Dissecting super-enhancer hierarchy based on chromatin interactions

Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically...

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Autores principales: Huang, Jialiang, Li, Kailong, Cai, Wenqing, Liu, Xin, Zhang, Yuannyu, Orkin, Stuart H., Xu, Jian, Yuan, Guo-Cheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838163/
https://www.ncbi.nlm.nih.gov/pubmed/29507293
http://dx.doi.org/10.1038/s41467-018-03279-9
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author Huang, Jialiang
Li, Kailong
Cai, Wenqing
Liu, Xin
Zhang, Yuannyu
Orkin, Stuart H.
Xu, Jian
Yuan, Guo-Cheng
author_facet Huang, Jialiang
Li, Kailong
Cai, Wenqing
Liu, Xin
Zhang, Yuannyu
Orkin, Stuart H.
Xu, Jian
Yuan, Guo-Cheng
author_sort Huang, Jialiang
collection PubMed
description Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.
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spelling pubmed-58381632018-03-08 Dissecting super-enhancer hierarchy based on chromatin interactions Huang, Jialiang Li, Kailong Cai, Wenqing Liu, Xin Zhang, Yuannyu Orkin, Stuart H. Xu, Jian Yuan, Guo-Cheng Nat Commun Article Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization. Nature Publishing Group UK 2018-03-05 /pmc/articles/PMC5838163/ /pubmed/29507293 http://dx.doi.org/10.1038/s41467-018-03279-9 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Huang, Jialiang
Li, Kailong
Cai, Wenqing
Liu, Xin
Zhang, Yuannyu
Orkin, Stuart H.
Xu, Jian
Yuan, Guo-Cheng
Dissecting super-enhancer hierarchy based on chromatin interactions
title Dissecting super-enhancer hierarchy based on chromatin interactions
title_full Dissecting super-enhancer hierarchy based on chromatin interactions
title_fullStr Dissecting super-enhancer hierarchy based on chromatin interactions
title_full_unstemmed Dissecting super-enhancer hierarchy based on chromatin interactions
title_short Dissecting super-enhancer hierarchy based on chromatin interactions
title_sort dissecting super-enhancer hierarchy based on chromatin interactions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838163/
https://www.ncbi.nlm.nih.gov/pubmed/29507293
http://dx.doi.org/10.1038/s41467-018-03279-9
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