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The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.

Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K
Nat Struct Mol Biol 15 1122-4 (2008)
Cited: 155 times
EuropePMC logo PMID: 18794842

Abstract

Histone methylation regulates chromatin function dependent on the site and degree of the modification. In addition to creating binding sites for proteins, methylated lysine residues are likely to influence chromatin structure directly. Here we present crystal structures of nucleosomes reconstituted with methylated histones and investigate the folding behavior of resulting arrays. We demonstrate that dimethylation of histone H3 at lysine residue 79 locally alters the nucleosomal surface, whereas trimethylation of H4 at lysine residue 20 affects higher-order structure.

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  1. Readers of histone modifications. Yun M, Wu J, Workman JL, Li B. Cell Res 21 564-578 (2011)
  2. Histones: at the crossroads of peptide and protein chemistry. Müller MM, Muir TW. Chem Rev 115 2296-2349 (2015)

Articles - 3c1c mentioned but not cited (3)



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  1. Writing, erasing and reading histone lysine methylations. Hyun K, Jeon J, Park K, Kim J. Exp Mol Med 49 e324 (2017)
  2. Histone core modifications regulating nucleosome structure and dynamics. Tessarz P, Kouzarides T. Nat Rev Mol Cell Biol 15 703-708 (2014)
  3. New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Luger K, Dechassa ML, Tremethick DJ. Nat Rev Mol Cell Biol 13 436-447 (2012)
  4. Determinants and dynamics of genome accessibility. Bell O, Tiwari VK, Thomä NH, Schübeler D. Nat Rev Genet 12 554-564 (2011)
  5. Histone post-translational modifications - cause and consequence of genome function. Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Nat Rev Genet 23 563-580 (2022)
  6. Nucleosome structure and function. McGinty RK, Tan S. Chem Rev 115 2255-2273 (2015)
  7. Epigenetic modifications of histones in cancer. Zhao Z, Shilatifard A. Genome Biol 20 245 (2019)
  8. Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity. Jørgensen S, Schotta G, Sørensen CS. Nucleic Acids Res 41 2797-2806 (2013)
  9. Histone H3 lysine 4 (H3K4) methylation in development and differentiation. Eissenberg JC, Shilatifard A. Dev Biol 339 240-249 (2010)
  10. PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. Beck DB, Oda H, Shen SS, Reinberg D. Genes Dev 26 325-337 (2012)
  11. Histone H2A variants in nucleosomes and chromatin: more or less stable? Bönisch C, Hake SB. Nucleic Acids Res 40 10719-10741 (2012)
  12. Fast signals and slow marks: the dynamics of histone modifications. Barth TK, Imhof A. Trends Biochem Sci 35 618-626 (2010)
  13. Nucleosome structure(s) and stability: variations on a theme. Andrews AJ, Luger K. Annu Rev Biophys 40 99-117 (2011)
  14. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Nat Rev Drug Discov 20 265-286 (2021)
  15. DOT1L and H3K79 Methylation in Transcription and Genomic Stability. Wood K, Tellier M, Murphy S. Biomolecules 8 E11 (2018)
  16. The winding path of protein methylation research: milestones and new frontiers. Murn J, Shi Y. Nat Rev Mol Cell Biol 18 517-527 (2017)
  17. Writing and reading H2B monoubiquitylation. Fuchs G, Oren M. Biochim Biophys Acta 1839 694-701 (2014)
  18. Nucleosome structural studies. Tan S, Davey CA. Curr Opin Struct Biol 21 128-136 (2011)
  19. Chromatin as an expansive canvas for chemical biology. Fierz B, Muir TW. Nat Chem Biol 8 417-427 (2012)
  20. The emerging roles of DOT1L in leukemia and normal development. McLean CM, Karemaker ID, van Leeuwen F. Leukemia 28 2131-2138 (2014)
  21. Toward convergence of experimental studies and theoretical modeling of the chromatin fiber. Schlick T, Hayes J, Grigoryev S. J Biol Chem 287 5183-5191 (2012)
  22. Nucleosome positioning in Saccharomyces cerevisiae. Jansen A, Verstrepen KJ. Microbiol Mol Biol Rev 75 301-320 (2011)
  23. The upstreams and downstreams of H3K79 methylation by DOT1L. Vlaming H, van Leeuwen F. Chromosoma 125 593-605 (2016)
  24. The tale of a tail: histone H4 acetylation and the repair of DNA breaks. Dhar S, Gursoy-Yuzugullu O, Parasuram R, Price BD. Philos Trans R Soc Lond B Biol Sci 372 20160284 (2017)
  25. Chemical approaches for studying histone modifications. Chatterjee C, Muir TW. J Biol Chem 285 11045-11050 (2010)
  26. Intergenerational epigenetic inheritance in models of developmental programming of adult disease. Fernandez-Twinn DS, Constância M, Ozanne SE. Semin Cell Dev Biol 43 85-95 (2015)
  27. The emerging role of lysine methyltransferase SETD8 in human diseases. Milite C, Feoli A, Viviano M, Rescigno D, Cianciulli A, Balzano AL, Mai A, Castellano S, Sbardella G. Clin Epigenetics 8 102 (2016)
  28. Histone citrullination: a new target for tumors. Zhu D, Zhang Y, Wang S. Mol Cancer 20 90 (2021)
  29. The folding and unfolding of eukaryotic chromatin. Bassett A, Cooper S, Wu C, Travers A. Curr Opin Genet Dev 19 159-165 (2009)
  30. Decoding the histone H4 lysine 20 methylation mark. Balakrishnan L, Milavetz B. Crit Rev Biochem Mol Biol 45 440-452 (2010)
  31. Histone Tail Conformations: A Fuzzy Affair with DNA. Ghoneim M, Fuchs HA, Musselman CA. Trends Biochem Sci 46 564-578 (2021)
  32. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. Kebede AF, Schneider R, Daujat S. FEBS J 282 1658-1674 (2015)
  33. Spreading chromatin into chemical biology. Allis CD, Muir TW. Chembiochem 12 264-279 (2011)
  34. A molecular engineering toolbox for the structural biologist. Debelouchina GT, Muir TW. Q Rev Biophys 50 e7 (2017)
  35. Synthesis of proteins with defined posttranslational modifications using the genetic noncanonical amino acid incorporation approach. Liu WR, Wang YS, Wan W. Mol Biosyst 7 38-47 (2011)
  36. Regulation of chromatin structure via histone post-translational modification and the link to carcinogenesis. Thompson LL, Guppy BJ, Sawchuk L, Davie JR, McManus KJ. Cancer Metastasis Rev 32 363-376 (2013)
  37. Chemical and biochemical approaches in the study of histone methylation and demethylation. Li KK, Luo C, Wang D, Jiang H, Zheng YG. Med Res Rev 32 815-867 (2012)
  38. SIR-nucleosome interactions: structure-function relationships in yeast silent chromatin. Oppikofer M, Kueng S, Gasser SM. Gene 527 10-25 (2013)
  39. Chemical mutagenesis: selective post-expression interconversion of protein amino acid residues. Chalker JM, Davis BG. Curr Opin Chem Biol 14 781-789 (2010)
  40. Histone tails: ideal motifs for probing epigenetics through chemical biology approaches. Voigt P, Reinberg D. Chembiochem 12 236-252 (2011)
  41. Implication of posttranslational histone modifications in nucleotide excision repair. Li S. Int J Mol Sci 13 12461-12486 (2012)
  42. Trimethyllysine: From Carnitine Biosynthesis to Epigenetics. Maas MN, Hintzen JCJ, Porzberg MRB, Mecinović J. Int J Mol Sci 21 E9451 (2020)
  43. Chemical and semisynthesis of modified histones. Maity SK, Jbara M, Brik A. J Pept Sci 22 252-259 (2016)
  44. Chromatin assembly on herpes simplex virus genomes during lytic infection. Lu X, Triezenberg SJ. Biochim Biophys Acta 1799 217-222 (2010)
  45. Lysine methyltransferase inhibitors: where we are now. Feoli A, Viviano M, Cipriano A, Milite C, Castellano S, Sbardella G. RSC Chem Biol 3 359-406 (2022)
  46. A modified epigenetics toolbox to study histone modifications on the nucleosome core. Frederiks F, Stulemeijer IJ, Ovaa H, van Leeuwen F. Chembiochem 12 308-313 (2011)
  47. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Ackermann BE, Debelouchina GT. Front Mol Biosci 8 741581 (2021)
  48. Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. Pick H, Kilic S, Fierz B. Biochim Biophys Acta 1839 644-656 (2014)
  49. Methylation across the central dogma in health and diseases: new therapeutic strategies. Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Signal Transduct Target Ther 8 310 (2023)
  50. Progress in the Development of Lysine Methyltransferase SETD8 Inhibitors. Milite C, Feoli A, Viviano M, Rescigno D, Mai A, Castellano S, Sbardella G. ChemMedChem 11 1680-1685 (2016)
  51. Is There a Histone Code for Cellular Quiescence? Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Front Cell Dev Biol 9 739780 (2021)
  52. One, two, three: how histone methylation is read. Fischle W. Epigenomics 4 641-653 (2012)
  53. Systematic analysis of histone modification readout. Nikolov M, Fischle W. Mol Biosyst 9 182-194 (2013)
  54. Chemistry-Driven Epigenetic Investigation of Histone and DNA Modifications. Sueoka T, Koyama K, Hayashi G, Okamoto A. Chem Rec 18 1727-1744 (2018)
  55. Chromatin Organization and Function in Drosophila. Llorens-Giralt P, Camilleri-Robles C, Corominas M, Climent-Cantó P. Cells 10 2362 (2021)
  56. Reprogramming chromatin. Ehrensberger AH, Svejstrup JQ. Crit Rev Biochem Mol Biol 47 464-482 (2012)
  57. Getting down to the core of histone modifications. Jack AP, Hake SB. Chromosoma 123 355-371 (2014)
  58. Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies. Musselman CA, Kutateladze TG. ACS Chem Biol 14 579-586 (2019)
  59. Chemical tools in chromatin research. Schwarzer D. J Pept Sci 16 530-537 (2010)
  60. Recent Advances in Investigating Functional Dynamics of Chromatin. Shi X, Zhai Z, Chen Y, Li J, Nordenskiöld L. Front Genet 13 870640 (2022)
  61. Remembering through the genome: the role of chromatin states in brain functions and diseases. Arzate-Mejia RG, Mansuy IM. Transl Psychiatry 13 122 (2023)
  62. Citric Acid: A Nexus Between Cellular Mechanisms and Biomaterial Innovations. Xu H, Yan S, Gerhard E, Xie D, Liu X, Zhang B, Shi D, Ameer GA, Yang J. Adv Mater 36 e2402871 (2024)
  63. Regulation of the heterochromatin spreading reaction by trans-acting factors. Hamali B, Amine AAA, Al-Sady B. Open Biol 13 230271 (2023)
  64. Lysine methylation modifications in tumor immunomodulation and immunotherapy: regulatory mechanisms and perspectives. Luo Y, Lu J, Lei Z, Zhu H, Rao D, Wang T, Fu C, Zhang Z, Xia L, Huang W. Biomark Res 12 74 (2024)
  65. Synthesis of ubiquitinated proteins for biochemical and functional analysis. Kriegesmann J, Brik A. Chem Sci 14 10025-10040 (2023)

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