The normal adult human mammary gland is a continuous bilayered epithelial 
system. Bipotent and myoepithelial progenitors are prominent and unique 
components of the outer (basal) layer. The inner (luminal) layer includes both 
luminal-restricted progenitors and a phenotypically separable fraction that 
lacks progenitor activity. We now report an epigenomic comparison of these three 
subsets with one another, with their associated stromal cells, and with three 
immortalized, non-tumorigenic human mammary cell lines. Each genome-wide 
analysis contains profiles for six histone marks, methylated DNA, and RNA 
transcripts. Analysis of these datasets shows that each cell type has unique 
features, primarily within genomic regulatory regions, and that the cell lines 
group together. Analyses of the promoter and enhancer profiles place the luminal 
progenitors in between the basal cells and the non-progenitor luminal subset. 
Integrative analysis reveals networks of subset-specific transcription factors.