The chromatin-based epigenome in development and aging

Child Health And Human Development

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Abstract

The past year has seen an increasing emphasis on studies that use human tissues from several clinical sources. Peripheral blood monocytes are obtained from newborns (cord blood) through a collaboration with the Perinatology Branch, NICHD, while monocytes from adults are available through the NIH Department of Transfusion Medicine. These cells are induced by the cytokines IL4 and GM-CSF to differentiate in vitro into antigen-presenting dendritic cells. Human skin fibroblasts from newborns and adults are procured, as needed, under a NICHD Institutional Review Board (IRB) approved protocol. The latter cells are studied with respect to serum responsiveness and growth properties.[unreadable] [unreadable] With these monocyte- and fibroblast-based experimental systems, RNA expression microarrays were successfully employed to search for instances of developmental and age-related change in gene regulation. The current focus of work is thus shifting to more detailed studies on whether such changes have an epigenetic basis. Cis-acting epigenetic states have several distinctive properties, and multiple strategies are used to evaluate their presence or absence: i) heterocellularity (variegation) in expression patterns: RNA FISH and cytohistochemistry are applicable techniques; ii) allele independence: single nucleotide polymorphisms (SNPs) are used to search for examples of allelic skewing; iii) memory of expression state settings: heterokaryons between cells from newborns and adults, or young and old adults, can be utilized to determine the independence of development- and age-specific expression levels. [unreadable] [unreadable] Complementary to these strategies are a variety of techniques in various stages of implementation. Chromatin immunoprecipitation (ChIP) studies are well advanced: both direct assays using an automated HPLC/fluorescence detection system and ChIP-on-chip platforms are used. For the latter, bioinformatics tools have been developed for the custom design of large deoxynucleotide probe arrays. A new, and potentially very powerful, approach based on single nucleotide sequencing (ChIP-Seq) should be initiated within several months. In addition, a major initiative for the upcoming year will be to incorporate studies of monozygotic (identical) and dizygotic (fraternal) twins. Detection of persistent gene expression differences in genetically identical twins especially if those differences exhibit one or more of the properties listed above constitutes very strong evidence for underlying epigenetic mechanisms.[unreadable] [unreadable] Results to date indicate that genes subject to both differentiation and developmental controls often exhibit a high degree of variance in expression levels during age-related transitions. That this occurs, at least in part, through epigenetic mechanisms is supported by cumulative evidence from chromatin mapping and data on heterocellularity and allelic skewing. In a general way, the well-studied combination of differentiation and developmental controls on fetal hemoglobin expression may prove to be an important paradigm. The emerging goal is to generalize this paradigm to address a range of current problems in Pediatrics and Medicine. The most likely, based on the genes currently under study, will be deficiencies in the innate immune systems of newborns; peripheral insulin resistance and diabetes in adolescents and young adults; and a spectrum of neurodegenerative processes, including Parkinsons and Alzheimers diseases, in the elderly.