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Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling

National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.

Address correspondence to Bruce Howard, MD, NICHD, NIH, Bldg. 31, Rm. 2A25, 6 Center Dr., Bethesda, MD 20892. E-mail: howard{at}helix.nih.gov

With completion of the human genome project, patterns of higher order chromatin structure can be easily related to other features of genome organization. A well-studied aspect of chromatin, histone H4 acetylation, is examined here on the basis of its role in setting competence for gene activation. Three applications of a new hybrid genome sampling–chromatin immunoprecipitation strategy are described. The first explores aspects of epigenome architecture in human fibroblasts. A second focuses on chromatin from HL-60 promyelocytic leukemia cells before and after differentiation into macrophage-like cells. A third application explores age-related epigenome change. In the latter, acetylation patterns are compared in human skin fibroblast chromatin from donors of various ages. Two sites are reported at which observed histone H4 acetylation differences suggest decreasing acetylation over time. The sites, located in chromosome 4p16.1 and 4q35.2 regions, appear to remodel during late fetal–early child development and from preadolescence through adult life, respectively.