摘要：SummaryMicrococcal 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.Graphical abstractDisplay OmittedHighlights•Naked DNA correction improved the accuracy of nucleosome map in partial digestion•Level of MNase digestion has effects on nucleosome organization•A type of strong nucleosomes (SNs) exist across different nucleosome maps•Nucleosome stability may be related to its location and the DNA sequenceBioinformatics; Biological sciences; Biological sciences research methodologies; Molecular biology; Molecular biology experimental approach
