ISWI catalyzes nucleosome sliding in condensed nucleosome arrays

Burak, Y., Ariel, G. & Andelman, D. Onset of DNA aggregation in presence of monovalent and multivalent counterions. Biophys. J. 85, 2100–2110 (2003).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Post, C. B. & Zimm, B. H. Theory of DNA condensation: collapse versus aggregation. Biopolymers 21, 2123–2137 (1982).

Article  CAS  PubMed  Google Scholar 

Woodcock, C. L. F. Ultrastructure of inactive chromatin. J. Cell Biol. 59, A368 (1973).

Google Scholar 

Olins, A. L. & Olins, D. E. Spheroid chromatin units (v bodies). Science 183, 330–332 (1974).

Article  CAS  PubMed  Google Scholar 

Finch, J. T. & Klug, A. Solenoidal model for superstructure in chromatin. Proc. Natl Acad. Sci. USA 73, 1897 (1976).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ou, H. D. et al. ChromEMT: visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357, eaag0025 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Maeshima, K. et al. Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J. 35, 1115–1132 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Adhireksan, Z., Sharma, D., Lee, P. L. & Davey, C. A. Near-atomic resolution structures of interdigitated nucleosome fibres. Nat. Commun. 11, 4747 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hsieh, T. H. S. et al. Mapping nucleosome resolution chromosome folding in yeast by Micro-C. Cell 162, 108 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ricci, M. A., Manzo, C., García-Parajo, M. F., Lakadamyali, M. & Cosma, M. P. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160, 1145–1158 (2015).

Article  CAS  PubMed  Google Scholar 

Gibson, B. A. et al. Organization of chromatin by intrinsic and regulated phase separation. Cell 179, 470–484.e21 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Strickfaden, H. et al. Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells. Cell 183, 1772–1784.e13 (2020).

Article  CAS  PubMed  Google Scholar 

Zhang, Y., Narlikar, G. J. & Kutateladze, T. G. Enzymatic reactions inside biological condensates. J. Mol. Biol. 433, 166624 (2021).

Article  CAS  PubMed  Google Scholar 

Hihara, S. et al. Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell Rep. 2, 1645–1656 (2012).

Article  CAS  PubMed  Google Scholar 

Kornberg, R. D. & Lorch, Y. Primary role of the nucleosome. Mol. Cell 79, 371–375 (2020).

Article  CAS  PubMed  Google Scholar 

Kim, J. M. et al. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 10, e69387 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Corona, D. F. V. et al. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3, 239–245 (1999).

Article  CAS  PubMed  Google Scholar 

Hamiche, A., Sandaltzopoulos, R., Gdula, D. A. & Wu, C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97, 833–842 (1999).

Article  CAS  PubMed  Google Scholar 

Ludwigsen, J., Hepp, N., Klinker, H., Pfennig, S. & Mueller-Planitz, F. Remodeling and repositioning of nucleosomes in nucleosomal arrays. Methods Mol. Biol. 1805, 349–370 (2018).

Article  CAS  PubMed  Google Scholar 

Mueller-Planitz, F., Klinker, H., Ludwigsen, J. & Becker, P. B. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat. Struct. Mol. Biol. 20, 82–89 (2013).

Article  CAS  PubMed  Google Scholar 

Schram, R. D., Klinker, H., Becker, P. B. & Schiessel, H. Computational study of remodeling in a nucleosomal array. Eur. Phys. J. E 38, 85 (2015).

Article  PubMed  Google Scholar 

Klinker, H. et al. ISWI remodelling of physiological chromatin fibres acetylated at lysine 16 of histone H4. PLoS ONE 9, e88411 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Boyer, L. A. et al. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes. J. Biol. Chem. 275, 18864–18870 (2000).

Article  CAS  PubMed  Google Scholar 

Logie, C., Tse, C., Hansen, J. C. & Peterson, C. L. The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes. Biochemistry 38, 2514–2522 (1999).

Article  CAS  PubMed  Google Scholar 

Peeples, W. & Rosen, M. K. Mechanistic dissection of increased enzymatic rate in a phase-separated compartment. Nat. Chem. Biol. 17, 693–702 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Poirier, M. G., Bussiek, M., Langowski, J. & Widom, J. Spontaneous access to DNA target sites in folded chromatin fibers. J. Mol. Biol. 379, 772–786 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Poirier, M. G., Oh, E., Tims, H. S. & Widom, J. Dynamics and function of compact nucleosome arrays. Nat. Struct. Mol. Biol. 16, 938–944 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hagerman, T. A. et al. Chromatin stability at low concentration depends on histone octamer saturation levels. Biophys. J. 96, 1944–1951 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gibson, B. A. et al. In diverse conditions, intrinsic chromatin condensates have liquid-like material properties. Proc. Natl Acad. Sci. USA 120, e2218085120 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Goins, A. B., Sanabria, H. & Waxham, M. N. Macromolecular crowding and size effects on probe microviscosity. Biophys. J. 95, 5362–5373 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, J. G. & Narlikar, G. J. FRET-based methods to study ATP-dependent changes in chromatin structure. Methods 41, 291–295 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, M. et al. Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography. Mol. Cell 82, 3000 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Weidemann, T. et al. Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging. J. Mol. Biol. 334, 229–240 (2003).

Article  CAS  PubMed  Google Scholar 

Leonard, J. D. & Narlikar, G. J. A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler. Mol. Cell 57, 850–859 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Larson, A. G. & Narlikar, G. J. The role of phase separation in heterochromatin formation, function, and regulation. Biochemistry 57, 2540–2548 (2018).

Article  CAS  PubMed  Google Scholar 

Grüne, T. et al. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12, 449–460 (2003).

Article  PubMed  Google Scholar 

Bhardwaj, S. K. et al. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat. Commun. 11, 5913 (2020).

Article  CAS  PubMed 

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