1 LTR ..
  19. Role of oxidative modifications to D-loop region in mTDNA replication in hypoxia
    Mykhaylo Ruchko; Fiscal Year: 2012
    ..Because the lesions are restricted to HREs associated with transcriptionally-active nucleosomes and since mimicking the effect of hypoxia by introducing modified bases in the HRE of the VEGF promoter leads ..
  20. Spinocerebellar ataxia 7 protein function.
    Patrick A Grant; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): In the eukaryotic cell nucleus, DMA is packaged by histones into nucleosomes, the repeating subunits of chromatin...
  21. Identifying disease-related functional regulatory variants in open chromatin
    Karen L Mohlke; Fiscal Year: 2010
    ..evidence indicates that many regulatory elements are located in regions of open chromatin, not bound by nucleosomes when in an active state...
  22. Epigenetics of Severe Systemic Inflammation
    CHARLES EMORY MCCALL; Fiscal Year: 2013
    ..H1, in concert with HMGB1, sustains heterochromatin assembly and transcription silencing by re-positioning nucleosomes and maintaining RelB and G9a binding at promoter sequences of TNFa and IL-1b...
  23. In vivo imaging of X inactivation
    Matthew Levy; Fiscal Year: 2013
    ..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 ..
  24. MOLECULAR CHARACTERIZATION OF THE DORSAL MORPHOGEN
    Michael S Levine; Fiscal Year: 2013
    ..In particular, we will test the idea that paused Pol II displaces inhibitory promoter-positioned nucleosomes (PPNs). We will also investigate the role of the promoter in developmental timing...
  25. PROTEIN SEQUENCING BY TANDEM MASS SPECTROMETRY
    Donald F Hunt; Fiscal Year: 2013
    ..to define the posttranslational modifications that exist on the histone, H3 variant, CENP-A, that is located in nucleosomes at the centromere and also continue our efforts to characterize post-translational modifications on histone and ..
  26. Chromatin and Coactivators in HSV-1 gene regulation
    STEVEN TRIEZENBERG; Fiscal Year: 2009
    ..a viral activator such as VP16 recruit chromatin modifying coactivator proteins to a DNA template that lacks nucleosomes? The overall goal of this project is to define the roles of histones and chromatin in HSV-1 gene regulation, ..
  27. Regulation of nucleosome positions and transcription during CTL differentiation
    MATTHEW EUGENE PIPKIN; Fiscal Year: 2013
    ..b>Nucleosomes are the fundamental repeating subunit of chromatin, and they directly bind DNA, which obscures encoded ..
  28. Mechanisms of RSC recruitment and its role in transcription
    CHHABI KUMAR GOVIND; Fiscal Year: 2013
    ..by elongating polymerases, and subsequently recognizes particular patterns of histone acetylation to target nucleosomes for remodeling or eviction...
  29. MECHANISM OF IMMUNOGLOBULIN HYPERMUTATION
    URSULA B STORB; Fiscal Year: 2012
    ..We will further investigate the role of nucleosomes that appear to be a barrier to SHM...
  30. Expanding Data Collection Via High-Throughput DNA Sequencing
    Stephan C Schuster; Fiscal Year: 2010
    ..Illumina GA IIx will be used to dramatically expand our capacity to produce genome-wide maps of nucleosomes and hundreds of transcription factors un- der a variety of environmental states from yeast to flies to humans, ..
  31. Mechanisms of Polycomb Silencing
    Yi Zhang; Fiscal Year: 2010
    ..This will be accomplished by using recombinant PRC2 and reconstituted nucleosomes containing H3 that is methylated to various levels on H3K27. 2...
  32. PROPERTIES AND REGULATION OF P53 IN TUMOR CELLS
    Carol Prives; Fiscal Year: 2013
    ..One particular issue that has not yet been well addressed is how and when p53 locates its site in nucleosomes within chromatin...
  33. Dynamics of nucleosome positioning and the role of chromatin in myogenesis
    DUSTIN EDWARD SCHONES; Fiscal Year: 2013
    ..The precise positioning of nucleosomes in functional regulatory regions of the genome can directly influence the transcriptional regulation of nearby ..
  34. ATP-dependent Chromatin Remodeling in Neural Development
    Gerald R Crabtree; Fiscal Year: 2012
    ..energy of ATP hydrolysis to control transitions between stable epigenetic states by exchanging or mobilizing nucleosomes thereby altering histone codes...
  35. Mammalian Centromere Assembly
    Don W Cleveland; Fiscal Year: 2013
    ..We will now determine if the structural rigidity and compactness of nucleosomes targeted to the centromere is sufficient to maintain centromere identity and function in mammalian cells...
  36. Structure and Function of the SAGA Deubiquitinating Module
    Cynthia Wolberger; Fiscal Year: 2013
    ..determination and in vivo assays will be used to identify the determinants in both the SAGA DUB module and in nucleosomes that are responsible for proper substrate recognition...
  37. Aromatic Amine-DNA Lesions: Mutagenicity and Repair
    Suse Broyde; Fiscal Year: 2013
    ..We will investigate the adducts in uncomplexed DNA as well as when complexed with histone proteins in nucleosomes, the fundamental DNA-organization unit in the cellular environment...
  38. COORDINATE GENE REGULATION IN ANIMAL CELLS
    John T Lis; Fiscal Year: 2013
    ..In Aim 2, the roles of DNA sequences, specific TFs, and nucleosomes in regulation will be tested by applying disruption or inhibition strategies and evaluating changes in ..
  39. DNA PHOTOLESION STRUCTURE-ACTIVITY RELATIONSHIPS
    JOHN STEPHEN ADOLFINO TAYLOR; Fiscal Year: 2013
    ..therefore be to elucidate the structure-activity relationships of photoproduct formation and deamination in nucleosomes and telomeres with regard to their mutagenic and epigenetic consequences...
  40. Interplay between Chromatin and Co-activator Complexes
    Michael F Carey; Fiscal Year: 2012
    ..the vast body of knowledge from mammalian gene regulation to craft and test hypotheses for how PICs assemble on nucleosomes and how covalent modifications of chromatin, and the machines that bind those modifications, regulate this ..
  41. BAYESIAN APPROACHES TO MODEL SELECTION FOR SURVIVAL DATA
    Joseph G Ibrahim; Fiscal Year: 2013
    ..Chromatin structure, in the form of positioning of nucleosomes in DNA, has long been known to play a huge role in protein-DNA binding, however, a quantitative assessment of ..
  42. Histone Tail Interactions and Functions in Chromatin
    Jeffrey J Hayes; Fiscal Year: 2013
    ..short ~200 bp segments around protein spools comprised of the core histone proteins into structures known as nucleosomes. Immensely long, genome-sized strings of nucleosomes are assembled into a hierarchy of higher-order chromatin ..
  43. Molecular Mechanisms of Chromosome Segregation in Yeast
    Jennifer L Gerton; Fiscal Year: 2012
    ..This histone variant is incorporated into nucleosomes with centromere sequence which is critical to direct the formation of the kinetochore, a multi-protein ..
  44. MOLECULAR ANALYSIS OF A YEAST TRANSCRIPTIONAL REGULATOR
    David T Auble; Fiscal Year: 2013
    ..Mot1 in chromatin structure regulation will be addressed, including the unexpected ability of Mot1 to bind to nucleosomes and to regulate the interaction of FACT with nucleosomes...
  45. SWI/SNF complex loss facilitates gene silencing during NSCLC development
    Bernard E Weissman; Fiscal Year: 2010
    ..Originally identified in yeast, the SWI/SNF complex alters chromatin structure by remodeling nucleosomes through an ATP-dependent process...
  46. The RNA polymerase II transcription complex
    Stephen Buratowski; Fiscal Year: 2013
    ..nearest the transcription start site, while dimethylation predominates further downstream through the next few nucleosomes. We will explore how Set1/COMPASS is recruited to transcription complexes and how this gradient of methylation ..
  47. Regulating Pathways and Fidelity of DNA Replication and Repair by Acetylation
    Lata Balakrishnan; Fiscal Year: 2013
    ..Jeffrey J. Hayes, to reconstitute DNA templates on nucleosomes will help me to test the effects of acetylation on replication and repair in a reconstituted chromatin ..
  48. Role of H3K4 methylation in transcriptional activation by FoxA
    Janice M Ascano; Fiscal Year: 2010
    ..Recently, it was found that FoxAl binds only to target sites that are enriched with nucleosomes bearing histone H3 that is mono- or dimethylated on lysines at position 4 (H3K4)...
  49. Analysis of Proline Isomerization in Epigenetics
    ROB CARL OSLUND; Fiscal Year: 2013
    ..An important type of chromatin regulatory mechanism takes place on the tails of histone proteins in nucleosomes. These histone tail post-translational modifications (PTMs) are essential for normal cellular function and ..
  50. Dynamics of nucleosome assembly/disassembly affected by chromatin modifications
    Tae Hee Lee; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Nucleosomes are the fundamental DNA packaging units of eukaryotic chromatin...
  51. Excision of Carcinogen-DNA Adducts in Nucleosomes
    Nicholas E Geacintov; Fiscal Year: 2013
    ..free DNA in aqueous environments;it is not known whether in biologically more relevant protein environments of nucleosomes, the fundamental sub-units of DNA packaging in the cell, similar hierarchies of NER will be observed with DNA ..
  52. REGULATION OF G1-SPECIFIC GENE EXPRESSION IN YEAST
    Curt Wittenberg; Fiscal Year: 2013
    ..analysis to study the influence of transcriptional repressors on histone modifying enzymes and their marks on nucleosomes. Finally, in the third Aim we will study the molecular basis for the differential regulation of SBF and MBF by ..
  53. Molecular Architecture of the Regional Kinetochore in Fission Yeast
    Xiangwei He; Fiscal Year: 2012
    ..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 ..
  54. Transcriptional elongation and splicing in human genes in situ
    Richard A Padgett; Fiscal Year: 2013
    ..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 ..
  55. Histone chaperones and epigenetic silencing
    Zhiguo Zhang; Fiscal Year: 2013
    ..Following DNA replication, parental and newly synthesized histones are deposited onto DNA strands to form nucleosomes, the basic unit of chromatin, and then higher order chromatin structures...
  56. Regulation of Nucleosome Assembly
    Zhiguo Zhang; Fiscal Year: 2013
    ..It is believed that the assembly of histones H3-H4 into nucleosomes is the rate-limiting step of nucleosome formation following gene transcription and DNA replication...
  57. Reprogramming of cardiac genome by Smyd1 in hypertrophy and failure
    Sarah Franklin; Fiscal Year: 2012
    ..The wrapping of DNA around nucleosomes and its organization into higher order structures is fundamentally influenced by chromatin remodeling enzymes...
  58. Biophysical Models for Prediction and Design of Eukaryotic Chromatin Structure an
    Alexandre V Morozov; Fiscal Year: 2012
    ..In eukaryotic genomes, transcriptional regulation is strongly affected by nucleosomes which function to compact DNA and to regulate access to it by simple physical occlusion and by providing the ..
  59. Structural Studies of epigenetic regulation of rRNA gene by TTF-I
    Carlos R Escalante; Fiscal Year: 2013
    ..site and recruits Cockayne Sindrome Protein B (CSB) that in an ATP dependent reaction modifies the position of nucleosomes in the promoter and activates transcription of the gene...
  60. Structural basis of signaling by ING2 PHD
    Tatiana G Kutateladze; Fiscal Year: 2010
    ..of the histone and IP6 recognition remains unexplored and the effect of IP6 interaction on ING2 targeting to nucleosomes is not known...
  61. NUCLEOSOME POSITIONING
    Olke C Uhlenbeck; Fiscal Year: 2012
    ..In eukaryotes, the genomic DNA is wrapped in nucleosomes, which occlude much of the surface of the wrapped DNA and strongly distort it;yet, nucleosomes also recruit ..
  62. Orbitrap Elite Mass Spectrometer for Chromatin Biology and Epigenetics Research
    Benjamin A Garcia; Fiscal Year: 2013
    ..technologies which currently include Functional Genomics, Robotics and High-throughput qPCR, Chromatin and Nucleosomes, and Computational Epigenetics...
  63. 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 ..
  64. 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 ..
  65. CHROMATIN HISTONE MODIFICATIONS AND HMG PROTEINS
    EDWIN BRADBURY; Fiscal Year: 1992
    ..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...
  66. 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...
  67. DNA STRUCTURE AND RECOMBINATIONAL INTERMEDIATES
    Brian Johnston; Fiscal Year: 1993
    ..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 ..
  68. 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...
  69. 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...
  70. 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 ..
  71. 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...
  72. FLUORESCENCE STUDIES OF NUCLEOSOME STRUCTURAL CHANGES
    ENOCH SMALL; Fiscal Year: 1992
    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...
  73. 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...
  74. 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...
  75. 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...
  76. 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...