NicE-C efficiently reveals open chromatin-associated chromosome interactions at high resolution

Enhancer-promoter communication is known to regulate spatiotemporal dynamics of gene expression. Several methods are available to capture enhancer-promoter interactions, but they either require large amounts of starting materials and are costly, or provide a relative low resolution in chromatin cont...

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Bibliographic Details
Published in:Genome research 2022-03, Vol.32 (3), p.534-544
Main Authors: Luo, Zhengyu, Zhang, Ran, Hu, Tengfei, Zhu, Yuting, Wu, Yueming, Li, Wenfei, Zhang, Zhi, Yao, Xuebiao, Liang, Haiyi, Song, Xiaoyuan
Format: Article
Language:English
Subjects:
Aging
Animal models
Animals
Chromatin
Chromatin - genetics
Chromosomes
Chromosomes - genetics
Conformation
Enhancer Elements, Genetic
Enzymes
Gene expression
Gene mapping
Kidneys
Method
Mice
Nicking endonuclease
Promoter Regions, Genetic
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Summary:Enhancer-promoter communication is known to regulate spatiotemporal dynamics of gene expression. Several methods are available to capture enhancer-promoter interactions, but they either require large amounts of starting materials and are costly, or provide a relative low resolution in chromatin contact maps. Here, we present nicking enzyme-assisted open chromatin interaction capture (NicE-C), a method that leverages nicking enzyme-mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of open chromatin interactions at high resolution, especially enhancer-promoter interactions. Using TNF stimulation and mouse kidney aging as models, we applied NicE-C to reveal characteristics of dynamic enhancer-promoter interactions.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.275986.121