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Human Molecular Genetics Advance Access published online on June 20, 2006
Human Molecular Genetics, doi:10.1093/hmg/ddl159
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© The Author 2006. Published by Oxford University Press. All rights reserved
Received March 7, 2006
Revised June 17, 2006
Accepted June 17, 2006

Article

Chromosome-wide, Allele-specific Analysis of the Histone Code on the Human X Chromosome

Cory M. Valley 1, Lisa M. Pertz 2, Bala S. Balakumaran 2, and Huntington F. Willard 3 *

1 Institute for Genome Sciences & Policy, Duke University, Durham NC 27708; Departments of Molecular Genetics & Microbiology,Duke University, Durham NC 27708
2 Institute for Genome Sciences & Policy, Duke University, Durham NC 27708
3 Institute for Genome Sciences & Policy, Duke University, Durham NC 27708; Departments of Molecular Genetics & Microbiology,Duke University, Durham NC 27708; Institute for Genome Sciences & Policy, Departments of Biology, Duke University, CIEMAS 2376, 101 Science Dr. Durham, NC 27708

* To whom correspondence should be addressed.
Huntington F. Willard, E-mail: hunt.Willard{at}duke.edu


  Abstract

Variation in the composition of chromatin has been proposed to generate a ‘histone code’ that epigenetically regulates gene expression in a variety of eukaryotic systems. As a result of the process of X chromosome inactivation, chromatin on the mammalian inactive X chromosome (Xi) is marked by several modifications, including histone hypoacetylation, trimethylation of lysine 9 on histone H3 (H3TrimK9), and substitution of core histone H2A with the histone variant MacroH2A. H3TrimK9 is a well-studied marker for heterochromatin in many organisms, but the distribution and function of MacroH2A are less clear. Cytologically, the Xi in human cells is comprised of alternating and largely non-overlapping ~10-15 Mb domains marked by MacroH2A and H3TrimK9. To examine the genomic deposition of MacroH2A, H3TrimK9, and acetylated histone H4 modifications on the Xi at higher resolution, we used chromatin immunoprecipitation in combination with a SNP-based assay to distinguish the Xi and active X (Xa) in a diploid female cell line and to determine quantitatively the relative enrichment of these histone code elements on the Xi relative to the Xa. While we found a majority of sites were enriched for either MacroH2A or H3TrimK9 in a manner consistent with the cytological appearance of the Xi, a range of different histone code types were detected at different sites along the X. These findings suggest that the nature of the heterochromatin histone code associated with X inactivation may be more heterogeneous than previously thought and imply that gene silencing can be achieved by a variety of different epigenetic mechanisms whose genomic, evolutionary or developmental basis is now amenable to investigation.


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