Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells
Abstract The exploration of single‐cell 3D genome maps reveals that chromatin domains are indeed physical structures presenting in single cells, and domain boundaries vary from cell to cell. However, systematic analysis of the association between regulatory factor binding and elements and the format...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-03-01
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| Series: | Advanced Science |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/advs.202205162 |
| _version_ | 1797870163887915008 |
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| author | Yusen Ye Shihua Zhang Lin Gao Yuqing Zhu Jin Zhang |
| author_facet | Yusen Ye Shihua Zhang Lin Gao Yuqing Zhu Jin Zhang |
| author_sort | Yusen Ye |
| collection | DOAJ |
| description | Abstract The exploration of single‐cell 3D genome maps reveals that chromatin domains are indeed physical structures presenting in single cells, and domain boundaries vary from cell to cell. However, systematic analysis of the association between regulatory factor binding and elements and the formation of chromatin domains in single cells has not yet emerged. To this end, a hierarchical chromatin domain structure identification algorithm (named as HiCS) is first developed from individual single‐cell Hi‐C maps, with superior performance in both accuracy and efficiency. The results suggest that in addition to the known CTCF‐cohesin complex, Polycomb, TrxG, pluripotent protein families, and other multiple factors also contribute to shaping chromatin domain boundaries in single embryonic stem cells. Different cooperation patterns of these regulatory factors drive genomic position categories with differential preferences forming boundaries, and the most extensive six types of retrotransposons are differentially distributed in these genomic position categories with preferential localization. The above results suggest that these different retrotransposons within genomic regions interplay with regulatory factors navigating the preference of genomic positions forming boundaries, driving the formation of higher‐order chromatin structures, and thus regulating cell functions in single mouse embryonic stem cells. |
| first_indexed | 2024-04-10T00:24:05Z |
| format | Article |
| id | doaj.art-3e3319cc9f6e4d4fbeea611302203ca7 |
| institution | Directory Open Access Journal |
| issn | 2198-3844 |
| language | English |
| last_indexed | 2024-04-10T00:24:05Z |
| publishDate | 2023-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj.art-3e3319cc9f6e4d4fbeea611302203ca72023-03-15T13:19:15ZengWileyAdvanced Science2198-38442023-03-01108n/an/a10.1002/advs.202205162Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem CellsYusen Ye0Shihua Zhang1Lin Gao2Yuqing Zhu3Jin Zhang4School of Computer Science and Technology Xidian University Xi'an Shaanxi 710071 P. R. ChinaNCMIS CEMS RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 P. R. ChinaSchool of Computer Science and Technology Xidian University Xi'an Shaanxi 710071 P. R. ChinaCenter for Stem Cell and Translational Medicine School of Life Sciences Anhui University Hefei Anhui 230601 P. R. ChinaCenter for Stem Cell and Regenerative Medicine Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital Zhejiang University School of Medicine Hangzhou Zhejiang 310003 P. R. ChinaAbstract The exploration of single‐cell 3D genome maps reveals that chromatin domains are indeed physical structures presenting in single cells, and domain boundaries vary from cell to cell. However, systematic analysis of the association between regulatory factor binding and elements and the formation of chromatin domains in single cells has not yet emerged. To this end, a hierarchical chromatin domain structure identification algorithm (named as HiCS) is first developed from individual single‐cell Hi‐C maps, with superior performance in both accuracy and efficiency. The results suggest that in addition to the known CTCF‐cohesin complex, Polycomb, TrxG, pluripotent protein families, and other multiple factors also contribute to shaping chromatin domain boundaries in single embryonic stem cells. Different cooperation patterns of these regulatory factors drive genomic position categories with differential preferences forming boundaries, and the most extensive six types of retrotransposons are differentially distributed in these genomic position categories with preferential localization. The above results suggest that these different retrotransposons within genomic regions interplay with regulatory factors navigating the preference of genomic positions forming boundaries, driving the formation of higher‐order chromatin structures, and thus regulating cell functions in single mouse embryonic stem cells.https://doi.org/10.1002/advs.202205162chromatin landscapehierarchical chromatin domainsmouse embryonic stem cellsregulatory factorsretrotransposonssingle cell 3D genome |
| spellingShingle | Yusen Ye Shihua Zhang Lin Gao Yuqing Zhu Jin Zhang Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells Advanced Science chromatin landscape hierarchical chromatin domains mouse embryonic stem cells regulatory factors retrotransposons single cell 3D genome |
| title | Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells |
| title_full | Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells |
| title_fullStr | Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells |
| title_full_unstemmed | Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells |
| title_short | Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells |
| title_sort | deciphering hierarchical chromatin domains and preference of genomic position forming boundaries in single mouse embryonic stem cells |
| topic | chromatin landscape hierarchical chromatin domains mouse embryonic stem cells regulatory factors retrotransposons single cell 3D genome |
| url | https://doi.org/10.1002/advs.202205162 |
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