Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity
Abstract Cell-specific super-enhancers (SEs) and master transcription factors (TFs) dynamically remodel embryonic stem cell (ESC) fate, yet their regulatory interplay remains unclear. By integrating multi-omics data (H3K27ac, Hi-C, scRNA-seq) across ESC states, we identified SEs interacting with mas...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60389-x |
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| author | Guangsong Su Bohan Chen Yingjie Song Qingqing Yin Wenbin Wang Xueyuan Zhao Sibo Fan Jie Lian Dongqing Li Jinfang Bi Peng Li Zhongfang Zhao Lei Zhang Jiandang Shi Wange Lu |
| author_facet | Guangsong Su Bohan Chen Yingjie Song Qingqing Yin Wenbin Wang Xueyuan Zhao Sibo Fan Jie Lian Dongqing Li Jinfang Bi Peng Li Zhongfang Zhao Lei Zhang Jiandang Shi Wange Lu |
| author_sort | Guangsong Su |
| collection | DOAJ |
| description | Abstract Cell-specific super-enhancers (SEs) and master transcription factors (TFs) dynamically remodel embryonic stem cell (ESC) fate, yet their regulatory interplay remains unclear. By integrating multi-omics data (H3K27ac, Hi-C, scRNA-seq) across ESC states, we identified SEs interacting with master TFs, exemplified by the Klf5-adjacent SE (K5aSE). K5aSE deletion impaired proliferation, differentiation, and Klf5 expression, partially rescued by KLF5 reintroduction. Despite phenotypic similarities between Klf5-KO and K5aSE-KO ESCs, scRNA-seq of embryoid bodies revealed distinct differentiation trajectories, suggesting K5aSE targets beyond Klf5. High-throughput 3D genome screening demonstrated K5aSE activates four distal genes via chromatin looping. CRISPRa-mediated activation of these targets rescued K5aSE-KO phenotypes and uncovered their regulatory roles. Furthermore, CTCF depletion disrupted topologically associated domains (TADs) near K5aSE, suppressing Klf5 and target gene expression, indicating CTCF-mediated TADs sustain K5aSE activity. Our study unveils a 3D genome-dependent mechanism by which SEs govern ESC identity through coordinated TF interaction and multi-gene regulation. |
| format | Article |
| id | doaj-art-bc523d9236d341cd80a437802e321309 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-bc523d9236d341cd80a437802e3213092025-08-20T03:37:37ZengNature PortfolioNature Communications2041-17232025-07-0116112110.1038/s41467-025-60389-xKlf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identityGuangsong Su0Bohan Chen1Yingjie Song2Qingqing Yin3Wenbin Wang4Xueyuan Zhao5Sibo Fan6Jie Lian7Dongqing Li8Jinfang Bi9Peng Li10Zhongfang Zhao11Lei Zhang12Jiandang Shi13Wange Lu14Department of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityDepartment of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityDepartment of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityDepartment of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityDepartment of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityState Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityDepartment of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen UniversityAbstract Cell-specific super-enhancers (SEs) and master transcription factors (TFs) dynamically remodel embryonic stem cell (ESC) fate, yet their regulatory interplay remains unclear. By integrating multi-omics data (H3K27ac, Hi-C, scRNA-seq) across ESC states, we identified SEs interacting with master TFs, exemplified by the Klf5-adjacent SE (K5aSE). K5aSE deletion impaired proliferation, differentiation, and Klf5 expression, partially rescued by KLF5 reintroduction. Despite phenotypic similarities between Klf5-KO and K5aSE-KO ESCs, scRNA-seq of embryoid bodies revealed distinct differentiation trajectories, suggesting K5aSE targets beyond Klf5. High-throughput 3D genome screening demonstrated K5aSE activates four distal genes via chromatin looping. CRISPRa-mediated activation of these targets rescued K5aSE-KO phenotypes and uncovered their regulatory roles. Furthermore, CTCF depletion disrupted topologically associated domains (TADs) near K5aSE, suppressing Klf5 and target gene expression, indicating CTCF-mediated TADs sustain K5aSE activity. Our study unveils a 3D genome-dependent mechanism by which SEs govern ESC identity through coordinated TF interaction and multi-gene regulation.https://doi.org/10.1038/s41467-025-60389-x |
| spellingShingle | Guangsong Su Bohan Chen Yingjie Song Qingqing Yin Wenbin Wang Xueyuan Zhao Sibo Fan Jie Lian Dongqing Li Jinfang Bi Peng Li Zhongfang Zhao Lei Zhang Jiandang Shi Wange Lu Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity Nature Communications |
| title | Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity |
| title_full | Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity |
| title_fullStr | Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity |
| title_full_unstemmed | Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity |
| title_short | Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity |
| title_sort | klf5 adjacent super enhancer functions as a 3d genome structure dependent transcriptional driver to safeguard esc identity |
| url | https://doi.org/10.1038/s41467-025-60389-x |
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