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Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260 (1997).
Dorigo, B. et al. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571–1573 (2004).
Chen, P., Li, W. & Li, G. Structures and functions of chromatin fibers. Annu. Rev. Biophys. 50, 95–116 (2021).
Vasudevan, D., Chua, E. Y. D. & Davey, C. A. Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. J. Mol. Biol. 403, 1–10 (2010).
Hood, L. & Galas, D. The digital code of DNA. Nature 421, 444–448 (2003).
Cosgrove, M. S., Boeke, J. D. & Wolberger, C. Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11, 1037–1043 (2004).
Zhang, Y. et al. Overview of histone modification. Adv. Exp. Med. Biol. 1283, 1–16 (2021).
Bannister, A. J. & Kouzarides, T. Regulation of chromatin by histone modifications. Cell Res. 21, 381–395 (2011).
Henikoff, S. & Smith, M. M. Histone variants and epigenetics. Cold Spring Harb. Perspect. Biol. 7, a019364 (2015).
Martire, S. & Banaszynski, L. A. The roles of histone variants in fine-tuning chromatin organization and function. Nat. Rev. Mol. Cell Biol. 21, 522–541 (2020).
Zhang, P. et al. An overview of chromatin-regulating proteins in cells. Curr. Protein Pept. Sci. 17, 401–410 (2016).
Meier, K. & Brehm, A. Chromatin regulation: how complex does it get? Epigenetics 9, 1485–1495 (2014).
Wilson, M. D. & Costa, A. Cryo-electron microscopy of chromatin biology. Acta Crystallogr. D. 73, 541–548 (2017).
Takizawa, Y. & Kurumizaka, H. Chromatin structure meets cryo-EM: dynamic building blocks of the functional architecture. Biochim. Biophys. Acta Gene. Regul. Mech. 1865, 194851 (2022).
Soman, A. et al. Columnar structure of human telomeric chromatin. Nature 609, 1048–1055 (2022).
Soman, A. et al. The human telomeric nucleosome displays distinct structural and dynamic properties. Nucleic Acids Res. 48, 5383–5396 (2020).
Zhou, K., Gaullier, G. & Luger, K. Nucleosome structure and dynamics are coming of age. Nat. Struct. Mol. Biol. 26, 3–13 (2018).
Morrison, E. A., Baweja, L., Poirier, M. G., Wereszczynski, J. & Musselman, C. A. Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility. Nucleic Acids Res. 49, 4750–4767 (2021).
Shi, X., Zhai, Z., Chen, Y., Li, J. & Nordenskiöld, L. Recent advances in investigating functional dynamics of chromatin. Front. Genet. 13, 870640 (2022).
Nozawa, K. et al. Cryo–electron microscopy structure of the H3-H4 octasome: a nucleosome-like particle without histones H2A and H2B. Proc. Natl Acad. Sci. USA 119, e2206542119 (2022).
Kelbauskas, L. et al. Sequence-dependent nucleosome structure and stability variations detected by Forster resonance energy transfer. Biochemistry 46, 2239–2248 (2007).
Shi, X. et al. Structure and dynamics in the nucleosome revealed by solid-state NMR. Angew. Chem. 57, 9734–9738 (2018).
Armeev, G. A., Kniazeva, A. S., Komarova, G. A., Kirpichnikov, M. P. & Shaytan, A. K. Histone dynamics mediate DNA unwrapping and sliding in nucleosomes. Nat. Commun. 12, 2387 (2021).
le Paige, U. B. et al. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magn. Reson. 2, 187–202 (2021).
Kitevski-LeBlanc, J. L. et al. Investigating the dynamics of destabilized nucleosomes using methyl-TROSY NMR. J. Am. Chem. Soc. 140, 4774–4777 (2018).
Langowski, J. et al. Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET. Nucleic Acids Res 48, 1551–1571 (2020).
Gansen, A. et al. High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes. Nat. Commun. 9, 4628 (2018).
Hansen, J. C., Maeshima, K. & Hendzel, M. J. The solid and liquid states of chromatin. Epigenetics Chromatin 14, 50 (2021).
Rippe, K. Liquid–liquid phase separation in chromatin. Cold Spring Harb. Perspect. Biol. 14, a040683 (2022).
Narlikar, G. J. Phase-separation in chromatin organization. J. Biosci. 45, (2020).
Gibson, B. A. et al. Organization of chromatin by intrinsic and regulated phase separation. Cell 179, 470–484.e421 (2019).
Strickfaden, H. et al. Condensed chromatin behaves like a solid on the mesoscale In vitro and in living cells. Cell 183, 1772–1784 (2020).
Chen, Q. et al. Chromatin liquid–liquid phase separation (LLPS) is regulated by ionic conditions and fiber length. Cells 11, 3145 (2022).
Xiang, S. et al. Site-specific studies of nucleosome interactions by solid-state NMR spectroscopy. Angew. Chem. 57, 4571–4575 (2018).
Smrt, S. T. et al. Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy. Front. Mol. Biosci. 9, 1106588 (2023).
Gao, M. et al. Histone H3 and H4 N-terminal tails in nucleosome arrays at cellular concentrations probed by magic angle spinning NMR spectroscopy. J. Am. Chem. Soc. 135, 15278–15281 (2013).
Ackermann, B. E. & Debelouchina, G. T. Emerging contributions of solid-state NMR spectroscopy to chromatin structural biology. Front. Mol. Biosci. 8, 741581 (2021).
Shoaib, M. et al. Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. Nat. Commun. 12, 4800 (2021).
Shi, X., Prasanna, C., Soman, A., Pervushin, K. & Nordenskiöld, L. Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA. Commun. Biol. 3, 639 (2020).
Furukawa, A. et al. Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome. Proc. Natl Acad. Sci. USA 117, 19661–19663 (2020).
Bertin, A., Mangenot, S., Renouard, M., Durand, D. & Livolant, F. Structure and phase diagram of nucleosome core particles aggregated by multivalent cations. Biophys. J. 93, 3652–3663 (2007).
Bohrmann, B., Haider, M. & Kellenberger, E. Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM. Ultramicroscopy 49, 235–251 (1993).
Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998).
Berezhnoy, N. V. et al. The influence of ionic environment and histone tails on columnar order of nucleosome core particles. Biophys. J. 110, 1720–1731 (2016).
Takegoshi, K., Nakamura, S. & Terao, T. 13C–1H dipolar-assisted rotational resonance in magic-angle spinning NMR. Chem. Phys. Lett. 344, 631–637 (2001).
Shi, X., Prasanna, C., Pervushin, K. & Nordenskiöld, L. Solid-state NMR 13C, 15N assignments of human histone H3 in the nucleosome core particle. Biomol. NMR Assign. 14, 99–104 (2020).
Verel, R., Ernst, M. & Meier, B. H. Adiabatic dipolar recoupling in solid-state NMR: the DREAM scheme. J. Mag. Reson. 150, 81–99 (2001).
Shen, Y. & Bax, A. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J. Biomol. NMR 56, 227–241 (2013).
Munowitz, M., Aue, W. P. & Griffin, R. G. Two-dimensional separation of dipolar and scaled isotropic chemical shift interactions in magic angle NMR spectra. J. Chem. Phys. 77, 1686–1689 (1982).
Schanda, P. & Ernst, M. Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: principles and applications to biomolecules. Prog. Nucl. Magn. Reson. Spectrosc. 96, 1–46 (2016).
Shi, X. & Rienstra, C. M. Site-specific internal motions in GB1 protein microcrystals revealed by 3D 2H-13C-13C solid-State NMR spectroscopy. J. Am. Chem. Soc. 138, 4105–4119 (2016).
Luger, K., Rechsteiner, T. J. & Richmond, T. J. Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1–16 (1999).
Vab Geet, A. L. calibration of the methanol and glycol nuclear magnetic resonance thermometers with a static thermistor probe. Anal. Chem. 40, 2227–2229 (1968).
Levitt, M. H. Symmetry-based pulse sequences in magic-anglespinning solid-state NMR. (2007).
Hou, G., Byeon, I. J., Ahn, J., Gronenborn, A. M. & Polenova, T. 1H-13C/1H-15N heteronuclear dipolar recoupling by R-symmetry sequences under fast magic angle spinning for dynamics analysis of biological and organic solids. J. Am. Chem. Soc. 133, 18646–18655 (2011).
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
Morcombe, C. R. & Zilm, K. W. Chemical shift referencing in MAS solid state NMR. J. Magn. Reson. 162, 479–486 (2003).
Bak, M., Rasmussen, J. T. & Nielsen, N. C. SIMPSON: a general simulation program for solid-state NMR spectroscopy. J. Magn. Reson. 147, 296–330 (2000).
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