全部 标题 作者
关键词 摘要

PLOS ONE  2013 

Solution Scattering and FRET Studies on Nucleosomes Reveal DNA Unwrapping Effects of H3 and H4 Tail Removal

DOI: 10.1371/journal.pone.0078587

Full-Text   Cite this paper   Add to My Lib

Abstract:

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.

References

[1]  Wolffe A (1992) Chromatin: Structure and Function. London: Academic Press. 213 pp.
[2]  Li G, Reinberg D (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 21: 175–186. doi:10.1016/j.gde.2011.01.022. PubMed: 21342762.
[3]  Schwarz PM, Felthauser A, Fletcher TM, Hansen JC (1996) Reversible oligonucleosome self-association:? Dependence on divalent cations and core histone tail domains. Biochemistry 35: 4009–4015. doi:10.1021/bi9525684. PubMed: 8672434.
[4]  Andrews AJ, Luger K (2011) Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys 40: 99–117. doi:10.1146/annurev-biophys-042910-155329. PubMed: 21332355.
[5]  Tan S, Davey CA (2011) Nucleosome structural studies. Curr Opin Struct BiolCurrent Opinion in Structural Biology 21: 128–136 16/j.sbi.2010.11.006.
[6]  Zheng C, Hayes JJ (2003) Structures and interactions of the core histone tail domains. Biopolymers 68: 539–546. doi:10.1002/bip.10303. PubMed: 12666178.
[7]  Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 ? resolution. J Mol Biol 319: 1097–1113 16/S0022-2836(02)00386-8.
[8]  Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A et al. (1984) Structure of the nucleosome core particle at 7 ? resolution. Nature 311: 532–537. doi:10.1038/311532a0. PubMed: 6482966.
[9]  Luger K, M?der AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 ? resolution. Nature 389: 251–260. doi:10.1038/38444. PubMed: 9305837.
[10]  Schalch T, Duda S, Sargent DF, Richmond TJ (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436: 138–141. doi:10.1038/nature03686. PubMed: 16001076.
[11]  Schlick T, Hayes J, Grigoryev S (2012) Toward convergence of experimental studies and theoretical modeling of the chromatin fiber. J Biol Chem 287: 5183–5191. doi:10.1074/jbc.R111.305763. PubMed: 22157002.
[12]  B?hm V, Hieb AR, Andrews AJ, Gansen A, Rocker A et al. (2011) Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res 39: 3093–102. doi:10.1093/nar/gkq1279. PubMed: 21177647.
[13]  Park Y-J, Dyer PN, Tremethick DJ, Luger K (2004) A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome. J Biol Chem 279: 24274–24282. doi:10.1074/jbc.M313152200. PubMed: 15020582.
[14]  Bowman GD (2010) Mechanisms of ATP-dependent nucleosome sliding. Curr Opin Struct Biol 20: 73–81. doi:10.1016/j.sbi.2009.12.002. PubMed: 20060707.
[15]  Li G, Widom J (2004) Nucleosomes facilitate their own invasion. Nat Struct Mol Biol 11: 763–769. doi:10.1038/nsmb801. PubMed: 15258568.
[16]  Li G, Levitus M, Bustamante C, Widom J (2005) Rapid spontaneous accessibility of nucleosomal. DNA - Nat Struct Mol Biol 12: 46–53. doi:10.1038/nsmb869.
[17]  Koopmans WJA, Buning R, Schmidt T, J van Noort (2009) spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes. Biophys J 97: 195–204. doi:10.1016/j.bpj.2009.04.030. PubMed: 19580757.
[18]  Buning R, van Noort J (2010) Single-pair FRET experiments on nucleosome conformational dynamics. Biochimie 92: 1729–1740. doi:10.1016/j.biochi.2010.08.010. PubMed: 20800089.
[19]  Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K (2011) Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes. Nucleic Acids Res 39: 4122–4135. doi:10.1093/nar/gkr005. PubMed: 21278419.
[20]  Kelbauskas L, Woodbury N, Lohr D (2009) DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysis. Biochem Cell Biol 87: 323–335. doi:10.1139/O08-126. PubMed: 19234544.
[21]  Widlund HR, Vitolo JM, Thiriet C, Hayes JJ (2000) DNA sequence-dependent contributions of core histone tails to nucleosome stability:? Differential effects of acetylation and proteolytic tail removal. Biochemistry 39: 3835–3841. doi:10.1021/bi991957l. PubMed: 10736184.
[22]  Gansen A, To ?th K, Schwarz N, Langowski J (2009) Structural variability of nucleosomes detected by single-pair Fo?rster resonance energy transfer: histone acetylation, sequence variation, and salt effects. J Phys Chem B 113: 2604–2613. doi:10.1021/jp7114737.
[23]  Choy JS, Wei S, Lee JY, Tan S, Chu S et al. (2010) DNA methylation increases nucleosome compaction and rigidity. J Am Chem Soc 132: 1782–1783. doi:10.1021/ja910264z. PubMed: 20095602.
[24]  Jimenez-Useche I, Yuan C (2012) The effect of DNA CpG methylation on the dynamic conformation of a nucleosome. Biophys J 103: 2502–2512. doi:10.1016/j.bpj.2012.11.012. PubMed: 23260052.
[25]  Bertin A, Leforestier A, Durand D, Livolant F (2004) Role of histone tails in the conformation and interactions of nucleosome core particles. Biochemistry 43: 4773–4780. doi:10.1021/bi036210g. PubMed: 15096046.
[26]  Brower-Toland B, Wacker DA, Fulbright RM, Lis JT, Kraus WL et al. (2005) Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol 346: 135–146. doi:10.1016/j.jmb.2004.11.056. PubMed: 15663933.
[27]  Bertin A, Renouard M, Pedersen JS, Livolant F, Durand D (2007) H3 and H4 histone tails play a central role in the interactions of recombinant NCPs. Biophys J 92: 2633–2645. doi:10.1529/biophysj.106.093815. PubMed: 17237203.
[28]  Tóth K, Brun N, Langowski J (2006) Chromatin compaction at the mononucleosome level. Biochemistry 45: 1591–1598. doi:10.1021/bi052110u. PubMed: 16460006.
[29]  Ferreira H, Somers J, Webster R, Flaus A, Owen-Hughes T (2007) Histone tails and the H3 αN helix regulate nucleosome mobility and stability. Mol Cell Biol 27: 4037–4048. doi:10.1128/MCB.02229-06. PubMed: 17387148.
[30]  Simon M, North JA, Shimko JC, Forties RA, Ferdinand MB et al. (2011) Histone fold modifications control nucleosome unwrapping and disassembly. Proc Natl Acad Sci U S A 108: 12711–12716. doi:10.1073/pnas.1106264108. PubMed: 21768347.
[31]  Kelbauskas L, Chan N, Bash R, DeBartolo P, Sun J et al. (2008) Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes. Biophys J 94: 147–158. doi:10.1529/biophysj.107.111906. PubMed: 17933873.
[32]  Mangenot S, Leforestier A, Vachette P, Durand D, Livolant F (2002) Salt-induced conformation and interaction changes of nucleosome core particles. Biophys J 82: 345–356. doi:10.1016/S0006-3495(02)75399-X. PubMed: 11751321.
[33]  Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, et al. (2003) Reconstitution of nucleosome core particles from recombinant histones and DNA. In: CD AllisC. Wu. Methods in Enzymology, volume 375. Academic Press. pp. 23–44.
[34]  Luger K, Rechsteiner TJ, Richmond TJ (1999) Preparation of nucleosome core particle from recombinant histones. In: M. PaulAPW Wassarman. Methods in Enzymology, volume 304. Academic Press. pp. 3–19.
[35]  Godde JS, Wolffe AP (1995) Disruption of reconstituted nucleosomes the effect of particle concentration, MgCl2 and KCl concentration, the histone tails, and temperature. J Biol Chem 270: 27399–27402. doi:10.1074/jbc.270.46.27399. PubMed: 7499192.
[36]  Howell SC, Andresen K, Jimenez-Useche I, Yuan C, Qiu X (2013) Elucidating Internucleosome Interactions and the Roles of Histone Tails. Biophys J 105: 194–199. doi:10.1016/j.bpj.2013.05.021. PubMed: 23823239.
[37]  Nielsen SS, Toft KN, Snakenborg D, Jeppesen MG, Jacobsen JK et al. (2009) BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis. J Appl Crystallogr 42: 959–964. doi:10.1107/S0021889809023863.
[38]  Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG et al. (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45: 342–350. doi:10.1107/S0021889812007662.
[39]  Svergun D, Barberato C, Koch MHJ (1995) CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28: 768–773. doi:10.1107/S0021889895007047.
[40]  Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT et al. (2009) High resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol 16: 124–129. doi:10.1038/nsmb.1526. PubMed: 19136959.
[41]  Voltz K, Trylska J, Calimet N, Smith JC, Langowski J (2012) Unwrapping of nucleosomal DNA ends: A multiscale molecular dynamics study. Biophys J 102: 849–858. doi:10.1016/j.bpj.2011.11.4028. PubMed: 22385856.
[42]  Wang X, Moore SC, Laszckzak M, Ausió J (2000) Acetylation increases the a-helical content of the histone tails of the nucleosome. J Biol Chem 275: 35013–35020. doi:10.1074/jbc.M004998200. PubMed: 10938086.
[43]  Zhou J, Fan JY, Rangasamy D, Tremethick DJ (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 14: 1070–1076. doi:10.1038/nsmb1323. PubMed: 17965724.
[44]  Nurse NP, Jimenez-Useche I, Smith IT, Yuan C (2013) Clipping of Flexible Tails of Histones H3 and H4 Affects the Structure and?Dynamics of the Nucleosome. Biophys J 104: 1081–1088. doi:10.1016/j.bpj.2013.01.019. PubMed: 23473491.

Full-Text

comments powered by Disqus