Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity
© 2022. The Author(s)..
The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:13 |
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| Enthalten in: |
Nature communications - 13(2022), 1 vom: 11. März, Seite 1293 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Li, Mingsen [VerfasserIn] |
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| Links: |
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| Themen: |
CCCTC-Binding Factor |
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| Anmerkungen: |
Date Completed 05.04.2022 Date Revised 10.11.2022 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1038/s41467-022-28966-6 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM338083197 |
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| 245 | 1 | 0 | |a Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity |
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| 520 | |a © 2022. The Author(s). | ||
| 520 | |a The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia | ||
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| 700 | 1 | |a Huang, Huaxing |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Bofeng |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Shaoshuai |e verfasserin |4 aut | |
| 700 | 1 | |a Guo, Huizhen |e verfasserin |4 aut | |
| 700 | 1 | |a Zhu, Liqiong |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Siqi |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Jiafeng |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Lan, Xihong |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Wang |e verfasserin |4 aut | |
| 700 | 1 | |a Zhu, Jin |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Fuxi |e verfasserin |4 aut | |
| 700 | 1 | |a Tan, Jieying |e verfasserin |4 aut | |
| 700 | 1 | |a Mao, Zhen |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Chunqiao |e verfasserin |4 aut | |
| 700 | 1 | |a Ji, Jianping |e verfasserin |4 aut | |
| 700 | 1 | |a Ding, Junjun |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Kang |e verfasserin |4 aut | |
| 700 | 1 | |a Yuan, Jin |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Yizhi |e verfasserin |4 aut | |
| 700 | 1 | |a Ouyang, Hong |e verfasserin |4 aut | |
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