Display options
Cite
Marr LT, Ocampo J, Clark DJ, et al. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin. 2021;14(1):5doi: 10.1186/s13072-020-00381-5.
Marr, L. T., Ocampo, J., Clark, D. J., & Hayes, J. J. (2021). Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics & chromatin, 14(1), 5. https://doi.org/10.1186/s13072-020-00381-5
Marr, Luke T, et al. "Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes." Epigenetics & chromatin vol. 14,1 (2021): 5. doi: https://doi.org/10.1186/s13072-020-00381-5
Marr LT, Ocampo J, Clark DJ, Hayes JJ. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin. 2021 Jan 11;14(1):5. doi: 10.1186/s13072-020-00381-5. PMID: 33430969; PMCID: PMC7802155.
Copy Download .nbib Format: NLM
Share it on

Epigenetics Chromatin. 2021 Jan 11;14(1):5. doi: 10.1186/s13072-020-00381-5.

Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes.

Epigenetics & chromatin

Luke T Marr, Josefina Ocampo, David J Clark, Jeffrey J Hayes

Affiliations

  1. Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
  2. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), C1428ADN, Buenos Aires, Argentina.
  3. Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
  4. Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA. [email protected].

PMID: 33430969 PMCID: PMC7802155 DOI: 10.1186/s13072-020-00381-5

Abstract

BACKGROUND: The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM).

RESULTS: Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A-H2B dimer/H3-H4 tetramer interface, and H3 A110C, resides at the H3-H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed.

CONCLUSIONS: Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.

Keywords: Chromatin structure; Remodelers; Subnucleosome; Transcription

References

  1. Oncogene. 2002 Jan 21;21(4):512-21 - PubMed
  2. Cell. 2005 Jan 14;120(1):37-48 - PubMed
  3. Mol Cell. 2000 Oct;6(4):769-80 - PubMed
  4. FEBS Lett. 1976 Jul 15;66(2):274-80 - PubMed
  5. Mol Cell Biol. 2011 Jun;31(12):2413-21 - PubMed
  6. Nucleic Acids Res. 2011 Apr;39(8):3093-102 - PubMed
  7. Genes Dev. 2002 Apr 1;16(7):806-19 - PubMed
  8. Cell. 2005 Nov 18;123(4):581-92 - PubMed
  9. Genome Res. 2019 Dec;29(12):1985-1995 - PubMed
  10. Mol Cell. 2004 Jun 4;14(5):667-73 - PubMed
  11. Cell. 1979 Apr;16(4):797-806 - PubMed
  12. Mol Biol Cell. 2016 Nov 1;27(21):3357-3368 - PubMed
  13. Biochem Biophys Res Commun. 2012 Feb 10;418(2):205-10 - PubMed
  14. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1238-43 - PubMed
  15. Methods. 2020 Dec 1;184:61-69 - PubMed
  16. Chromosoma. 2014 Jun;123(3):225-37 - PubMed
  17. Biophys J. 2010 Sep 22;99(6):1896-905 - PubMed
  18. J Biol Chem. 2008 Dec 12;283(50):34532-40 - PubMed
  19. EMBO J. 2016 May 17;35(10):1115-32 - PubMed
  20. J Mol Biol. 1987 Jul 20;196(2):399-411 - PubMed
  21. Nucleic Acids Res. 2016 Jun 2;44(10):4625-35 - PubMed
  22. Genes Dev. 2018 May 1;32(9-10):695-710 - PubMed
  23. Nature. 1980 Aug 28;286(5776):854-60 - PubMed
  24. J Biol Chem. 1991 Apr 5;266(10):6489-98 - PubMed
  25. Proc Natl Acad Sci U S A. 2018 Dec 4;115(49):12447-12452 - PubMed
  26. J Mol Biol. 1987 Jul 20;196(2):379-88 - PubMed
  27. Cell. 2000 Oct 13;103(2):263-71 - PubMed
  28. Mol Cell Biol. 1998 Aug;18(8):4629-38 - PubMed
  29. Elife. 2015 Mar 30;4:e06073 - PubMed
  30. Structure. 2020 Jan 7;28(1):44-53.e4 - PubMed
  31. Mol Biol Cell. 2009 Aug;20(15):3503-13 - PubMed
  32. Genes Dev. 1988 Feb;2(2):150-9 - PubMed
  33. J Biol Chem. 1986 Jul 25;261(21):9904-14 - PubMed
  34. EMBO J. 2008 Jan 9;27(1):100-10 - PubMed
  35. Nucleic Acids Res. 2014 Nov 10;42(20):12512-22 - PubMed
  36. Mol Cell. 2006 Feb 3;21(3):417-25 - PubMed
  37. EMBO J. 2007 Feb 7;26(3):730-40 - PubMed
  38. Philos Trans A Math Phys Eng Sci. 2006 Oct 15;364(1847):2615-33 - PubMed
  39. Genome Res. 2014 Oct;24(10):1637-49 - PubMed
  40. Cell. 2001 May 4;105(3):403-14 - PubMed
  41. Cell. 1979 Apr;16(4):807-14 - PubMed
  42. Methods Enzymol. 2012;513:145-68 - PubMed
  43. Mol Cell Biol. 2003 Nov;23(22):8323-33 - PubMed
  44. Nat Struct Mol Biol. 2019 Aug;26(8):744-754 - PubMed
  45. Biochem Biophys Res Commun. 1973 May 15;52(2):504-10 - PubMed
  46. J Biol Chem. 1988 Oct 25;263(30):15643-51 - PubMed
  47. Science. 2014 Apr 25;344(6182):376-80 - PubMed
  48. Nucleic Acids Res. 2011 Mar;39(5):1680-91 - PubMed
  49. Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11325-30 - PubMed
  50. Genome Res. 2015 Mar;25(3):381-90 - PubMed
  51. Mol Cell. 2006 Nov 17;24(4):559-68 - PubMed
  52. Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9 - PubMed
  53. Mol Cell. 2019 Jan 17;73(2):238-249.e3 - PubMed
  54. Genes Dev. 2017 Mar 1;31(5):451-462 - PubMed
  55. J Biol Chem. 1990 Apr 5;265(10):5736-46 - PubMed
  56. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8872-7 - PubMed
  57. Sci Rep. 2015 Feb 17;5:8512 - PubMed
  58. EMBO J. 2003 Apr 15;22(8):1846-56 - PubMed
  59. Genome Res. 2010 Jan;20(1):90-100 - PubMed
  60. Nucleic Acids Res. 1978 Nov;5(11):4431-49 - PubMed
  61. J Mol Biol. 1987 Jul 20;196(2):389-97 - PubMed
  62. Cell Rep. 2016 Nov 15;17(8):2112-2124 - PubMed
  63. Mol Cell. 2005 Dec 22;20(6):971-8 - PubMed
  64. Nat Struct Mol Biol. 2020 Feb;27(2):109-118 - PubMed
  65. FEBS Lett. 1989 Oct 23;257(1):141-4 - PubMed
  66. Nat Methods. 2013 Dec;10(12):1213-8 - PubMed
  67. Biophys J. 2018 May 22;114(10):2326-2335 - PubMed
  68. Nat Methods. 2012 Mar 04;9(4):357-9 - PubMed
  69. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4947-52 - PubMed
  70. Mol Cell Biol. 2002 Sep;22(18):6458-70 - PubMed
  71. Science. 2003 Aug 22;301(5636):1096-9 - PubMed
  72. Mol Cell Biol. 2012 Sep;32(17):3479-85 - PubMed
  73. Nature. 2007 Dec 13;450(7172):1031-5 - PubMed
  74. Mol Cell. 2002 Mar;9(3):541-52 - PubMed
  75. Chromosoma. 2014 Mar;123(1-2):3-13 - PubMed
  76. Science. 2003 Aug 22;301(5636):1090-3 - PubMed
  77. Nature. 1999 Nov 25;402(6760):418-21 - PubMed
  78. Soft Matter. 2020 May 13;16(18):4366-4372 - PubMed
  79. Cell. 2012 Jun 22;149(7):1461-73 - PubMed
  80. Mol Cell. 2006 Nov 3;24(3):481-7 - PubMed
  81. Genome Biol. 2019 Sep 13;20(1):198 - PubMed
  82. Nature. 2000 Jan 6;403(6765):41-5 - PubMed
  83. Mol Biol Cell. 2018 Jul 1;29(13):1652-1663 - PubMed
  84. Nucleic Acids Res. 2014 Jul;42(13):8767-76 - PubMed
  85. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91 - PubMed
  86. Genome Res. 2007 Jun;17(6):877-85 - PubMed
  87. Genome Res. 2019 Mar;29(3):407-417 - PubMed
  88. Mol Cell Biol. 2007 Oct;27(20):6987-95 - PubMed
  89. Biotechniques. 2004 Feb;36(2):212-3 - PubMed
  90. PLoS Biol. 2008 Mar 18;6(3):e65 - PubMed
  91. PLoS Comput Biol. 2008 Nov;4(11):e1000216 - PubMed
  92. Sci Rep. 2018 Jan 24;8(1):1543 - PubMed
  93. Mol Cell Biol. 2006 Feb;26(4):1496-509 - PubMed
  94. Biopolymers. 1982 Feb;21(2):343-58 - PubMed
  95. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4285-8 - PubMed
  96. Nucleic Acids Res. 2012 Nov;40(21):10753-64 - PubMed
  97. Cell. 2005 Nov 18;123(4):593-605 - PubMed
  98. Nature. 1997 Sep 18;389(6648):251-60 - PubMed
  99. J Cell Biol. 2001 Jun 25;153(7):1341-53 - PubMed
  100. Cell. 2015 Jul 2;162(1):108-19 - PubMed
  101. Nature. 2011 Jan 20;469(7330):368-73 - PubMed
  102. Epigenetics. 2013 Jan;8(1):10-5 - PubMed
  103. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  104. Methods Enzymol. 2012;513:233-50 - PubMed
  105. Mol Cell. 2018 Dec 6;72(5):902-915.e7 - PubMed
  106. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8266-70 - PubMed
  107. Nat Commun. 2016 May 06;7:11485 - PubMed
  108. Science. 2006 Feb 10;311(5762):844-7 - PubMed
  109. Cell Cycle. 2006 Jul;5(13):1361-5 - PubMed
  110. Genes Dev. 2005 Mar 15;19(6):677-82 - PubMed
  111. Mol Cell. 2014 Dec 4;56(5):653-66 - PubMed
  112. Nucleic Acids Res. 2014 Apr;42(8):4922-33 - PubMed
  113. Cell. 2009 May 1;137(3):445-58 - PubMed
  114. Genetics. 2015 Jun;200(2):505-21 - PubMed
  115. Genes Dev. 1999 Sep 15;13(18):2369-74 - PubMed
  116. J Mol Biol. 2007 Aug 24;371(4):971-88 - PubMed
  117. Cell. 2014 Dec 4;159(6):1377-88 - PubMed
  118. J Biol Chem. 2004 Jun 4;279(23):24274-82 - PubMed
  119. Mol Cell Biol. 2004 Dec;24(23):10111-7 - PubMed

Publication Types

Grant support