Routes to DNA Accessibility: Alternative Pathways for Nucleosome Unwinding

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2014 Jul 17

PMID 25028880

Citations 5

Authors

Daniel J Schlingman

Andrew H Mack

Masha Kamenetska

Simon G J Mochrie

Lynne Regan

Affiliations

Soon will be listed here.

Abstract

The dynamic packaging of DNA into chromatin is a key determinant of eukaryotic gene regulation and epigenetic inheritance. Nucleosomes are the basic unit of chromatin, and therefore the accessible states of the nucleosome must be the starting point for mechanistic models regarding these essential processes. Although the existence of different unwound nucleosome states has been hypothesized, there have been few studies of these states. The consequences of multiple states are far reaching. These states will behave differently in all aspects, including their interactions with chromatin remodelers, histone variant exchange, and kinetic properties. Here, we demonstrate the existence of two distinct states of the unwound nucleosome, which are accessible at physiological forces and ionic strengths. Using optical tweezers, we measure the rates of unwinding and rewinding for these two states and show that the rewinding rates from each state are different. In addition, we show that the probability of unwinding into each state is dependent on the applied force and ionic strength. Our results demonstrate not only that multiple unwound states exist but that their accessibility can be differentially perturbed, suggesting possible roles for these states in gene regulation. For example, different histone variants or modifications may facilitate or suppress access to DNA by promoting unwinding into one state or the other. We anticipate that the two unwound states reported here will be the basis for future models of eukaryotic transcriptional control.

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References

English C, Maluf N, Tripet B, Churchill M, Tyler J . ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3-H4 heterotetramer on DNA. Biochemistry. 2005; 44(42):13673-82. PMC: 4445473. DOI: 10.1021/bi051333h. View

Dalal Y, Wang H, Lindsay S, Henikoff S . Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol. 2007; 5(8):e218. PMC: 1933458. DOI: 10.1371/journal.pbio.0050218. View

Thastrom A, Lowary P, Widom J . Measurement of histone-DNA interaction free energy in nucleosomes. Methods. 2004; 33(1):33-44. DOI: 10.1016/j.ymeth.2003.10.018. View

Wechser M, Kladde M, Alfieri J, Peterson C . Effects of Sin- versions of histone H4 on yeast chromatin structure and function. EMBO J. 1997; 16(8):2086-95. PMC: 1169811. DOI: 10.1093/emboj/16.8.2086. View

Mack A, Schlingman D, Kamenetska M, Collins R, Regan L, Mochrie S . The molecular yo-yo method: live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions. Rev Sci Instrum. 2013; 84(8):085119. DOI: 10.1063/1.4819026. View

Elsasser S, Huang H, Lewis P, Chin J, Allis C, Patel D . DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition. Nature. 2012; 491(7425):560-5. PMC: 4056191. DOI: 10.1038/nature11608. View

Mochrie S, Mack A, Schlingman D, Collins R, Kamenetska M, Regan L . Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants. Phys Rev E Stat Nonlin Soft Matter Phys. 2013; 87(1):012710. PMC: 3902847. DOI: 10.1103/PhysRevE.87.012710. View

Schlingman D, Mack A, Mochrie S, Regan L . A new method for the covalent attachment of DNA to a surface for single-molecule studies. Colloids Surf B Biointerfaces. 2010; 83(1):91-5. PMC: 3902852. DOI: 10.1016/j.colsurfb.2010.11.002. View

Sternberg P, Stern M, Clark I, Herskowitz I . Activation of the yeast HO gene by release from multiple negative controls. Cell. 1987; 48(4):567-77. DOI: 10.1016/0092-8674(87)90235-2. View

10.

Bintu L, Ishibashi T, Dangkulwanich M, Wu Y, Lubkowska L, Kashlev M . Nucleosomal elements that control the topography of the barrier to transcription. Cell. 2012; 151(4):738-749. PMC: 3508686. DOI: 10.1016/j.cell.2012.10.009. View

11.

Conde E Silva N, Black B, Sivolob A, Filipski J, Cleveland D, Prunell A . CENP-A-containing nucleosomes: easier disassembly versus exclusive centromeric localization. J Mol Biol. 2007; 370(3):555-73. DOI: 10.1016/j.jmb.2007.04.064. View

12.

Williams S, Tyler J . Transcriptional regulation by chromatin disassembly and reassembly. Curr Opin Genet Dev. 2007; 17(2):88-93. DOI: 10.1016/j.gde.2007.02.001. View

13.

Mack A, Schlingman D, Ilagan R, Regan L, Mochrie S . Kinetics and thermodynamics of phenotype: unwinding and rewinding the nucleosome. J Mol Biol. 2012; 423(5):687-701. PMC: 3902851. DOI: 10.1016/j.jmb.2012.08.021. View

14.

Bohm V, Hieb A, Andrews A, Gansen A, Rocker A, Toth K . Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res. 2010; 39(8):3093-102. PMC: 3082900. DOI: 10.1093/nar/gkq1279. View

15.

Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y . Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 2004; 116(1):51-61. DOI: 10.1016/s0092-8674(03)01064-x. View

16.

Brower-Toland B, Smith C, Yeh R, Lis J, Peterson C, Wang M . Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci U S A. 2002; 99(4):1960-5. PMC: 122302. DOI: 10.1073/pnas.022638399. View

17.

Sheinin M, Li M, Soltani M, Luger K, Wang M . Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun. 2013; 4:2579. PMC: 3848035. DOI: 10.1038/ncomms3579. View

18.

Prior C, Cantor C, Johnson E, Littau V, Allfrey V . Reversible changes in nucleosome structure and histone H3 accessibility in transcriptionally active and inactive states of rDNA chromatin. Cell. 1983; 34(3):1033-42. DOI: 10.1016/0092-8674(83)90561-5. View

19.

Lavelle C, Victor J, Zlatanova J . Chromatin fiber dynamics under tension and torsion. Int J Mol Sci. 2010; 11(4):1557-79. PMC: 2871131. DOI: 10.3390/ijms11041557. View

20.

Yin H, Wang M, Svoboda K, Landick R, Block S, Gelles J . Transcription against an applied force. Science. 1995; 270(5242):1653-7. DOI: 10.1126/science.270.5242.1653. View