BACKGROUND: The interplay between epigenetic modifications and chromatin 
structure are integral to our understanding of genome function. Methylation of 
cytosine (5mC) at CG dinucleotides, traditionally associated with 
transcriptional repression, is the most highly studied chemical modification of 
DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated 
regions (HMRs) often occur in CG islands (CGIs), however, they also occur 
outside of CGIs and function as cell-type specific enhancers. During the process 
of differentiation, reorganization of chromatin and nucleosome arrangement at 
regulatory regions is thought to occur in order for the establishment of 
cell-type specific transcriptional programs. However, the specifics regarding 
the organization of nucleosomes at HMRs and the potential mechanisms regulating 
nucleosome occupancy in these regions are unknown. Here, we have investigated 
nucleosome organization around hypomethylated regions (HMRs) identified in two 
mouse primary cells.
RESULTS: Microccocal nuclease (MNase) digested mononucleosomes from primary 
cultures of new-born female mouse dermal fibroblasts and keratinocytes were 
mapped and compared to the HMRs obtained from single base-pair resolution 
methylomes. In both cell types, we find that nucleosomes are enriched at HMR 
boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, 
HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, 
with phased nucleosomes propagating into the methylated region. Nucleosomes are 
enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types 
suggesting that nucleosome organization surrounding HMR boundaries is 
independent of methylation status. In addition, we find potential transcription 
factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries.
CONCLUSIONS: Our results show that intrinsic nucleosome occupancy score (INOS) 
positively correlate with the nucleosome organization surrounding non-CGI 
TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs 
in the genome. Since nucleosomes impact all processes involving the genome, our 
results provide a link between epigenetic modifications, chromatin structure, 
and regulatory function.