XB-ART-58422
Mol Cell
2021 Nov 04;8121:4377-4397.e12. doi: 10.1016/j.molcel.2021.08.010.
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Structural features of nucleosomes in interphase and metaphase chromosomes.
Arimura Y
,
Shih RM
,
Froom R
,
Funabiki H
.
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Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
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R35 GM132111 NIGMS NIH HHS
Species referenced: Xenopus laevis
Genes referenced: h2ac21
GO keywords: nucleosome [+]
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References [+] :
Adams,
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative.
1995, Pubmed
Adams, Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. 1995, Pubmed
Adhireksan, Near-atomic resolution structures of interdigitated nucleosome fibres. 2020, Pubmed
Ali-Ahmad, CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail. 2019, Pubmed
An, Linker histone protects linker DNA on only one side of the core particle and in a sequence-dependent manner. 1998, Pubmed
Arimura, The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism. 2019, Pubmed
Arimura, Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome. 2012, Pubmed
Arimura, Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. 2018, Pubmed
Armache, Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. 2019, Pubmed
Ayala, Structure and regulation of the human INO80-nucleosome complex. 2018, Pubmed
Baker, Electrostatics of nanosystems: application to microtubules and the ribosome. 2001, Pubmed
Bancaud, Nucleosome chiral transition under positive torsional stress in single chromatin fibers. 2007, Pubmed
Basu, Measuring DNA mechanics on the genome scale. 2021, Pubmed
Bednar, Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. 2017, Pubmed , Xenbase
Bell, High resolution single particle refinement in EMAN2.1. 2016, Pubmed
Bepler, Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. 2019, Pubmed
Buckwalter, Regulation of chromatin folding by conformational variations of nucleosome linker DNA. 2017, Pubmed
Cai, Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo. 2018, Pubmed
Cai, The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. 2018, Pubmed
Cardone, One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. 2013, Pubmed
Chen, Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail-H2A Acidic Patch Interaction. 2017, Pubmed , Xenbase
Chicano, Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure. 2019, Pubmed
Choppakatla, Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. 2021, Pubmed , Xenbase
Chua, 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM. 2016, Pubmed , Xenbase
Chua, The mechanics behind DNA sequence-dependent properties of the nucleosome. 2012, Pubmed , Xenbase
Corujo, Post-Translational Modifications of H2A Histone Variants and Their Role in Cancer. 2018, Pubmed
de la Rosa-Trevín, Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. 2016, Pubmed
D'Imprima, Protein denaturation at the air-water interface and how to prevent it. 2019, Pubmed
Dodonova, Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. 2020, Pubmed
Dolinsky, PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. 2004, Pubmed
Dorigo, Nucleosome arrays reveal the two-start organization of the chromatin fiber. 2004, Pubmed , Xenbase
Dworkin-Rastl, The maternal histone H1 variant, H1M (B4 protein), is the predominant H1 histone in Xenopus pregastrula embryos. 1994, Pubmed , Xenbase
Ekundayo, Capturing Structural Heterogeneity in Chromatin Fibers. 2017, Pubmed
Eltsov, Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ. 2008, Pubmed
Eltsov, Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections. 2018, Pubmed
Emsley, Coot: model-building tools for molecular graphics. 2004, Pubmed
Eustermann, Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. 2018, Pubmed
Falk, Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. 2015, Pubmed
Farnung, Nucleosome-Chd1 structure and implications for chromatin remodelling. 2017, Pubmed
Fujii, Direct visualization of secondary structures of F-actin by electron cryomicroscopy. 2010, Pubmed
Funabiki, Nucleosome-Dependent Pathways That Control Mitotic Progression. 2017, Pubmed
Furuyama, Reconstitution of hemisomes on budding yeast centromeric DNA. 2013, Pubmed
Gagnon, Undetectable histone O-GlcNAcylation in mammalian cells. 2015, Pubmed
Gibbs, Linker histones as liquid-like glue for chromatin. 2018, Pubmed
Gibcus, A pathway for mitotic chromosome formation. 2018, Pubmed , Xenbase
Gibson, Organization of Chromatin by Intrinsic and Regulated Phase Separation. 2019, Pubmed
Glotzer, Cyclin is degraded by the ubiquitin pathway. 1991, Pubmed , Xenbase
Goloborodko, Compaction and segregation of sister chromatids via active loop extrusion. 2016, Pubmed
Gong, Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection. 2016, Pubmed
Grigorieff, Frealign: An Exploratory Tool for Single-Particle Cryo-EM. 2016, Pubmed
Grigoryev, Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles. 2018, Pubmed
Grigoryev, Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. 2009, Pubmed
Hall, High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. 2009, Pubmed
Han, Cryo-EM structure of SWI/SNF complex bound to a nucleosome. 2020, Pubmed , Xenbase
Hayashi-Takanaka, Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies. 2015, Pubmed
He, Structure of nucleosome-bound human BAF complex. 2020, Pubmed
Herrero Del Valle, Prospects for antimicrobial development in the cryo-EM era - a focus on the ribosome. 2020, Pubmed
Hirano, A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro. 1994, Pubmed , Xenbase
Hirano, Condensins and the evolution of torsion-mediated genome organization. 2014, Pubmed
Hite, Structural Titration of Slo2.2, a Na+-Dependent K+ Channel. 2017, Pubmed
Ho, Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. 2021, Pubmed
Hyman, Preparation of modified tubulins. 1991, Pubmed
Jenness, HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. 2018, Pubmed , Xenbase
Kastritis, Capturing protein communities by structural proteomics in a thermophilic eukaryote. 2017, Pubmed
Kato, Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. 2017, Pubmed
Kelly, Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. 2010, Pubmed , Xenbase
Kelly, Glycosylation of chromosomal proteins: localization of O-linked N-acetylglucosamine in Drosophila chromatin. 1989, Pubmed
Klug, A low resolution structure for the histone core of the nucleosome. 1980, Pubmed
Koslover, Local geometry and elasticity in compact chromatin structure. 2010, Pubmed
Krietenstein, Mesoscale organization of the chromatin fiber. 2020, Pubmed
Kujirai, Structural basis of the nucleosome transition during RNA polymerase II passage. 2018, Pubmed
Kyrilis, Integrative biology of native cell extracts: a new era for structural characterization of life processes. 2019, Pubmed
Kyte, A simple method for displaying the hydropathic character of a protein. 1982, Pubmed
Lavelle, Chromatin polymorphism and the nucleosome superfamily: a genealogy. 2007, Pubmed
Liebschner, Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. 2019, Pubmed
Lilic, The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. 2020, Pubmed
Liu, Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. 2017, Pubmed
Luger, Crystal structure of the nucleosome core particle at 2.8 A resolution. 1997, Pubmed
Lyumkis, Likelihood-based classification of cryo-EM images using FREALIGN. 2013, Pubmed
Maeshima, Packaging the genome: the structure of mitotic chromosomes. 2008, Pubmed
Maresca, Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts. 2005, Pubmed , Xenbase
Marrero, The crystal structure of human α2-macroglobulin reveals a unique molecular cage. 2012, Pubmed
McGinty, Nucleosome structure and function. 2015, Pubmed
Murray, Cell cycle extracts. 1991, Pubmed
Nakane, Single-particle cryo-EM at atomic resolution. 2020, Pubmed
Nguyen, Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex. 2019, Pubmed
Nishino, Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. 2012, Pubmed
Ohno, Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs. 2019, Pubmed
Olins, Chromatin history: our view from the bridge. 2003, Pubmed
Pettersen, UCSF Chimera--a visualization system for exploratory research and analysis. 2004, Pubmed
Piovesan, The RING 2.0 web server for high quality residue interaction networks. 2016, Pubmed
Punjani, 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. 2021, Pubmed
Punjani, cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. 2017, Pubmed
Renz, Involvement of histone H1 in the organization of the chromosome fiber. 1977, Pubmed
Ricci, Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. 2015, Pubmed
Richmond, Structure of the nucleosome core particle at 7 A resolution. , Pubmed
Risca, Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. 2017, Pubmed
Robinson, EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure. 2006, Pubmed
Samejima, Functional analysis after rapid degradation of condensins and 3D-EM reveals chromatin volume is uncoupled from chromosome architecture in mitosis. 2018, Pubmed
Sanulli, HP1 reshapes nucleosome core to promote phase separation of heterochromatin. 2019, Pubmed
Schalch, X-ray structure of a tetranucleosome and its implications for the chromatin fibre. 2005, Pubmed , Xenbase
Scheffer, Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei. 2011, Pubmed
Scheres, RELION: implementation of a Bayesian approach to cryo-EM structure determination. 2012, Pubmed
Scheres, Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. 2007, Pubmed
Schneider, NIH Image to ImageJ: 25 years of image analysis. 2012, Pubmed
Schwanhäusser, Global quantification of mammalian gene expression control. 2011, Pubmed
Shamu, Sister chromatid separation in frog egg extracts requires DNA topoisomerase II activity during anaphase. 1992, Pubmed , Xenbase
Shechter, A distinct H2A.X isoform is enriched in Xenopus laevis eggs and early embryos and is phosphorylated in the absence of a checkpoint. 2009, Pubmed , Xenbase
Shevchenko, In-gel digestion for mass spectrometric characterization of proteins and proteomes. 2006, Pubmed
Sinha, Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler. 2017, Pubmed , Xenbase
Skrajna, Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. 2020, Pubmed
Song, Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. 2014, Pubmed , Xenbase
Su, A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. 2021, Pubmed
Takahashi, Folding the genome into mitotic chromosomes. 2019, Pubmed
Tan, Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. 2023, Pubmed
Tropea, Expression and purification of soluble His(6)-tagged TEV protease. 2009, Pubmed
Turner, Highly disordered histone H1-DNA model complexes and their condensates. 2018, Pubmed
Vargas, Efficient initial volume determination from electron microscopy images of single particles. 2014, Pubmed
Verbeke, Classification of Single Particles from Human Cell Extract Reveals Distinct Structures. 2018, Pubmed
Verbeke, Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections. 2020, Pubmed
Wang, Histone modifications and mitosis: countermarks, landmarks, and bookmarks. 2013, Pubmed
Wangkanont, Structures of Xenopus Embryonic Epidermal Lectin Reveal a Conserved Mechanism of Microbial Glycan Recognition. 2016, Pubmed , Xenbase
Waterhouse, SWISS-MODEL: homology modelling of protein structures and complexes. 2018, Pubmed
Weber, Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. 2014, Pubmed
Willcockson, H1 histones control the epigenetic landscape by local chromatin compaction. 2021, Pubmed
Willhoft, Structure and dynamics of the yeast SWR1-nucleosome complex. 2018, Pubmed
Woods, Elucidating the influence of linker histone variants on chromatosome dynamics and energetics. 2020, Pubmed
Wühr, Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. 2014, Pubmed , Xenbase
Yan, Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling. 2019, Pubmed
Ye, Structure of the RSC complex bound to the nucleosome. 2019, Pubmed
Yi, Electron microscopy snapshots of single particles from single cells. 2019, Pubmed
Yusufova, Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. 2021, Pubmed
Zheng, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. 2017, Pubmed
Zhiteneva, Mitotic post-translational modifications of histones promote chromatin compaction in vitro. 2017, Pubmed
Zhou, Structural Mechanisms of Nucleosome Recognition by Linker Histones. 2015, Pubmed
Zhou, Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment. 2019, Pubmed
Zhou, Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2. 2021, Pubmed
Zierhut, Nucleosomal regulation of chromatin composition and nuclear assembly revealed by histone depletion. 2014, Pubmed , Xenbase
Zlatanova, The nucleosome family: dynamic and growing. 2009, Pubmed
Zou, Direct Observation of H3-H4 Octasome by High-Speed AFM. 2018, Pubmed