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| Status |
Public on Dec 21, 2023 |
| Title |
ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry (RNA-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF depletion, revealed that ZNF143 and CTCF collaborate to regulate higher-order genome organization. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate TAD formation and genome compartmentalization whereas directional recognition of DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.
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| Overall design |
We generated CTCF-AID cells by merging the AID tag with the CTCF gene in TiR1-expressing HEC-1-B cells.. We performed RNA sequencing on the cells to investigate changes in gene that treated with auxin for 0h or 24h.
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| Web link |
https://www.sciencedirect.com/science/article/pii/S2211124723016741?via%3Dihub
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| Contributor(s) |
Zhang M, Wu Q |
| Citation(s) |
38206813 |
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| Submission date |
Nov 27, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Mo Zhang |
| E-mail(s) |
zhangmo@alumni.sjtu.edu.cn
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| Organization name |
Shanghai Jiaotong University
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| Street address |
800 Dongchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE248737 |
ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry |
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| Relations |
| BioProject |
PRJNA1045677 |
