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Nucleic Acids Research Advance Access originally published online on March 12, 2009
Nucleic Acids Research 2009 37(9):2818-2829; doi:10.1093/nar/gkp113
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Nucleic Acids Research, 2009, Vol. 37, No. 9 2818-2829
© Published by Oxford University Press 2009
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Gene Regulation, Chromatin and Epigenetics

Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA

Feng Cui and Victor B. Zhurkin*

Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA

*To whom correspondence should be addressed. Tel: +1 301 496 8913; Fax: +1 301 402 4724; Email: zhurkin{at}nih.gov

Received October 30, 2008. Revised January 21, 2009. Accepted February 9, 2009.

Linker histones (LHs) bind to the DNA entry/exit points of nucleosomes and demonstrate preference for AT-rich DNA, although the recognized sequence patterns remain unknown. These patterns are expected to be more pronounced in metazoan nucleosomes with abundant LHs, compared to yeast nucleosomes with few LHs. To test this hypothesis, we compared the nucleosome core particle (NCP) sequences from chicken, Drosophila and yeast, extending them by the flanking sequences extracted from the genomes. We found that the known ~10-bp periodic oscillation of AT-rich elements goes beyond the ends of yeast nucleosomes, but is distorted in metazoan sequences where the ‘out-of-phase’ AT-peaks appear at the NCP ends. The observed difference is likely to be associated with sequence-specific LH binding. We therefore propose a new structural model for LH binding to metazoan nucleosomes, postulating that the highly conserved nonpolar ‘wing’ region of the LH globular domain (tetrapeptide GVGA) recognizes AT-rich fragments through hydrophobic interactions with the thymine methyl groups. These interactions lead to DNA bending at the NCP ends and formation of a ‘stem-like’ structure. The same mechanism accounts for the high affinity of LH to methylated DNA—a feature critical for stabilization of the higher-order structure of chromatin and for repression of transcription.


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