title: Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes.
abstract: The architecture of higher-order chromatin in eukaryotic cell nuclei is largely unknown. Here, we use electron microscopy-assisted nucleosome interaction capture (EMANIC) cross-linking experiments in combination with mesoscale chromatin modeling of 96-nucleosome arrays to investigate the internal organization of condensed chromatin in interphase cell nuclei and metaphase chromosomes at nucleosomal resolution. The combined data suggest a novel hierarchical looping model for chromatin higher-order folding, similar to rope flaking used in mountain climbing and rappelling. Not only does such packing help to avoid tangling and self-crossing, it also facilitates rope unraveling. Hierarchical looping is characterized by an increased frequency of higher-order internucleosome contacts for metaphase chromosomes compared with chromatin fibers in vitro and interphase chromatin, with preservation of a dominant two-start zigzag organization associated with the 30-nm fiber. Moreover, the strong dependence of looping on linker histone concentration suggests a hierarchical self-association mechanism of relaxed nucleosome zigzag chains rather than longitudinal compaction as seen in 30-nm fibers. Specifically, concentrations lower than one linker histone per nucleosome promote self-associations and formation of these looped networks of zigzag fibers. The combined experimental and modeling evidence for condensed metaphase chromatin as hierarchical loops and bundles of relaxed zigzag nucleosomal chains rather than randomly coiled threads or straight and stiff helical fibers reconciles aspects of other models for higher-order chromatin structure; it constitutes not only an efficient storage form for the genomic material, consistent with other genome-wide chromosome conformation studies that emphasize looping, but also a convenient organization for local DNA unraveling and genome access.
authors.affiliation: Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033; sag17@psu.edu schlick@nyu.edu.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Grigoryev
authors.affiliation: Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY 10012;
authors.forename: Gavin
authors.initials: G
authors.lastname: Bascom
authors.affiliation: Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033;
authors.forename: Jenna M
authors.initials: JM
authors.lastname: Buckwalter
authors.affiliation: Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033;
authors.forename: Michael B
authors.initials: MB
authors.lastname: Schubert
authors.affiliation: Biology Department, University of Massachusetts, Amherst, MA 01003;
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Woodcock
authors.affiliation: Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY 10012; NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China sag17@psu.edu schlick@nyu.edu.
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D000818:Animals; D002645:Chickens; D002843:Chromatin / Q000737:chemistry; D002877:Chromosomes, Human; D004912:Erythrocytes / Q000648:ultrastructure; D006367:HeLa Cells; D006801:Humans; D008677:Metaphase; D008854:Microscopy, Electron; D009707:Nucleosomes / Q000737:chemistry*
chemical_list: D002843:Chromatin; D009707:Nucleosomes
keywords: chromatin higher-order structure; electron microscopy; linker histone; mesoscale modeling; nucleosome