GSE49836
Hematopoietic stem/progenitor cells HELP-tagging cytosine methylation data
Using HELP-Tagging, we defined the cytosine methylation profiles of hematopoietic stem/progenitor cells (CD34+) from umbilical cord blood in 29 healthy newborns.  We found substantial variation of DNA methylation to occur in human CD34+ hematopoietic stem and progenitor cells from different individuals. Empirical annotation of the genome of this cell type reveals the variability to be targeted to candidate promoters and to candidate enhancer sequences of genes expressed at lower levels. The variability of DNA methylation at candidate enhancers was low for housekeeping genes but high for genes associated with leukocyte differentiation. The enrichment of DNA methylation variability at loci  with intermediate methylation values, occurring at apparently “poised” enhancers, suggests cell subpopulation heterogeneity between individuals as the basis for the epigenomic variability observed. The “meta-epigenome” present even in purified cells complicates the design and interpretation of epigenome-wide association studies, but also allows insights into the gene expression characteristics and the number of cell types comprising the cell population analyzed. One Sentence Summary: Variability in epigenomic patterns between different individuals occurs predominantly at promoters and enhancers, reflecting cell subpopulation heterogeneity. Overall design: 29 HpaII test