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. Yang F, Kemp C, Henikoff S. Doxorubicin enhances nucleosome turnover around promoters. Curr Biol. 2013;23:782-7 pubmed publisher
    ..Our results suggest that anthracycline intercalation promotes nucleosome turnover around promoters by its effect on DNA topology, with possible implications for mechanisms of cell killing during cancer chemotherapy...
  2. Hasson D, Panchenko T, Salimian K, Salman M, Sekulic N, Alonso A, et al. The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013;20:687-95 pubmed publisher
    ..Conflicting evidence has emerged regarding the histone composition and stoichiometry of CENP-A nucleosomes. Here we show that the predominant form of the CENP-A particle at human centromeres is an octameric nucleosome...
  3. Teves S, Henikoff S. Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol. 2014;21:88-94 pubmed publisher
    As RNA polymerase II (Pol II) transcribes a gene, it encounters an array of well-ordered nucleosomes. How it traverses through this array in vivo remains unresolved...
  4. Johnson S, Chen Y, Phillips R. Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLoS ONE. 2013;8:e75799 pubmed publisher
  5. Jimenez Useche I, Ke J, Tian Y, Shim D, Howell S, Qiu X, et al. DNA methylation regulated nucleosome dynamics. Sci Rep. 2013;3:2121 pubmed publisher
    ..conformation, but significant conformational differences were observed between the unmethylated and methylated nucleosomes. These findings suggest that the correlation between nucleosome positioning and DNA methylation patterns can ..
  6. Yang D, Fang Q, Wang M, Ren R, Wang H, He M, et al. N?-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Nat Struct Mol Biol. 2013;20:1116-8 pubmed publisher
    ..By X-ray crystallography, we show here that the acetylated N terminus of Sir3 does not interact with the nucleosome directly. Instead, it stabilizes a nucleosome-binding loop in the BAH domain. ..
  7. D Arcy S, Martin K, Panchenko T, Chen X, Bergeron S, Stargell L, et al. Chaperone Nap1 shields histone surfaces used in a nucleosome and can put H2A-H2B in an unconventional tetrameric form. Mol Cell. 2013;51:662-77 pubmed publisher
    ..The organization of the complex reveals that Nap1 competes with histone-DNA and interhistone interactions observed in the nucleosome, thereby regulating the availability of histones for chromatin assembly. ..
  8. Ozonov E, van Nimwegen E. Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput Biol. 2013;9:e1003181 pubmed publisher
    Because DNA packaging in nucleosomes modulates its accessibility to transcription factors (TFs), unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation...
  9. Yen K, Vinayachandran V, Pugh B. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 2013;154:1246-56 pubmed publisher
    ..Z from the first nucleosome at the start of genes. How they target and engage these +1 nucleosomes is unclear...

More Information

Publications62

  1. van Nuland R, Schram A, van Schaik F, Jansen P, Vermeulen M, Marc Timmers H. Multivalent engagement of TFIID to nucleosomes. PLoS ONE. 2013;8:e73495 pubmed publisher
    ..contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated...
  2. Ivankin A, Carson S, Kinney S, Wanunu M. Fast, label-free force spectroscopy of histone-DNA interactions in individual nucleosomes using nanopores. J Am Chem Soc. 2013;135:15350-2 pubmed publisher
    Herein we report a novel approach for fast, label-free probing of DNA-histone interactions in individual nucleosomes. We use solid-state nanopores to unravel individual DNA/histone complexes for the first time and find that the ..
  3. Hepat R, Song J, Lee D, Kim Y. A viral histone h4 joins to eukaryotic nucleosomes and alters host gene expression. J Virol. 2013;87:11223-30 pubmed publisher
    ..This study analyzed its molecular interaction with eukaryotic host nucleosomes and subsequent regulation of host gene expression...
  4. Moyle Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck O, Holmgren R, et al. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc Natl Acad Sci U S A. 2013;110:20158-63 pubmed publisher
    Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S...
  5. Luo Y, North J, Rose S, Poirier M. Nucleosomes accelerate transcription factor dissociation. Nucleic Acids Res. 2014;42:3017-27 pubmed publisher
    ..We investigated TF binding and dissociation dynamics at their recognition sequence within duplex DNA, single nucleosomes and short nucleosome arrays with single molecule total internal reflection fluorescence (smTIRF) microscopy...
  6. Formosa T. The role of FACT in making and breaking nucleosomes. Biochim Biophys Acta. 2013;1819:247-55 pubmed
    ..FACT was identified as a factor that destabilizes nucleosomes in vitro, but it has now also been implicated as a central factor in the deposition of histones to form ..
  7. Pang B, Qiao X, Janssen L, Velds A, Groothuis T, Kerkhoven R, et al. Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nat Commun. 2013;4:1908 pubmed publisher
    ..We define a novel mechanism of action of anthracycline anticancer drugs doxorubicin and daunorubicin on chromatin biology, with important consequences for DNA damage responses, epigenetics, transcription, side effects and cancer therapy...
  8. Stephan F, Marsman G, Bakker L, Bulder I, Stavenuiter F, Aarden L, et al. Cooperation of factor VII-activating protease and serum DNase I in the release of nucleosomes from necrotic cells. Arthritis Rheumatol. 2014;66:686-93 pubmed publisher
    ..The plasma protease factor VII-activating protease (FSAP) can release nucleosomes from late apoptotic cells...
  9. Byeon B, Wang W, Barski A, Ranallo R, Bao K, Schones D, et al. The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. J Biol Chem. 2013;288:23182-93 pubmed publisher
    ..However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression...
  10. Hizume K, Yagura M, Araki H. Concerted interaction between origin recognition complex (ORC), nucleosomes and replication origin DNA ensures stable ORC-origin binding. Genes Cells. 2013;18:764-79 pubmed publisher
    ..Molecular imaging using atomic force microscopy (AFM) shows that ORC associates with the adjacent nucleosomes and forms a larger complex. Moreover, stable binding of ORC to chromatin requires linker DNA...
  11. Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R. PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics. 2013;29:2049-50 pubmed publisher
    ..We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR...
  12. Zasadzińska E, Barnhart Dailey M, Kuich P, Foltz D. Dimerization of the CENP-A assembly factor HJURP is required for centromeric nucleosome deposition. EMBO J. 2013;32:2113-24 pubmed publisher
    ..The deposition of new centromeric nucleosomes requires the CENP-A-specific chromatin assembly factor HJURP (Holliday junction recognition protein)...
  13. Ranjan A, Mizuguchi G, FitzGerald P, Wei D, Wang F, Huang Y, et al. Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell. 2013;154:1232-45 pubmed publisher
    The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known to catalyze ATP-dependent deposition of H2A...
  14. Hansen A, O Shea E. Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol Syst Biol. 2013;9:704 pubmed publisher
  15. Zhang T, Talbert P, Zhang W, Wu Y, Yang Z, Henikoff J, et al. The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci U S A. 2013;110:E4875-83 pubmed publisher
    ..sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3)...
  16. Thomas C, Kotova E, Andrake M, Adolf Bryfogle J, Glaser R, Regnard C, et al. Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. Mol Cell. 2014;53:831-42 pubmed publisher
    ..We propose that chromatin loosening and associated initiation of gene expression is activated by phosphorylation of H2Av in a nucleosome positioned in promoter regions of PARP-1-dependent genes...
  17. Lacoste N, Woolfe A, Tachiwana H, Garea A, Barth T, Cantaloube S, et al. Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX. Mol Cell. 2014;53:631-44 pubmed publisher
    ..Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments. ..
  18. Creamer K, Job G, Shanker S, Neale G, Lin Y, Bartholomew B, et al. The Mi-2 homolog Mit1 actively positions nucleosomes within heterochromatin to suppress transcription. Mol Cell Biol. 2014;34:2046-61 pubmed publisher
    ..and conserved chromatin tethering domains, including a previously unrecognized chromodomain, to remodel nucleosomes and silence transcription...
  19. Song F, Chen P, Sun D, Wang M, Dong L, Liang D, et al. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science. 2014;344:376-80 pubmed publisher
    ..H1-dependent left-handed twist of the repeating tetranucleosomal structural units, within which the four nucleosomes zigzag back and forth with a straight linker DNA...
  20. Wittwer C, Boeck S, Heinemann V, Haas M, Stieber P, Nagel D, et al. Circulating nucleosomes and immunogenic cell death markers HMGB1, sRAGE and DNAse in patients with advanced pancreatic cancer undergoing chemotherapy. Int J Cancer. 2013;133:2619-30 pubmed publisher
    ..Circulating nucleosomes and immunogenic cell death markers, high-mobility group box 1 (HMGB1), soluble receptors of advanced glycation ..
  21. Kato H, Jiang J, Zhou B, Rozendaal M, Feng H, Ghirlando R, et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science. 2013;340:1110-3 pubmed publisher
    ..Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through hydrophobic interactions facilitated by nucleosome docking...
  22. Goutte Gattat D, Shuaib M, Ouararhni K, Gautier T, Skoufias D, Hamiche A, et al. Phosphorylation of the CENP-A amino-terminus in mitotic centromeric chromatin is required for kinetochore function. Proc Natl Acad Sci U S A. 2013;110:8579-84 pubmed publisher
  23. Ballaré C, Zaurin R, Vicent G, Beato M. More help than hindrance: nucleosomes aid transcriptional regulation. Nucleus. 2013;4:189-94 pubmed publisher
    ..In contrast with this vision, we have shown that PR requires nucleosomes for optimal binding and function...
  24. Miell M, Fuller C, Guse A, Barysz H, Downes A, Owen Hughes T, et al. CENP-A confers a reduction in height on octameric nucleosomes. Nat Struct Mol Biol. 2013;20:763-5 pubmed publisher
    b>Nucleosomes with histone H3 replaced by CENP-A direct kinetochore assembly...
  25. Choi K, Zhao X, Kelly K, Venn O, Higgins J, Yelina N, et al. Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters. Nat Genet. 2013;45:1327-36 pubmed publisher
    ..Crossovers were asymmetric around promoters and were most frequent over CTT-repeat motifs and H2A.Z nucleosomes. Pollen typing, segregation and cytogenetic analysis showed decreased numbers of crossovers in the arp6 H2A...
  26. Weber C, Ramachandran S, Henikoff S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell. 2014;53:819-30 pubmed publisher
    b>Nucleosomes are barriers to transcription in vitro; however, their effects on RNA polymerase in vivo are unknown...
  27. Zhou B, Feng H, Kato H, Dai L, Yang Y, Zhou Y, et al. Structural insights into the histone H1-nucleosome complex. Proc Natl Acad Sci U S A. 2013;110:19390-5 pubmed publisher
  28. Watanabe S, Radman Livaja M, Rando O, Peterson C. A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme. Science. 2013;340:195-9 pubmed publisher
    ..Z or H2A can be exchanged from nucleosomes. This result was confirmed in vivo, where genome-wide analysis demonstrated widespread decreases in H2A...
  29. Padeganeh A, Ryan J, Boisvert J, Ladouceur A, Dorn J, Maddox P. Octameric CENP-A nucleosomes are present at human centromeres throughout the cell cycle. Curr Biol. 2013;23:764-9 pubmed publisher
    ..Here we show that natively assembled human CENP-A nucleosomes are octameric throughout the cell cycle...
  30. Harshman S, Young N, Parthun M, Freitas M. H1 histones: current perspectives and challenges. Nucleic Acids Res. 2013;41:9593-609 pubmed publisher
    ..We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry. ..
  31. Arnaudo N, Fern ndez I, McLaughlin S, Peak Chew S, Rhodes D, Martino F. The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle. Nat Struct Mol Biol. 2013;20:1119-21 pubmed publisher
    ..Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis...
  32. Foulds C, Feng Q, Ding C, Bailey S, Hunsaker T, Malovannaya A, et al. Proteomic analysis of coregulators bound to ER? on DNA and nucleosomes reveals coregulator dynamics. Mol Cell. 2013;51:185-99 pubmed publisher
    ..discovered the mechanism whereby H3K4me3 stimulates ER?-mediated transcription as compared with unmodified nucleosomes. H3K4me3 templates promote specific CoR dynamics in the presence of ATP and AcCoA, as manifested by CBP/p300 ..
  33. Gan L, Ladinsky M, Jensen G. Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes. Chromosoma. 2013;122:377-86 pubmed publisher
    ..organization is central to many conserved biological processes, but it is generally unknown how the underlying nucleosomes are arranged in situ...
  34. Wang F, Li G, Altaf M, Lu C, Currie M, Johnson A, et al. Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci U S A. 2013;110:8495-500 pubmed publisher
    ..of H4R17 and R19 with alanine abolish silencing in vivo, but have little or no effect on binding of Sir3 to nucleosomes or histone H4 peptides in vitro...
  35. Gansen A, Hieb A, Böhm V, Toth K, Langowski J. Closing the gap between single molecule and bulk FRET analysis of nucleosomes. PLoS ONE. 2013;8:e57018 pubmed publisher
    ..Recent FRET experiments on nucleosomes have given valuable insight into the structural transformations they can adopt...
  36. Aravamudhan P, Felzer Kim I, Joglekar A. The budding yeast point centromere associates with two Cse4 molecules during mitosis. Curr Biol. 2013;23:770-4 pubmed publisher
    ..conformation of CENP-A chromatin has been proposed by different studies as hemisomes, canonical, or heterotypic nucleosomes. A clear understanding of the in vivo architecture of CENP-A chromatin is important, because it influences the ..
  37. Cui F, Zhurkin V. Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res. 2014;42:836-47 pubmed publisher
    ..DNA, we sought to understand if the two groups of p53 sites differ in their accessibility when embedded in nucleosomes. To this aim, we analyzed the sequence-dependent bending anisotropy of human genomic DNA containing p53 sites...
  38. Bönisch C, Hake S. Histone H2A variants in nucleosomes and chromatin: more or less stable?. Nucleic Acids Res. 2012;40:10719-41 pubmed publisher
  39. Riposo J, Mozziconacci J. Nucleosome positioning and nucleosome stacking: two faces of the same coin. Mol Biosyst. 2012;8:1172-8 pubmed publisher
    b>Nucleosomes are regularly spaced along eukaryotic genomes...
  40. Di Rienzi S, Lindstrom K, Mann T, Noble W, Raghuraman M, Brewer B. Maintaining replication origins in the face of genomic change. Genome Res. 2012;22:1940-52 pubmed publisher
    ..We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved...
  41. Eidahl J, Crowe B, North J, McKee C, Shkriabai N, Feng L, et al. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res. 2013;41:3924-36 pubmed publisher
    ..We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin...
  42. Luger K, Dechassa M, Tremethick D. New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?. Nat Rev Mol Cell Biol. 2012;13:436-47 pubmed publisher
    ..b>Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components...
  43. Collings C, Waddell P, Anderson J. Effects of DNA methylation on nucleosome stability. Nucleic Acids Res. 2013;41:2918-31 pubmed publisher
    ..in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to ..
  44. Xu J, Yanagisawa Y, Tsankov A, Hart C, Aoki K, Kommajosyula N, et al. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 2012;13:R27 pubmed publisher
    ..DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood...
  45. Wyrick J, Kyriss M, Davis W. Ascending the nucleosome face: recognition and function of structured domains in the histone H2A-H2B dimer. Biochim Biophys Acta. 2012;1819:892-901 pubmed publisher
  46. Correll S, Schubert M, Grigoryev S. Short nucleosome repeats impose rotational modulations on chromatin fibre folding. EMBO J. 2012;31:2416-26 pubmed publisher
    In eukaryotic cells, DNA is organized into arrays of repeated nucleosomes where the shorter nucleosome repeat length (NRL) types are associated with transcriptionally active chromatin...
  47. Voigt P, LeRoy G, Drury W, Zee B, Son J, Beck D, et al. Asymmetrically modified nucleosomes. Cell. 2012;151:181-93 pubmed publisher
    ..We demonstrate that nucleosomes in embryonic stem cells, fibroblasts, and cancer cells exist in both symmetrically and asymmetrically modified ..
  48. Choi E, Strålfors A, Catania S, Castillo A, Svensson J, Pidoux A, et al. Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast. PLoS Genet. 2012;8:e1002985 pubmed publisher
    Specialized chromatin containing CENP-A nucleosomes instead of H3 nucleosomes is found at all centromeres...
  49. Mattiroli F, Vissers J, van Dijk W, Ikpa P, Citterio E, Vermeulen W, et al. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell. 2012;150:1182-95 pubmed publisher
    ..Using a mutant of RNF168 unable to target histones but still catalyzing ubiquitin chains at DSBs, we show that ubiquitin chains per se are insufficient for signaling, but RNF168 target ubiquitination is required for DDR...
  50. Morra R, Lee B, Shaw H, Tuma R, Mancini E. Concerted action of the PHD, chromo and motor domains regulates the human chromatin remodelling ATPase CHD4. FEBS Lett. 2012;586:2513-21 pubmed publisher
    ..Our results demonstrate functional interdependency between domains within a chromatin remodeller. ..
  51. Bassett E, Denizio J, Barnhart Dailey M, Panchenko T, Sekulic N, Rogers D, et al. HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev Cell. 2012;22:749-62 pubmed publisher
    ..are defined by the presence of chromatin containing the histone H3 variant, CENP-A, whose assembly into nucleosomes requires the chromatin assembly factor HJURP...
  52. Volle C, Delaney S. CAG/CTG repeats alter the affinity for the histone core and the positioning of DNA in the nucleosome. Biochemistry. 2012;51:9814-25 pubmed publisher
    ..and the histone core, we determined the efficiency with which various TNR-containing DNA substrates form nucleosomes, revealing that even short CAG/CTG tracts are robust incorporators...
  53. Cole H, Howard B, Clark D. Genome-wide mapping of nucleosomes in yeast using paired-end sequencing. Methods Enzymol. 2012;513:145-68 pubmed publisher
    ..Nucleosome cores are regularly spaced along the DNA in vivo, separated by linker DNA. Nucleosomes are compact structures capable of blocking access to the DNA that they contain...