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Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.

Publication ,  Journal Article
Grigoryev, SA; Arya, G; Correll, S; Woodcock, CL; Schlick, T
Published in: Proceedings of the National Academy of Sciences of the United States of America
August 2009

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 vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.

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Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

August 2009

Volume

106

Issue

32

Start / End Page

13317 / 13322

Related Subject Headings

  • Nucleosomes
  • Nucleic Acid Conformation
  • Models, Molecular
  • Histones
  • Chickens
  • Cations
  • Animals
 

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Grigoryev, S. A., Arya, G., Correll, S., Woodcock, C. L., & Schlick, T. (2009). Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proceedings of the National Academy of Sciences of the United States of America, 106(32), 13317–13322. https://doi.org/10.1073/pnas.0903280106
Grigoryev, Sergei A., Gaurav Arya, Sarah Correll, Christopher L. Woodcock, and Tamar Schlick. “Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.Proceedings of the National Academy of Sciences of the United States of America 106, no. 32 (August 2009): 13317–22. https://doi.org/10.1073/pnas.0903280106.
Grigoryev SA, Arya G, Correll S, Woodcock CL, Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proceedings of the National Academy of Sciences of the United States of America. 2009 Aug;106(32):13317–22.
Grigoryev, Sergei A., et al. “Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 32, Aug. 2009, pp. 13317–22. Epmc, doi:10.1073/pnas.0903280106.
Grigoryev SA, Arya G, Correll S, Woodcock CL, Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proceedings of the National Academy of Sciences of the United States of America. 2009 Aug;106(32):13317–13322.
Journal cover image

Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

August 2009

Volume

106

Issue

32

Start / End Page

13317 / 13322

Related Subject Headings

  • Nucleosomes
  • Nucleic Acid Conformation
  • Models, Molecular
  • Histones
  • Chickens
  • Cations
  • Animals