NicE-C efficiently reveals open chromatin-associated chromosome interactions at high resolution
- Zhengyu Luo1,
- Ran Zhang2,
- Tengfei Hu1,
- Yuting Zhu1,
- Yueming Wu1,
- Wenfei Li3,
- Zhi Zhang4,
- Xuebiao Yao5,
- Haiyi Liang2 and
- Xiaoyuan Song1,6
- 1 MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China;
- 2 CAS Key Laboratory of Mechanical Behavior and Design of Materials, University of Science and Technology of China;
- 3 Affiliated Psychological Hospital of Anhui Medical University, Hefei Fourth People's Hospital, Anhui Mental Health Center;
- 4 CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China;
- 5 MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Anhui Key Laboratory for Cellular Dynamics and Chemical Biology
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.
- Received August 10, 2021.
- Accepted January 25, 2022.
- Published by Cold Spring Harbor Laboratory Press
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