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• W2899399102 abstract "•Crystal structure of a 6-nucleosome array was determined in complex with histone H1•The array adopts a ladder-like conformation half as compact as a twisted 30-nm fiber•Cryo-EM, biophysical, and biochemical experiments confirm the ladder-like structure•A shift in ionic conditions induces the array to switch to a compact twisted state Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber. Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber. Eukaryotic nuclear DNA is packaged in nucleosomes, which in turn condense into higher-complexity structures. At low ionic strength, purified chromatin forms 11-nm “beads on a string” filaments with an open zigzag conformation (Griffith, 1975Griffith J.D. Chromatin structure: deduced from a minichromosome.Science. 1975; 187: 1202-1203Crossref PubMed Scopus (276) Google Scholar, Ris and Kubai, 1970Ris H. Kubai D.F. Chromosome structure.Annu. Rev. Genet. 1970; 4: 263-294Crossref PubMed Scopus (145) Google Scholar, Thoma et al., 1979Thoma F. Koller T. Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.J. Cell Biol. 1979; 83: 403-427Crossref PubMed Scopus (1179) Google Scholar, Makarov et al., 1983Makarov V.L. Dimitrov S.I. Petrov P.T. Salt-induced conformational transitions in chromatin. A flow linear dichroism study.Eur. J. Biochem. 1983; 133: 491-497Crossref PubMed Scopus (43) Google Scholar). Raising the ionic strength leads progressively to a closed zigzag structure, further compaction, and the formation of 30-nm fibers (Greulich et al., 1987Greulich K.O. Wachtel E. Ausio J. Seger D. Eisenberg H. Transition of chromatin from the “10 nm” lower order structure, to the “30 nm” higher order structure as followed by small angle X-ray scattering.J. Mol. Biol. 1987; 193: 709-721Crossref PubMed Scopus (31) Google Scholar, Thoma et al., 1979Thoma F. Koller T. Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.J. Cell Biol. 1979; 83: 403-427Crossref PubMed Scopus (1179) Google Scholar, Makarov et al., 1983Makarov V.L. Dimitrov S.I. Petrov P.T. Salt-induced conformational transitions in chromatin. A flow linear dichroism study.Eur. J. Biochem. 1983; 133: 491-497Crossref PubMed Scopus (43) Google Scholar). Under physiological conditions, chromatin extracted from diverse cell types adopts a 30-nm fiber configuration (Thoma et al., 1979Thoma F. Koller T. Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.J. Cell Biol. 1979; 83: 403-427Crossref PubMed Scopus (1179) Google Scholar, Belmont and Bruce, 1994Belmont A.S. Bruce K. Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure.J. Cell Biol. 1994; 127: 287-302Crossref PubMed Scopus (277) Google Scholar, Belmont et al., 1987Belmont A.S. Sedat J.W. Agard D.A. A three-dimensional approach to mitotic chromosome structure: evidence for a complex hierarchical organization.J. Cell Biol. 1987; 105: 77-92Crossref PubMed Scopus (149) Google Scholar, Bednar et al., 1998Bednar J. Horowitz R.A. Grigoryev S.A. Carruthers L.M. Hansen J.C. Koster A.J. Woodcock C.L. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin.Proc. Natl. Acad. Sci. USA. 1998; 95: 14173-14178Crossref PubMed Scopus (446) Google Scholar), which consequently has been intensely studied as a paradigm of higher-order chromatin structure. In vivo, 30-nm fibers are notably absent from many eukaryotic nuclei, where chromatin appears to form irregularly folded chains (Eltsov et al., 2008Eltsov M. Maclellan K.M. Maeshima K. Frangakis A.S. Dubochet J. Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ.Proc. Natl. Acad. Sci. USA. 2008; 105: 19732-19737Crossref PubMed Scopus (282) Google Scholar, Fussner et al., 2012Fussner E. Strauss M. Djuric U. Li R. Ahmed K. Hart M. Ellis J. Bazett-Jones D.P. Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres.EMBO Rep. 2012; 13: 992-996Crossref PubMed Scopus (120) Google Scholar, Gan et al., 2013Gan L. Ladinsky M.S. Jensen G.J. Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes.Chromosoma. 2013; 122: 377-386Crossref PubMed Scopus (40) Google Scholar, Nishino et al., 2012Nishino Y. Eltsov M. Joti Y. Ito K. Takata H. Takahashi Y. Hihara S. Frangakis A.S. Imamoto N. Ishikawa T. Maeshima K. Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure.EMBO J. 2012; 31: 1644-1653Crossref PubMed Scopus (223) Google Scholar, Ou et al., 2017Ou H.D. Phan S. Deerinck T.J. Thor A. Ellisman M.H. O’Shea C.C. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.Science. 2017; 357: eaag0025Crossref PubMed Scopus (452) Google Scholar, Cai et al., 2018Cai S. Böck D. Pilhofer M. Gan L. The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin.bioRxiv. 2018; https://doi.org/10.1101/334490Crossref Google Scholar) with zigzag features (Hsieh et al., 2015Hsieh T.H. Weiner A. Lajoie B. Dekker J. Friedman N. Rando O.J. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.Cell. 2015; 162: 108-119Abstract Full Text Full Text PDF PubMed Scopus (348) Google Scholar, Grigoryev et al., 2016Grigoryev S.A. Bascom G. Buckwalter J.M. Schubert M.B. Woodcock C.L. Schlick T. Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes.Proc. Natl. Acad. Sci. USA. 2016; 113: 1238-1243Crossref PubMed Scopus (92) Google Scholar, Cai et al., 2018Cai S. Böck D. Pilhofer M. Gan L. The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin.bioRxiv. 2018; https://doi.org/10.1101/334490Crossref Google Scholar). However, the nuclei of certain terminally differentiated cells contain well-defined 30-nm fibers (Langmore and Schutt, 1980Langmore J.P. Schutt C. The higher order structure of chicken erythrocyte chromosomes in vivo.Nature. 1980; 288: 620-622Crossref PubMed Scopus (62) Google Scholar, Woodcock, 1994Woodcock C.L. Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length.J. Cell Biol. 1994; 125: 11-19Crossref PubMed Scopus (98) Google Scholar, Kizilyaprak et al., 2010Kizilyaprak C. Spehner D. Devys D. Schultz P. In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.PLoS ONE. 2010; 5: e11039Crossref PubMed Scopus (51) Google Scholar, Scheffer et al., 2011Scheffer M.P. Eltsov M. Frangakis A.S. Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei.Proc. Natl. Acad. Sci. USA. 2011; 108: 16992-16997Crossref PubMed Scopus (101) Google Scholar), suggesting a role for such structures in transcriptionally silent chromatin. Indeed, recent data suggest that H3K9me3-marked repressed chromatin regions are associated with compact two-start helical fiber structures (Risca et al., 2017Risca V.I. Denny S.K. Straight A.F. Greenleaf W.J. Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping.Nature. 2017; 541: 237-241Crossref PubMed Scopus (99) Google Scholar). More generally, the wide variety of chromatin configurations observed in vitro and in vivo underscores the great structural plasticity of chromatin, whose molecular basis, however, remains only poorly understood. Whereas atomic details are known for how nucleosomal DNA wraps around the core histone octamer (Luger et al., 1997Luger K. Mäder A.W. Richmond R.K. Sargent D.F. Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution.Nature. 1997; 389: 251-260Crossref PubMed Scopus (6885) Google Scholar) and interacts with linker histones (Zhou et al., 2013Zhou B.R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar, Zhou et al., 2015Zhou B.R. Jiang J. Feng H. Ghirlando R. Xiao T.S. Bai Y. Structural mechanisms of nucleosome recognition by linker histones.Mol. Cell. 2015; 59: 628-638Abstract Full Text Full Text PDF PubMed Scopus (151) Google Scholar, Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar), how a flexible array of nucleosomes condenses into a more compact chromatin fiber remains elusive. In vitro studies have primarily supported one of two configurations for the 30-nm chromatin fiber: a one-start helix with a consecutive arrangement of nucleosomes (Finch and Klug, 1976Finch J.T. Klug A. Solenoidal model for superstructure in chromatin.Proc. Natl. Acad. Sci. USA. 1976; 73: 1897-1901Crossref PubMed Scopus (951) Google Scholar, Robinson et al., 2006Robinson P.J. Fairall L. Huynh V.A. Rhodes D. EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure.Proc. Natl. Acad. Sci. USA. 2006; 103: 6506-6511Crossref PubMed Scopus (368) Google Scholar) and a two-start structure comprising two separate nucleosomal stacks (Worcel et al., 1981Worcel A. Strogatz S. Riley D. Structure of chromatin and the linking number of DNA.Proc. Natl. Acad. Sci. USA. 1981; 78: 1461-1465Crossref PubMed Scopus (163) Google Scholar, Williams et al., 1986Williams S.P. Athey B.D. Muglia L.J. Schappe R.S. Gough A.H. Langmore J.P. Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length.Biophys. J. 1986; 49: 233-248Abstract Full Text PDF PubMed Scopus (169) Google Scholar, Dorigo et al., 2004Dorigo B. Schalch T. Kulangara A. Duda S. Schroeder R.R. Richmond T.J. Nucleosome arrays reveal the two-start organization of the chromatin fiber.Science. 2004; 306: 1571-1573Crossref PubMed Scopus (426) Google Scholar, Schalch et al., 2005Schalch T. Duda S. Sargent D.F. Richmond T.J. X-ray structure of a tetranucleosome and its implications for the chromatin fibre.Nature. 2005; 436: 138-141Crossref PubMed Scopus (594) Google Scholar, Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar, Ekundayo et al., 2017Ekundayo B. Richmond T.J. Schalch T. Capturing Structural Heterogeneity in Chromatin Fibers.J. Mol. Biol. 2017; 429: 3031-3042Crossref PubMed Scopus (40) Google Scholar). Data have also been reported supporting a heteromorphic combination of one- and two-start structures within the same fiber (Grigoryev et al., 2009Grigoryev S.A. Arya G. Correll S. Woodcock C.L. Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.Proc. Natl. Acad. Sci. USA. 2009; 106: 13317-13322Crossref PubMed Scopus (188) Google Scholar) as well as a polymorphic fiber model that incorporates variability in nucleosome repeat length (Collepardo-Guevara and Schlick, 2014Collepardo-Guevara R. Schlick T. Chromatin fiber polymorphism triggered by variations of DNA linker lengths.Proc. Natl. Acad. Sci. USA. 2014; 111: 8061-8066Crossref PubMed Scopus (99) Google Scholar). Taken together, the above studies suggest that nucleosomal arrays adopt a diversity of configurations depending on the precise biochemical context. Studies of H1-bound chromatin extracted from cell nuclei revealed that the salt-dependent compaction and electro-optical properties of nucleosome arrays undergo a sharp transition when the number of nucleosomes increases from 5 to 6 (Marion and Roux, 1978Marion C. Roux B. Nucleosomes arrangement in chromatin.Nucleic Acids Res. 1978; 5: 4431-4449Crossref PubMed Scopus (42) Google Scholar, Butler and Thomas, 1980Butler P.J. Thomas J.O. Changes in chromatin folding in solution.J. Mol. Biol. 1980; 140: 505-529Crossref PubMed Scopus (178) Google Scholar), suggesting that the minimal unit recapitulating key features of an extended chromatin fiber in vitro is a hexanucleosome. In living cells, nucleosomes have been found to cluster in discrete domains, termed “clutches,” along the chromatin fiber, with a mean clutch size ranging from 4 to 8 nucleosomes, depending on the cell type (Ricci et al., 2015Ricci 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. 2015; 160: 1145-1158Abstract Full Text Full Text PDF PubMed Scopus (388) Google Scholar). Thus, the study of short chromatin fragments such as a 6-nucleosome array may provide useful insights into the fundamental properties of chromatin. In this study, we report the crystal structure of a hexanucleosome bound to linker histone H1 together with in vitro studies of H1-bound 6-, 12-, and 24-nucleosome arrays. Our crystal structure reveals a two-start configuration in which nucleosomes stack through uniform interfaces and adopt a flat zigzag organization whose packing density is half of that reported for twisted 30-nm fibers. We confirm the uniform stacking and two-start organization using a procedure that couples disulfide crosslinking with qPCR, and we verify the flat and extended array conformation in biophysical experiments. High-resolution footprinting data indicate that the globular H1 domain localizes to the dyad axes of the 6-nucleosome array, resembling the binding mode observed for H1- and GH5-bound mononucleosomes (GH5 is the globular domain of H5; Zhou et al., 2015Zhou B.R. Jiang J. Feng H. Ghirlando R. Xiao T.S. Bai Y. Structural mechanisms of nucleosome recognition by linker histones.Mol. Cell. 2015; 59: 628-638Abstract Full Text Full Text PDF PubMed Scopus (151) Google Scholar, Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar) but distinct from that observed for a condensed 12-nucleosome array (Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar). Using cryoelectron microscopy (cryo-EM), we identify ionic conditions in which the flat array co-exists with a twisted conformation characteristic of a compact 30-nm fiber and show that a small increase in Mg2+ concentration preferentially stabilizes the twisted state. Taken together, our results confirm a two-start organization for short nucleosome arrays in vitro and suggest a possible pathway by which these condense into a 30-nm fiber. Furthermore, our findings provide insights into how chromatin may switch between different conformations in response to small changes in local environment. We determined the crystal structure of a 6-nucleosome array in stoichiometric complex with full-length H1 (Figure 1A). The array was reconstituted from recombinant human core histones, Xenopus laevis linker histone H1.0b, and six tandem repeats of a 187-bp DNA duplex comprising the 601 positioning sequence (Lowary and Widom, 1998Lowary P.T. Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.J. Mol. Biol. 1998; 276: 19-42Crossref PubMed Scopus (1203) Google Scholar) plus 40 bp of linker DNA. Diffraction data were collected at 9.7 Å resolution (Table 1), and the structure was solved by molecular replacement using the nucleosome core particle (NCP) as a search model. The resulting map revealed strong linker DNA density for the core-proximal DNA helical turn and weaker density for the distal turn, yielding sufficiently clear connectivity between nucleosomes to allow reliable tracing of the DNA path (Figure 1B; Video S1). In contrast, the density for histone H1 was too weak to allow interpretation, presumably reflecting the two-fold disorder that results from the ability of H1 to adopt two dyad-related orientations on each nucleosome (Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar).Table 1Crystallographic StatisticsPDB: 6HKTData CollectionaValues in parentheses are for the highest-resolution shell.Synchrotron beamlineESRF ID23-1Wavelength (Å)0.99187Space groupP22121Unit cell dimensionsa = 111.1 Å, b = 238.8 Å, c = 674.4 ÅResolution range (Å)49.1–9.70(Outer shell)(10.85–9.70)Number of measured reflections72,005 (21,507)Number of unique reflections11,252 (3,152)Multiplicity6.4 (6.8)Completeness (%)99.2 (100)Mean I/sigma(I)7.0 (2.3)Rmerge0.211 (0.881)Rmeas0.230 (0.954)Rpim0.090 (0.362)CC1/20.998 (0.604)RefinementResolution used for refinement49.1–9.7Reflections used (total/Rfree)10,632/572Rwork/Rfree26.18/29.07Number of Atoms/Mean B-FactorAll82,014/540Core histones36,012/451Core DNA35,833/574Linker DNA9676/736RMS deviations0.004Bond distances (Å)Bond angles (o)0.721Ramachandran analysis (%)97.2/0.3Favored/outliersMolprobity analysis12.67/1.77Clash Score/overall scorea Values in parentheses are for the highest-resolution shell. Open table in a new tab eyJraWQiOiI4ZjUxYWNhY2IzYjhiNjNlNzFlYmIzYWFmYTU5NmZmYyIsImFsZyI6IlJTMjU2In0.eyJzdWIiOiIzN2M2MTA3YzJkYWFiMDI4YWI2NmYwY2MwMzAwOGM2ZSIsImtpZCI6IjhmNTFhY2FjYjNiOGI2M2U3MWViYjNhYWZhNTk2ZmZjIiwiZXhwIjoxNjc4MDQ3Nzk5fQ.WGfWQsvhEzw75WuARkr5DYPgqVhru-P7F46E22Yc-CQECKg6ELD8uE5j2QaHI-WGqDokzFVivb4fJXGYBg3Pp4WDDb9TBilgy36DLPCMJLWanuEelnYJv-hciRRXffRYGbeqofWv95d5S_hTHz_I1DFjNJyeGJS-oT0YuGGkP86ogdOoY5GSVJ3Z6hL2CqMdFC93WTcisH1yw27XVZaFgVnWmXXdiK36Hb6NHTI0xj8SFO7gHrbtkqVC0eyY9q2zkRJQqdGbEVAEY9ZWujpRmwoBY9x6J_44H6QTNy27m5VVetA8kLkphEOV_FP9o7GQ_PhksiZfn1o_fS-4nsKeig Download .mp4 (27.36 MB) Help with .mp4 files Video S1. Electron Density of the 6-Nucleosome Array, Related to Figure 1Composite 2Fo-Fc omit map calculated in Phenix (Adams et al., 2010) by iteratively omitting regions accounting for 5% of the entire structure. The omitted regions were then assembled to generate a map unbiased by the atomic model (Terwilliger et al., 2008). The map is shown contoured at 1.0, 0.8 and 0.6 sigma. The hexanucleosome forms a two-start helix in which consecutive nucleosomes are related by pseudo-2-fold screw symmetry about the fiber axis (Figures 1C, 1D, and S1), giving rise to a remarkably flat structure whose depth is roughly the diameter of a single nucleosome. The structure deviates from perfect helical symmetry in that the dyad axes of the central nucleosomes (N3 and N4) are orthogonal to the fiber axis, whereas those of the peripheral nucleosomes are tilted by 20°–30° (Figure S1; angle α). These tilted nucleosome orientations yield favorable stacking interactions between neighboring arrays in the crystal and are presumably induced or stabilized by crystallization (Figure S2). The DNA linkers exhibit a pronounced bend midway along their length, comprising two angles: a uniform (∼45°) bend in the plane perpendicular to the fiber axis (Figures S3A and S3B, angle φ) and a variable (−35° to +28°) bend in the orthogonal plane (Figure S3C, angle ψ) that compensates for the tilted orientations of the peripheral nucleosomes (Figure S3D) and is absent from the central N3-N4 linker (ψ = 0°). The above deviations from ideal helical geometry suggest a dynamic conformational landscape in solution in which the peripheral nucleosome orientations fluctuate significantly compared with the more highly constrained central nucleosomes. Nevertheless, the fact that the hexanucleosome crystallized indicates that it forms a relatively stable structure, consistent with its ability to recapitulate biophysical properties of longer nucleosome arrays (Marion and Roux, 1978Marion C. Roux B. Nucleosomes arrangement in chromatin.Nucleic Acids Res. 1978; 5: 4431-4449Crossref PubMed Scopus (42) Google Scholar, Butler and Thomas, 1980Butler P.J. Thomas J.O. Changes in chromatin folding in solution.J. Mol. Biol. 1980; 140: 505-529Crossref PubMed Scopus (178) Google Scholar). The degree of nucleosome array condensation strongly depends on the ionic environment (Butler and Thomas, 1980Butler P.J. Thomas J.O. Changes in chromatin folding in solution.J. Mol. Biol. 1980; 140: 505-529Crossref PubMed Scopus (178) Google Scholar, Korolev et al., 2010Korolev N. Allahverdi A. Yang Y. Fan Y. Lyubartsev A.P. Nordenskiöld L. Electrostatic origin of salt-induced nucleosome array compaction.Biophys. J. 2010; 99: 1896-1905Abstract Full Text Full Text PDF PubMed Scopus (49) Google Scholar, Allahverdi et al., 2015Allahverdi A. Chen Q. Korolev N. Nordenskiöld L. Chromatin compaction under mixed salt conditions: opposite effects of sodium and potassium ions on nucleosome array folding.Sci. Rep. 2015; 5: 8512Crossref PubMed Scopus (52) Google Scholar). Our crystals were obtained by hanging drop vapor diffusion in the absence of divalent cations under conditions in which the NaCl concentration gradually increased from 50 to 100 mM during vapor equilibration. In this concentration range and up to 125 mM NaCl, H1-bound hexanucleosomes have been reported to become increasingly compact with increasing ionic strength (Butler and Thomas, 1980Butler P.J. Thomas J.O. Changes in chromatin folding in solution.J. Mol. Biol. 1980; 140: 505-529Crossref PubMed Scopus (178) Google Scholar), suggesting that the crystal conformation may represent that of an incompletely condensed array. Indeed, consecutive nucleosomes in the crystal structure are separated by a mean helical rise of 28 Å (Figure S1B, distance h), corresponding to a packing density of 3.9 nucleosomes per 11 nm. This is markedly lower than previous estimates for condensed chromatin fibers (6.5–12.7 nucleosomes/11 nm) (Gerchman and Ramakrishnan, 1987Gerchman S.E. Ramakrishnan V. Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy.Proc. Natl. Acad. Sci. USA. 1987; 84: 7802-7806Crossref PubMed Scopus (112) Google Scholar, Grigoryev et al., 2009Grigoryev S.A. Arya G. Correll S. Woodcock C.L. Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.Proc. Natl. Acad. Sci. USA. 2009; 106: 13317-13322Crossref PubMed Scopus (188) Google Scholar, Robinson et al., 2006Robinson P.J. Fairall L. Huynh V.A. Rhodes D. EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure.Proc. Natl. Acad. Sci. USA. 2006; 103: 6506-6511Crossref PubMed Scopus (368) Google Scholar, Scheffer et al., 2011Scheffer M.P. Eltsov M. Frangakis A.S. Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei.Proc. Natl. Acad. Sci. USA. 2011; 108: 16992-16997Crossref PubMed Scopus (101) Google Scholar, Woodcock et al., 1984Woodcock C.L. Frado L.L. Rattner J.B. The higher-order structure of chromatin: evidence for a helical ribbon arrangement.J. Cell Biol. 1984; 99: 42-52Crossref PubMed Scopus (263) Google Scholar) and only approximately half that observed in the cryo-EM structure of a condensed 12 × 187 bp nucleosome array (7 nucleosomes/11 nm; Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar). Although the structure by Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar and our hexanucleosome structure (for convenience referred to below as “condensed 12-mer” and “6-mer,” respectively) share the same left-handed topology, they exhibit striking conformational differences. These include an ∼30° difference in nucleosome orientation relative to the fiber axis and a 12° difference in azimuthal rotation angle relating consecutive nucleosomes (Figure S1B, angles β and θ, respectively). The latter difference equates to a dramatic change in helical periodicity (2 nucleosomes per helical turn for the 6-mer versus ∼13 for the condensed 12-mer). This is most easily visualized by extrapolating the helical geometry of the 6-mer to generate a hypothetical extended array: whereas the two nucleosomal stacks twist around each other in the condensed 12-mer, they adopt a parallel, zigzag configuration in the 6-mer-derived model (Figures 2A and 2B). This lack of twist rationalizes the lower nucleosome packing density of the 6-mer. Notably, the ladder-like appearance of the 6-mer-derived model is highly reminiscent of the “double track” structures observed for chromatin fibers isolated from chicken erythrocytes in 40 mM NaCl (Scheffer et al., 2012Scheffer M.P. Eltsov M. Bednar J. Frangakis A.S. Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitro.J. Struct. Biol. 2012; 178: 207-214Crossref PubMed Scopus (34) Google Scholar) and of a hypothetical fiber model based on the crystal packing of a GH5-bound mononucleosome (Zhou et al., 2018Zhou B.R. Jiang J. Ghirlando R. Norouzi D. Sathish Yadav K.N. Feng H. Wang R. Zhang P. Zhurkin V. Bai Y. Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.J. Mol. Biol. 2018; 430: 3093-3110Crossref PubMed Scopus (25) Google Scholar), both characterized by nucleosomes that stack in parallel columns. The nucleosome stacking arrangement is a distinguishing feature of our 6-mer structure. In the condensed 12-mer, nucleosomes stack through two types of interface: a tight interface within each tetranucleosome unit and a looser interface between such units, hereafter designated “type I” and “type II,” respectively (Figure 2C; Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar). Both are included in a recent survey of NCP-NCP interactions (Korolev et al., 2018Korolev N. Lyubartsev A.P. Nordenskiöld L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure.Sci. Rep. 2018; 8: 1543Crossref PubMed Scopus (29) Google Scholar). By contrast, the stacking interfaces in our 6-mer are highly uniform and of the type II class (Figure 2D). This agrees with the finding that isolated NCPs in 150 mM NaCl preferentially associate through a type II-like interface, whereas few or no type I associations were observed (Bilokapic et al., 2018Bilokapic S. Strauss M. Halic M. Cryo-EM of nucleosome core particle interactions in trans.Sci. Rep. 2018; 8: 7046Crossref PubMed Scopus (37) Google Scholar). In the condensed 12-mer, the type II interface is stabilized by interactions between basic H4 tail residues and the H2A-H2B acidic patch on the adjacent nucleosome (Song et al., 2014Song F. Chen P. S" @default.
• W2899399102 created "2018-11-09" @default.
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• W2899399102 date "2018-12-01" @default.
• W2899399102 modified "2023-10-18" @default.
• W2899399102 title "Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation" @default.
• W2899399102 cites W1660678623 @default.
• W2899399102 cites W1773400868 @default.
• W2899399102 cites W1824325020 @default.
• W2899399102 cites W1965555526 @default.
• W2899399102 cites W1971651847 @default.
• W2899399102 cites W1975767286 @default.
• W2899399102 cites W1977038370 @default.
• W2899399102 cites W1981037598 @default.
• W2899399102 cites W1982126789 @default.
• W2899399102 cites W1988997227 @default.
• W2899399102 cites W1990107720 @default.
• W2899399102 cites W1993646828 @default.
• W2899399102 cites W1993822465 @default.
• W2899399102 cites W2003569868 @default.
• W2899399102 cites W2012525958 @default.
• W2899399102 cites W2016329387 @default.
• W2899399102 cites W2017314177 @default.
• W2899399102 cites W2017991357 @default.
• W2899399102 cites W2018626566 @default.
• W2899399102 cites W2018816634 @default.
• W2899399102 cites W2024224240 @default.
• W2899399102 cites W2030023744 @default.
• W2899399102 cites W2031237705 @default.
• W2899399102 cites W2037573299 @default.
• W2899399102 cites W2038132544 @default.
• W2899399102 cites W2043264912 @default.
• W2899399102 cites W2050091361 @default.
• W2899399102 cites W2052842503 @default.
• W2899399102 cites W2056216005 @default.
• W2899399102 cites W2066088601 @default.
• W2899399102 cites W2067301744 @default.
• W2899399102 cites W2072674961 @default.
• W2899399102 cites W2080479776 @default.
• W2899399102 cites W2084392610 @default.
• W2899399102 cites W2093158813 @default.
• W2899399102 cites W2093351957 @default.
• W2899399102 cites W2094950254 @default.
• W2899399102 cites W2097041586 @default.
• W2899399102 cites W2099114692 @default.
• W2899399102 cites W2106751755 @default.
• W2899399102 cites W2117554090 @default.
• W2899399102 cites W2121003260 @default.
• W2899399102 cites W2124026197 @default.
• W2899399102 cites W2124618141 @default.
• W2899399102 cites W2125372868 @default.
• W2899399102 cites W2129098490 @default.
• W2899399102 cites W2135453959 @default.
• W2899399102 cites W2136567909 @default.
• W2899399102 cites W2139542530 @default.
• W2899399102 cites W2144792857 @default.
• W2899399102 cites W2147403429 @default.
• W2899399102 cites W2152814571 @default.
• W2899399102 cites W2154062872 @default.
• W2899399102 cites W2157089275 @default.
• W2899399102 cites W2159425665 @default.
• W2899399102 cites W2163341755 @default.
• W2899399102 cites W2165451373 @default.
• W2899399102 cites W2180229411 @default.
• W2899399102 cites W2233692211 @default.
• W2899399102 cites W2265882490 @default.
• W2899399102 cites W2305834606 @default.
• W2899399102 cites W2411795946 @default.
• W2899399102 cites W2480057469 @default.
• W2899399102 cites W2515958533 @default.
• W2899399102 cites W2564237126 @default.
• W2899399102 cites W2595894340 @default.
• W2899399102 cites W2610586915 @default.
• W2899399102 cites W2738317363 @default.
• W2899399102 cites W2739969873 @default.
• W2899399102 cites W2751246228 @default.
• W2899399102 cites W2774050918 @default.
• W2899399102 cites W2800190619 @default.
• W2899399102 cites W2801304553 @default.
• W2899399102 cites W2802136660 @default.
• W2899399102 cites W2810220176 @default.
• W2899399102 cites W2810921664 @default.
• W2899399102 cites W4210675630 @default.
• W2899399102 cites W4235591502 @default.
• W2899399102 cites W4248872320 @default.
• W2899399102 doi "https://doi.org/10.1016/j.molcel.2018.09.027" @default.

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