Nucleosome wrapping states encode principles of 3D genome organization

Zengqi Wen (), Ruixin Fang, Ruxin Zhang, Xinqian Yu, Fanli Zhou and Haizhen Long ()
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Zengqi Wen: Sun Yat-Sen University, Shenzhen
Ruixin Fang: Shenzhen Bay Laboratory
Ruxin Zhang: Shenzhen Bay Laboratory
Xinqian Yu: Shenzhen Bay Laboratory
Fanli Zhou: Sun Yat-Sen University, Shenzhen
Haizhen Long: Shenzhen Bay Laboratory

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract Nucleosome is the basic structural unit of the genome. During processes like DNA replication and gene transcription, the conformation of nucleosomes undergoes dynamic changes, including DNA unwrapping and rewrapping, as well as histone disassembly and assembly. However, the wrapping characteristics of nucleosomes across the entire genome, including region-specificity and their correlation with higher-order chromatin organization, remains to be studied. In this study, we investigate the wrapping length of DNA on nucleosomes across the whole genome using wrapping-seq. We discover that the chromatin of mouse ES cells forms Nucleosome Wrapping Domains (NRDs), which can also be observed in yeast and fly genomes. We find that the degree of nucleosome wrapping decreases after DNA replication and is promoted by transcription. Furthermore, we observe that nucleosome wrapping domains delineate Hi-C compartments and replication timing domains. In conclusion, we have unveiled a previously unrecognized domainization principle of the chromatin, encoded by nucleosome wrapping states.

Date: 2025
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DOI: 10.1038/s41467-024-54735-8

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