Palm, W. & de Lange, T. How shelterin protects mammalian telomeres. Annu. Rev. Genet. 42, 301–334 (2008).
Google Scholar
Pisano, S., Galati, A. & Cacchione, S. Telomeric nucleosomes: forgotten players at chromosome ends. Cell. Mol. Life Sci. 65, 3553–3563 (2008).
Google Scholar
Hewitt, G. et al. Telomeres are favoured targets of a persistent DNA damage response in ageing and stress-induced senescence. Nat. Commun. 3, 708 (2012).
Google Scholar
Takai, H., Smogorzewska, A. & de Lange, T. DNA damage foci at dysfunctional telomeres. Curr. Biol. 13, 1549–1556 (2003).
Google Scholar
Longhese, M. P. DNA damage response at functional and dysfunctional telomeres. Genes Dev. 22, 125–140 (2008).
Google Scholar
Samassekou, O., Gadji, M., Drouin, R. & Yan, J. Sizing the ends: normal length of human telomeres. Ann. Anat. 192, 284–291 (2010).
Google Scholar
Blasco, M. A. The epigenetic regulation of mammalian telomeres. Nat. Rev. Genet. 8, 299–309 (2007).
Google Scholar
d’Adda di Fagagna, F. et al. A DNA damage checkpoint response in telomere-initiated senescence. Nature 426, 194–198 (2003).
Google Scholar
Widom, J. A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc. Natl Acad. Sci. USA 89, 1095–1099 (1992).
Google Scholar
Valouev, A. et al. Determinants of nucleosome organization in primary human cells. Nature 474, 516–520 (2011).
Google Scholar
Robinson, P. J. J. & Rhodes, D. Structure of the ‘30 nm’ chromatin fibre: a key role for the linker histone. Curr. Opin. Struct. Biol. 16, 346–343 (2006).
Google Scholar
Garcia-Saez, I. et al. Structure of an H1-bound 6-nucleosome array reveals an untwisted two-start chromatin fiber conformation. Mol. Cell 72, 902–915 (2018).
Google Scholar
Song, F. et al. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science 344, 376–380 (2014).
Google Scholar
Ekundayo, B., Richmond, T. J. & Schalch, T. Capturing structural heterogeneity in chromatin fibers. J. Mol. Biol. 429, 3031–3042 (2017).
Google Scholar
Robinson, P. J. J., Fairall, L., Huynh, V. A. T. & Rhodes, D. EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure. Proc. Natl Acad. Sci. USA 103, 6506–6511 (2006).
Google Scholar
Kruithof, M. et al. Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nat. Struct. Mol. Biol. 16, 534–540 (2009).
Google Scholar
Konrad, S. F., Vanderlinden, W. & Lipfert, J. Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging. Biophys. J. 121, 841–851 (2022).
Google Scholar
Bedoyan, J. K., Lejnine, S., Makarov, V. L. & Langmore, J. P. Condensation of rat telomere-specific nucleosomal arrays containing unusually short DNA repeats and histone H1. J. Biol. Chem. 271, 18485–18493 (1996).
Google Scholar
Makarov, V. L., Lejnine, S., Bedoyan, J. & Langmore, J. P. Nucleosomal organization of telomere-specific chromatin in rat. Cell 73, 775–787 (1993).
Google Scholar
Soman, A. et al. The human telomeric nucleosome displays distinct structural and dynamic properties. Nucleic Acids Res. 48, 5383–5396 (2020).
Google Scholar
Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).
Google Scholar
Vasudevan, D., Chua, E. Y. & Davey, C. A. Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. J. Mol. Biol. 403, 1–10 (2010).
Google Scholar
Pisano, S. et al. Telomeric nucleosomes are intrinsically mobile. J. Mol. Biol. 369, 1153–1162 (2007).
Google Scholar
Huynh, V. A. T., Robinson, P. J. J. & Rhodes, D. A method for the in vitro reconstitution of a defined “30 nm” chromatin fibre containing stoichiometric amounts of the linker histone. J. Mol. Biol. 345, 957–968 (2005).
Google Scholar
Brouwer, T. et al. A critical role for linker DNA in higher-order folding of chromatin fibers. Nucleic Acids Res. 49, 2537–2551 (2021).
Google Scholar
Pope, L. H. et al. Single chromatin fiber stretching reveals physically distinct populations of disassembly events. Biophys. J. 88, 3572–3583 (2005).
Google Scholar
Korolev, N., Lyubartsev, A. P. & Nordenskiöld, L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep. 8, 1543 (2018).
Google Scholar
Dorigo, B. et al. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571–1573 (2004).
Google Scholar
Koopmans, W. J. A., Buning, R., Schmidt, T. & van Noort, J. spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes. Biophys. J. 97, 195–204 (2009).
Google Scholar
Huang, Y.-C. et al. The effect of linker DNA on the structure and interaction of nucleosome core particles. Soft Matter 14, 9096–9106 (2018).
Google Scholar
Tatchell, K. & Van Holde, K. E. Compact oligomers and nucleosome phasing. Proc. Natl Acad. Sci. USA 75, 3583–3587 (1978).
Google Scholar
Bowerman, S., Wereszczynski, J. & Luger, K. Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways. eLife 10, e65587 (2021).
Google Scholar
Mattiroli, F. et al. Structure of histone-based chromatin in Archaea. Science 357, 609–612 (2017).
Google Scholar
Edayathumangalam, R. S., Weyermann, P., Gottesfeld, J. M., Dervan, P. B. & Luger, K. Molecular recognition of the nucleosomal “supergroove”. Proc. Natl Acad. Sci. USA 101, 6864–6869 (2004).
Google Scholar
Vancevska, A., Douglass, K. M., Pfeiffer, V., Manley, S. & Lingner, J. The telomeric DNA damage response occurs in the absence of chromatin decompaction. Genes Dev. 31, 567–577 (2017).
Google Scholar
Cacchione, S., Biroccio, A. & Rizzo, A. Emerging roles of telomeric chromatin alterations in cancer. J. Exp. Clin. Cancer Res. 38, 21 (2019).
Google Scholar
Skrajna, A. et al. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res. 48, 9415–9432 (2020).
Google Scholar
Liu, W. H. et al. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Nat. Commun. 11, 5244 (2020).
Google Scholar
Court, R., Chapman, L., Fairall, L. & Rhodes, D. How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high-resolution crystal structures. EMBO Rep. 6, 39–45 (2005).
Google Scholar
Willhoft, O. et al. Structure and dynamics of the yeast SWR1–nucleosome complex. Science 362, eaat7716 (2018).
Google Scholar
Hübner, B. et al. Ultrastructure and nuclear architecture of telomeric chromatin revealed by correlative light and electron microscopy. Nucleic Acids Res. 50, 5047–5063 (2022).
Google Scholar
Fajkus, J. & Trifonov, E. N. Columnar packing of telomeric nucleosomes. Biochem. Biophys. Res. Comm. 280, 961–963 (2001).
Google Scholar
Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3–19 (1999).
Google Scholar
Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2004).
Google Scholar
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Google Scholar
OriginPro v.2019 (OriginLab Corp., 2019).
Ou, H. D. et al. ChromEMT: visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357, eaag0025 (2017).
Google Scholar
Zhou, B. R. et al. Revisit of reconstituted 30-nm nucleosome arrays reveals an ensemble of dynamic structures. J. Mol. Biol. 430, 3093–3110 (2018).
Google Scholar
de la Rosa-Trevín, J. M. et al. Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 195, 93–99 (2016).
Google Scholar
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Google Scholar
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Google Scholar
de la Rosa-Trevín, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013).
Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comp. Chem. 25, 1605–1612 (2004).
Google Scholar
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Google Scholar
Casañal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1069–1078 (2020).
Google Scholar
Burnley, T., Palmer, C. M. & Winn, M. Recent developments in the CCP-EM software suite. Acta Crystallogr. D Struct. Biol. 73, 469–477 (2017).
Google Scholar
Vagin, A. A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D Biol. Crystallogr. 60, 2184–2195 (2004).
Google Scholar
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Google Scholar
Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78, 1606–1619 (2000).
Google Scholar
Brautigam, C. A. Calculations and publication-quality illustrations for analytical ultracentrifugation data. Methods Enzymol. 562, 109–133 (2015).
Google Scholar
Laue, T. M., Shah, B., Ridgeway, T. M. & Pelletier, S. L. in Analytical Ultracentrifugation in Biochemistry and Polymer Science (eds S. E. Harding, S.E. et al.) 90–125 (Royal Society of Chemistry, 1992).
Kaczmarczyk, A., Brouwer, T. B., Pham, C., Dekker, N. H. & van Noort, J. Probing chromatin structure with magnetic tweezers. Methods Mol. Biol. 1814, 297–323 (2018).
Google Scholar
Brouwer, T. B., Kaczmarczyk, A., Pham, C. & van Noort, J. Unraveling DNA organization with single-molecule force spectroscopy using magnetic tweezers. Methods Mol. Biol. 1837, 317–349 (2018).
Google Scholar
Meng, H., Andresen, K. & van Noort, J. Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers. Nucleic Acids Res. 43, 3578–3590 (2015).
Google Scholar
Brouwer, T. B., Hermans, N. & van Noort, J. Multiplexed nanometric 3D tracking of microbeads using an FFT-phasor algorithm. Biophys. J. 118, 2245–2257 (2020).
Google Scholar
Kaczmarczyk, A. et al. Single-molecule force spectroscopy on histone H4 tail cross-linked chromatin reveals fiber folding. J. Biol. Chem. 292, 17506–17513 (2017).
Google Scholar
Evans, E. Probing the relation between force—lifetime—and chemistry in single molecular bonds. Annu. Rev. Biophys. Biomol. Struct. 30, 105–128 (2001).
Google Scholar
Brower-Toland, B. D. et al. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl Acad. Sci. USA 99, 1960–1965 (2002).
Google Scholar