Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

Sergei A. Grigoryev, Gavin Bascom, Jenna M. Buckwalter, Michael B. Schubert, Christopher L. Woodcock, Tamar Schlick

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1238-1243
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number5
DOIs
StatePublished - Feb 2 2016

Fingerprint

Nucleosomes
Metaphase
Chromatin
Chromosomes
Interphase
Cell Nucleus
Histones
Genome
Chromatin Assembly and Disassembly
Eukaryotic Cells
Electron Microscopy
DNA

Keywords

  • Chromatin higher-order structure
  • Electron microscopy
  • Linker histone
  • Mesoscale modeling
  • Nucleosome

ASJC Scopus subject areas

  • General

Cite this

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes. / Grigoryev, Sergei A.; Bascom, Gavin; Buckwalter, Jenna M.; Schubert, Michael B.; Woodcock, Christopher L.; Schlick, Tamar.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 5, 02.02.2016, p. 1238-1243.

Research output: Contribution to journalArticle

Grigoryev, Sergei A. ; Bascom, Gavin ; Buckwalter, Jenna M. ; Schubert, Michael B. ; Woodcock, Christopher L. ; Schlick, Tamar. / Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 5. pp. 1238-1243.
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