Nucleosome wrapping states encode principles of 3D genome organization
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 charact...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54735-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559215209971712 |
|---|---|
| author | Zengqi Wen Ruixin Fang Ruxin Zhang Xinqian Yu Fanli Zhou Haizhen Long |
| author_facet | Zengqi Wen Ruixin Fang Ruxin Zhang Xinqian Yu Fanli Zhou Haizhen Long |
| author_sort | Zengqi Wen |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-650bd9c6848f430eb6139ba298975080 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-650bd9c6848f430eb6139ba2989750802025-01-05T12:40:55ZengNature PortfolioNature Communications2041-17232025-01-0116111110.1038/s41467-024-54735-8Nucleosome wrapping states encode principles of 3D genome organizationZengqi Wen0Ruixin Fang1Ruxin Zhang2Xinqian Yu3Fanli Zhou4Haizhen Long5School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, ShenzhenInstitute of Molecular Physiology, Shenzhen Bay LaboratoryInstitute of Molecular Physiology, Shenzhen Bay LaboratoryInstitute of Molecular Physiology, Shenzhen Bay LaboratorySchool of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, ShenzhenInstitute of Molecular Physiology, Shenzhen Bay LaboratoryAbstract 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.https://doi.org/10.1038/s41467-024-54735-8 |
| spellingShingle | Zengqi Wen Ruixin Fang Ruxin Zhang Xinqian Yu Fanli Zhou Haizhen Long Nucleosome wrapping states encode principles of 3D genome organization Nature Communications |
| title | Nucleosome wrapping states encode principles of 3D genome organization |
| title_full | Nucleosome wrapping states encode principles of 3D genome organization |
| title_fullStr | Nucleosome wrapping states encode principles of 3D genome organization |
| title_full_unstemmed | Nucleosome wrapping states encode principles of 3D genome organization |
| title_short | Nucleosome wrapping states encode principles of 3D genome organization |
| title_sort | nucleosome wrapping states encode principles of 3d genome organization |
| url | https://doi.org/10.1038/s41467-024-54735-8 |
| work_keys_str_mv | AT zengqiwen nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization AT ruixinfang nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization AT ruxinzhang nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization AT xinqianyu nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization AT fanlizhou nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization AT haizhenlong nucleosomewrappingstatesencodeprinciplesof3dgenomeorganization |