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Mol Cell
2017 May 04;663:384-397.e8. doi: 10.1016/j.molcel.2017.04.012.
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Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C, Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R, Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C, Dimitrov S.
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Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.
Abrishami,
Alignment of direct detection device micrographs using a robust Optical Flow approach.
2015, Pubmed
Abrishami,
Alignment of direct detection device micrographs using a robust Optical Flow approach.
2015,
Pubmed Adams,
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
2010,
Pubmed Allan,
The structure of histone H1 and its location in chromatin.
1980,
Pubmed Allan,
Roles of H1 domains in determining higher order chromatin structure and H1 location.
1986,
Pubmed Bednar,
Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy.
1995,
Pubmed Bednar,
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
2018,
Pubmed Bednar,
Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin.
1998,
Pubmed Biasini,
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.
2014,
Pubmed Brown,
Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo.
2006,
Pubmed Buckle,
Site-directed mutagenesis studies on the binding of the globular domain of linker histone H5 to the nucleosome.
1992,
Pubmed Caterino,
Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain.
2011,
Pubmed
,
Xenbase Christophorou,
Citrullination regulates pluripotency and histone H1 binding to chromatin.
2014,
Pubmed Chua,
The mechanics behind DNA sequence-dependent properties of the nucleosome.
2012,
Pubmed
,
Xenbase de Vries,
The HADDOCK web server for data-driven biomolecular docking.
2010,
Pubmed Emsley,
Features and development of Coot.
2010,
Pubmed Evans,
Scaling and assessment of data quality.
2006,
Pubmed Fang,
DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain.
2012,
Pubmed
,
Xenbase Hamiche,
Linker histone-dependent DNA structure in linear mononucleosomes.
1996,
Pubmed Hendzel,
The C-terminal domain is the primary determinant of histone H1 binding to chromatin in vivo.
2004,
Pubmed Hubbard,
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.
1991,
Pubmed Izzo,
The histone H1 family: specific members, specific functions?
2008,
Pubmed Kabsch,
XDS.
2010,
Pubmed Kucukelbir,
Quantifying the local resolution of cryo-EM density maps.
2014,
Pubmed Lee,
Targeted cross-linking and DNA cleavage within model chromatin complexes.
1999,
Pubmed
,
Xenbase Li,
Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
2013,
Pubmed Liu,
SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes.
2011,
Pubmed Lone,
Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1.
2013,
Pubmed
,
Xenbase Lowary,
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.
1998,
Pubmed Ludtke,
EMAN: semiautomated software for high-resolution single-particle reconstructions.
1999,
Pubmed Luger,
Crystal structure of the nucleosome core particle at 2.8 A resolution.
1997,
Pubmed Makarov,
Salt-induced conformational transitions in chromatin. A flow linear dichroism study.
1983,
Pubmed Maresca,
Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts.
2005,
Pubmed
,
Xenbase McCoy,
Phaser crystallographic software.
2007,
Pubmed Méndez,
Assessment of blind predictions of protein-protein interactions: current status of docking methods.
2003,
Pubmed Mindell,
Accurate determination of local defocus and specimen tilt in electron microscopy.
2003,
Pubmed Mirzabekov,
Chromatin superstructure-dependent crosslinking with DNA of the histone H5 residues Thr1, His25 and His62.
1990,
Pubmed Morin,
Collaboration gets the most out of software.
2013,
Pubmed Pettersen,
UCSF Chimera--a visualization system for exploratory research and analysis.
2004,
Pubmed Pruss,
An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres.
1996,
Pubmed
,
Xenbase Ramakrishnan,
Crystal structure of globular domain of histone H5 and its implications for nucleosome binding.
1993,
Pubmed Scheres,
RELION: implementation of a Bayesian approach to cryo-EM structure determination.
2012,
Pubmed Schröder,
Super-resolution biomolecular crystallography with low-resolution data.
2010,
Pubmed Shukla,
The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling.
2011,
Pubmed Simpson,
Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones.
1978,
Pubmed Song,
Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.
2014,
Pubmed
,
Xenbase Staynov,
Footprinting of linker histones H5 and H1 on the nucleosome.
1988,
Pubmed Syed,
The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome.
2009,
Pubmed
,
Xenbase Syed,
Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome.
2010,
Pubmed Tachiwana,
Crystal structure of the human centromeric nucleosome containing CENP-A.
2011,
Pubmed Thoma,
Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.
1979,
Pubmed Thomas,
Selective radiolabelling and identification of a strong nucleosome binding site on the globular domain of histone H5.
1986,
Pubmed Tremethick,
Higher-order structures of chromatin: the elusive 30 nm fiber.
2007,
Pubmed Trott,
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
2010,
Pubmed Valdar,
Scoring residue conservation.
2002,
Pubmed van Heel,
A new generation of the IMAGIC image processing system.
1996,
Pubmed Van Heel,
Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction.
1987,
Pubmed Vasudevan,
Crystal structures of nucleosome core particles containing the '601' strong positioning sequence.
2010,
Pubmed
,
Xenbase Wang,
Acetylation mimics within individual core histone tail domains indicate distinct roles in regulating the stability of higher-order chromatin structure.
2008,
Pubmed
,
Xenbase White,
A quantitative investigation of linker histone interactions with nucleosomes and chromatin.
2016,
Pubmed Wisniewski,
Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function.
2008,
Pubmed Wisniewski,
Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue.
2007,
Pubmed Woodcock,
Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length.
2006,
Pubmed Wriggers,
Conventions and workflows for using Situs.
2012,
Pubmed Zhou,
A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome.
2016,
Pubmed Zhou,
Position and orientation of the globular domain of linker histone H5 on the nucleosome.
1998,
Pubmed Zhou,
Structural Mechanisms of Nucleosome Recognition by Linker Histones.
2015,
Pubmed Zhou,
Structural insights into the histone H1-nucleosome complex.
2013,
Pubmed
