Method

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

    • 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
Published February 1, 2022. https://doi.org/10.1101/gr.275986.121
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cover of Genome Research Vol 36 Issue 6
Current Issue:
June 2026, Vol. 36, No. 6
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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.

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