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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896462/ https://www.ncbi.nlm.nih.gov/pubmed/35105668 http://dx.doi.org/10.1101/gr.275986.121 |
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author | Luo, Zhengyu Zhang, Ran Hu, Tengfei Zhu, Yuting Wu, Yueming Li, Wenfei Zhang, Zhi Yao, Xuebiao Liang, Haiyi Song, Xiaoyuan |
author_facet | Luo, Zhengyu Zhang, Ran Hu, Tengfei Zhu, Yuting Wu, Yueming Li, Wenfei Zhang, Zhi Yao, Xuebiao Liang, Haiyi Song, Xiaoyuan |
author_sort | Luo, Zhengyu |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8896462 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-88964622022-09-01 NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution Luo, Zhengyu Zhang, Ran Hu, Tengfei Zhu, Yuting Wu, Yueming Li, Wenfei Zhang, Zhi Yao, Xuebiao Liang, Haiyi Song, Xiaoyuan Genome Res Method 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. Cold Spring Harbor Laboratory Press 2022-03 /pmc/articles/PMC8896462/ /pubmed/35105668 http://dx.doi.org/10.1101/gr.275986.121 Text en © 2022 Luo et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) . |
spellingShingle | Method Luo, Zhengyu Zhang, Ran Hu, Tengfei Zhu, Yuting Wu, Yueming Li, Wenfei Zhang, Zhi Yao, Xuebiao Liang, Haiyi Song, Xiaoyuan NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title | NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title_full | NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title_fullStr | NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title_full_unstemmed | NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title_short | NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution |
title_sort | nice-c efficiently reveals open chromatin–associated chromosome interactions at high resolution |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896462/ https://www.ncbi.nlm.nih.gov/pubmed/35105668 http://dx.doi.org/10.1101/gr.275986.121 |
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