THE CHROMATIN-BASED EPIGENOME IN DEVELOPMENT AND AGING
, Head, Section on Human Genetics
Valya Russanova, PhD, Staff Scientist
Analia Porrás, MD, PhD, Research Fellow
Hariklia Dimitropoulos, PhD, Postdoctoral Fellow
Sarah Kozar, BS, Postbaccalaureate Fellow
The normal human lifespan is marked by a complex series of developmental transitions, relative stability during adulthood, and, ultimately, a gradual decline in viability. Clock-like mechanisms presumably underlie the developmental events that occur through childhood and adolescence. Further, instabilities in such mechanisms are likely to be an integral part of the aging process and probably contribute to many common degenerative diseases of later life. A breakthrough in this area would have remarkable implications. Thus, there is widespread interest in the prospect that epigenetics—and the rapidly evolving field of epigenomics—holds the key to further progress.
Linking gene expression to cis-acting epigenetic states
The past year has seen an increasing emphasis on studies that use human tissues from several clinical sources. Through a collaboration with NICHD’s Program in Perinatal Research and Obstetrics, we obtain peripheral blood monocytes from newborns (cord blood) while monocytes from adults are available through the NIH Department of Transfusion Medicine. Using the cytokines IL4 and GM-CSF, we induce these cells to differentiate in vitro into antigen-presenting dendritic cells. We procure human skin fibroblasts from newborns and adults, as needed, under an NICHD Institutional Review Board (IRB)–approved protocol. We study the latter cells with respect to serum responsiveness and growth properties.
With our monocyte- and fibroblast-based experimental systems, we successfully employed RNA expression microarrays to search for instances of developmental and age-related changes in gene regulation. Our work is therefore shifting to more detailed studies on whether such changes have an epigenetic basis. Cis-acting epigenetic states have several distinctive properties, and we use several strategies to evaluate their presence or absence: (1) heterocellularity (variegation) in expression patterns: RNA FISH and cytohistochemistry are applicable techniques; (2) allele independence: single nucleotide polymorphisms (SNPs) are used to search for examples of allelic skewing; (3) memory of expression state settings: heterokaryons between cells from newborns and adults or from young and old adults are used to determine the independence of development- and age-specific expression levels.
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. For the latter, we have developed bioinformatics tools for the custom design of large deoxynucleotide probe arrays. Within several months, we should be able to initiate a new and potentially very powerful approach based on single-nucleotide sequencing (ChIP-Seq). In addition, a major initiative for the upcoming year will 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—would constitute particularly strong evidence for underlying epigenetic mechanisms.
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 of fetal hemoglobin expression may prove to be an important paradigm. The emerging goal is to generalize the paradigm to address a range of current problems in pediatrics and medicine. The most likely topics for pursuit, 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 Parkinson’s and Alzheimer’s diseases, in the elderly.
Humphrey GW, Wang YH, Hirai T, Padmanabhan R, Panchision DM, Newell LF, McKay RDG, Howard BH. Complementary roles for histone deacetylases 1,2, and 3 in differentiation of pluripotent stem cells. Differentiation 2007 [E-pub ahead of print].
COLLABORATORS
Jonathan Epstein, MS, Unit on Biological Computation, NICHD, Bethesda, MD
Ronald D.G. McKay, PhD, Laboratory of Molecular Biology, NINDS, Bethesda, MD
Keiko Ozato, PhD, Program in Genomics of Differentiation, NICHD, Bethesda, MD
Roberto Romero, MD, Program in Perinatal Research and Obstetrics, NICHD, Detroit, MI
For further information, contact howard@helix.nih.gov.
