Nucleosome positioning changes during human embryonic stem cell differentiation

Nucleosomes are the basic unit of chromatin. Nucleosome positioning (NP) plays a key role in transcriptional regulation and other biological processes. To better understand NP we used MNase-seq to investigate changes that occur as human embryonic stem cells (hESCs) transition to nascent mesoderm and then to smooth muscle cells (SMCs). Compared to differentiated cell derivatives, nucleosome occupancy at promoters and other notable genic sites, such as exon/intron junctions and adjacent regions, in hESCs shows a stronger correlation with transcript abundance and is less influenced by sequence content. Upon hESC differentiation, genes being silenced, but not genes being activated, display a substantial change in nucleosome occupancy at their promoters. Genome-wide, we detected a shift of NP to regions of higher G+C content as hESCs differentiate to SMCs. Notably, genomic regions with higher nucleosome occupancy harbor twice as many G↔C changes but fewer than half A↔T changes, compared to regions with lower nucleosome occupancy. Finally, our analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes. Our study reveals another unique feature of hESC chromatin, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.

核小体是染色质的基本结构单位。核小体定位（Nucleosome Positioning, NP）在转录调控及其他生物学过程中发挥关键作用。为深入解析核小体定位的调控机制，我们采用微球菌核酸酶测序（MNase-seq）技术，系统探究人类胚胎干细胞（hESCs）向新生中胚层分化、继而转化为平滑肌细胞（SMCs）过程中发生的核小体定位变化。相较于分化后的细胞子代，人类胚胎干细胞中启动子及其他重要基因位点（如外显子/内含子剪接位点及其邻近区域）的核小体占据率，与转录本丰度的相关性更强，且受序列组成的影响更弱。在人类胚胎干细胞分化进程中，仅发生沉默的基因（而非被激活的基因），其启动子区域的核小体占据率会出现显著改变。全基因组层面，我们观测到随着人类胚胎干细胞向平滑肌细胞分化，核小体定位向高G+C含量的基因组区域发生偏移。值得注意的是，与低核小体占据率区域相比，高核小体占据率的基因组区域中G↔C碱基替换的数量为其两倍，而A↔T碱基替换的数量则不足其一半。最终，我们的分析表明人类胚胎干细胞基因组未发生重排，其序列突变率与正常人类基因组水平相近。本研究揭示了人类胚胎干细胞染色质的又一独特特征，同时为核小体占据率与序列G+C含量之间的关联提供了新的研究视角。