Wang Lin, Dong Chunnan, Lu Chaolong, Li Shujin, Fu Lihong, Cong Bin
College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
Department of Pathogen Biology, Hebei Medical University, Shijiazhuang 050017, China.
iScience. 2022 Jun 13;25(7):104593. doi: 10.1016/j.isci.2022.104593. eCollection 2022 Jul 15.
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability.
微球菌核酸酶（MNase）被广泛用于绘制核小体图谱。然而，核小体具有高度动态性且易受实验条件影响，导致核小体图谱之间存在极大差异，这使得生成准确的核小体组织数据变得复杂。我们使用改进的MNase-seq技术对不同个体的核小体进行了绘制。改进措施包括设置不同的消化水平（低、中、高）以及进行裸DNA校正，以去除实验操作引起的噪声，并通过比较图谱来获得全基因组中强核小体（SNs）的准确位置和占有率。此外，还进一步挖掘了SNs的特征。SNs在Alu元件中富集，且靠近Chr12的着丝粒。SNs包含一些特定序列，其GC含量与动态核小体不同。这些发现表明，基因组中的核小体位置和DNA序列可能会影响核小体的稳定性。
