DataVXAdvanced SciencePaper
journal article·2023-03Open access

Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells

Yusen Ye, Shihua Zhang, Lin Gao, Yuqing Zhu, Jin Zhang

Advanced Science· Volume 10· Issue 8
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Abstract

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.
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Research context

OpenAlex topics: Genomics and Chromatin Dynamics · Chromosomal and Genetic Variations · Single-cell and spatial transcriptomics

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

School of Computer Science and Technology Xidian University Xi'an Shaanxi 710071 P. R. China

NCMIS CEMS RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 P. R. China

School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 P. R. China

Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 P. R. China

Center for Stem Cell and Translational Medicine School of Life Sciences Anhui University Hefei Anhui 230601 P. R. China

Center 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. China

Zhejiang Laboratory for Systems and Precision Medicine Zhejiang University Medical Center Hangzhou Zhejiang 311121 P. R. China

Institute of Hematology Zhejiang University Hangzhou Zhejiang 310058 P. R. China

Center of Gene/Cell Engineering and Genome Medicine Hangzhou Zhejiang 310058 P. R. China

Funding

National Natural Science Foundation of China · National Key Research and Development Program of China

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