NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo1,7,
- Ran Zhang2,7,
- Tengfei Hu3,7,
- Yuting Zhu3,
- Yueming Wu3,
- Wenfei Li4,
- Zhi Zhang5,
- Xuebiao Yao6,
- Haiyi Liang2 and
- Xiaoyuan Song1,3
- 1Department of Urology, the First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China;
- 2CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, 230027, China;
- 3MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China;
- 4Affiliated Psychological Hospital of Anhui Medical University, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui, 230022, China;
- 5CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China;
- 6MOE Key Laboratory for Cellular Dynamics, University of Science and Technology of China, Hefei, Anhui, 230027, China
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↵7 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275986.121.
- Received August 10, 2021.
- Accepted January 25, 2022.
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