Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Sergei A. Grigoryev, Gaurav Arya, Sarah Correll, Christopher L. Woodcock, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i ± 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i ± 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivomaymediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.

Original languageEnglish (US)
Pages (from-to)13317-13322
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume106
Issue number32
DOIs
StatePublished - Aug 11 2009

Keywords

  • Chromatin structure
  • Electron microscopy
  • Linker histone
  • Mesoscopic modeling
  • Monte carlo simulations

ASJC Scopus subject areas

  • General

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