Changes in global nucleosome positioning during human embryonic stem cell differentiation. Homo sapiens

Nucleosome positioning (NP) is a fundamental parameter in the chromatin packing/unpacking, playing key roles in transcriptional regulation and maintenance of genomic integrity. However, it is not as well studied as other levels of epigenetic controls such as histone modifications and DNA methylation. To better understand NP, we investigated how it changes during a human embryonic stem cell (hESC) differentiation system: WA09 hESCs->ISL1+ nascent mesoderm (INM)->smooth muscle cells (SMCs), by paired-end sequencing of mononucleosomal DNA fragments generated by micrococcal nuclease (MNase)-digestion (MNase-seq). The analysis reveals that at the promoter and gene body, NP is correlated primarily with transcriptional activity and secondarily with the GC content of the sequence. Pluripotent hESCs exhibit a more dynamic NP than their differentiated derivatives, indicating that more genes can be readily activated or silenced once differentiation starts. Surprisingly, mononucleosomal DNA of hESC is ~10bp (one helix turn) longer than its differentiated WA09-SMC on average. Moreover, as fragment length increases, both the GC content and the number of CpG also increase. We hypothesize that longer mononucleosomal DNA arises from a larger histone core and that this varies between the cell types.