The fundamental repeating unit of eukaryotic chromatin is the nucleosome. 
Besides being involved in packaging DNA, nucleosome organization plays an 
important role in transcriptional regulation and cellular identity. Currently, 
there is much debate about the major determinants of the nucleosome architecture 
of a genome and its significance with little being known about its role in stem 
cells. To address these questions, we performed ultra-deep sequencing of 
nucleosomal DNA in two human embryonic stem cell lines and integrated our data 
with numerous epigenomic maps. Our analyses have revealed that the genome is a 
determinant of nucleosome organization with transcriptionally inactive regions 
characterized by a "ground state" of nucleosome profiles driven by underlying 
DNA sequences. DNA sequence preferences are associated with heterogeneous 
chromatin organization around transcription start sites. Transcription, histone 
modifications, and DNA methylation alter this "ground state" by having distinct 
effects on both nucleosome positioning and occupancy. As the transcriptional 
rate increases, nucleosomes become better positioned. Exons transcribed and 
included in the final spliced mRNA have distinct nucleosome profiles in 
comparison to exons not included at exon-exon junctions. Genes marked by the 
active modification H3K4m3 are characterized by lower nucleosome occupancy 
before the transcription start site compared to genes marked by the inactive 
modification H3K27m3, while bivalent domains, genes associated with both marks, 
lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin 
states) are associated with unique nucleosome profiles. Nucleosome organization 
varies around transcription factor binding in enhancers versus promoters. DNA 
methylation is associated with increasing nucleosome occupancy and different 
types of methylations have distinct location preferences within the nucleosome 
core particle. Finally, computational analysis of nucleosome organization alone 
is sufficient to elucidate much of the circuitry of pluripotency. Our results, 
suggest that nucleosome organization is associated with numerous genomic and 
epigenomic processes and can be used to elucidate cellular identity.