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1. Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation.

Author

Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA, Bednar J, Hamiche A, Angelov D, Petosa C, and Dimitrov S

Subjects
Animals, Binding Sites, Cloning, Molecular, Cryoelectron Microscopy, Crystallography, X-Ray, DNA genetics, DNA metabolism, Escherichia coli genetics, Escherichia coli metabolism, Gene Expression, Genetic Vectors chemistry, Genetic Vectors metabolism, Histones genetics, Histones metabolism, Humans, Hydroxyl Radical chemistry, Models, Molecular, Nucleosome Assembly Protein 1 genetics, Nucleosome Assembly Protein 1 metabolism, Nucleosomes chemistry, Nucleosomes metabolism, Osmolar Concentration, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Protein Multimerization, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Xenopus laevis, DNA chemistry, Histones chemistry, Nucleosome Assembly Protein 1 chemistry, Nucleosomes ultrastructure
Abstract

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., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Published
2018
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3. Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.

Author

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, and Dimitrov S

Subjects
Animals, Base Pairing, Binding Sites, Chromatin chemistry, Chromatin genetics, Chromatin ultrastructure, Cryoelectron Microscopy, DNA chemistry, DNA genetics, Histones chemistry, Humans, Models, Molecular, Nucleosomes chemistry, Nucleosomes genetics, Nucleosomes ultrastructure, Protein Binding, Protein Interaction Domains and Motifs, Structure-Activity Relationship, Time Factors, Xenopus laevis genetics, Xenopus laevis metabolism, Chromatin metabolism, Chromatin Assembly and Disassembly, DNA metabolism, Histones metabolism, Nucleosomes metabolism
Abstract

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., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Published
2017
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