Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions

Stretched histone regions, such as super-enhancers and broad H3K4me3 domains, are associated with maintenance of cell identity and cancer. We connected super-enhancers and broad H3K4me3 domains in the K562 chronic myelogenous leukemia cell line as well as the MCF-7 breast cancer cell line with chrom...

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Main Authors: Cao, Fan, Fang, Yiwen, Tan, Hong Kee, Goh, Yufen, Choy, Jocelyn Yeen Hui, Koh, Bryan Thean Howe, Hao Tan, Jiong, Bertin, Nicolas, Ramadass, Aroul, Hunter, Ewan, Green, Jayne, Salter, Matthew, Akoulitchev, Alexandre, Wang, Wilson, Chng, Wee Joo, Tenen, Daniel G., Fullwood, Melissa Jane
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2017
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Online Access:https://hdl.handle.net/10356/83768
http://hdl.handle.net/10220/42747
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-837682023-02-28T17:03:16Z Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions Cao, Fan Fang, Yiwen Tan, Hong Kee Goh, Yufen Choy, Jocelyn Yeen Hui Koh, Bryan Thean Howe Hao Tan, Jiong Bertin, Nicolas Ramadass, Aroul Hunter, Ewan Green, Jayne Salter, Matthew Akoulitchev, Alexandre Wang, Wilson Chng, Wee Joo Tenen, Daniel G. Fullwood, Melissa Jane School of Biological Sciences Chronic myeloid leukaemia Genome informatics Stretched histone regions, such as super-enhancers and broad H3K4me3 domains, are associated with maintenance of cell identity and cancer. We connected super-enhancers and broad H3K4me3 domains in the K562 chronic myelogenous leukemia cell line as well as the MCF-7 breast cancer cell line with chromatin interactions. Super-enhancers and broad H3K4me3 domains showed higher association with chromatin interactions than their typical counterparts. Interestingly, we identified a subset of super-enhancers that overlap with broad H3K4me3 domains and show high association with cancer-associated genes including tumor suppressor genes. Besides cell lines, we could observe chromatin interactions by a Chromosome Conformation Capture (3C)-based method, in primary human samples. Several chromatin interactions involving super-enhancers and broad H3K4me3 domains are constitutive and can be found in both cancer and normal samples. Taken together, these results reveal a new layer of complexity in gene regulation by super-enhancers and broad H3K4me3 domains. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2017-06-27T09:19:08Z 2019-12-06T15:31:38Z 2017-06-27T09:19:08Z 2019-12-06T15:31:38Z 2017 Journal Article Cao, F., Fang, Y., Tan, H. K., Goh, Y., Choy, J. Y. H., Koh, B. T. H., et al. (2017). Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions. Scientific Reports, 7, 2186-. 2045-2322 https://hdl.handle.net/10356/83768 http://hdl.handle.net/10220/42747 10.1038/s41598-017-02257-3 en Scientific Reports © 2017 The Author(s) (Nature Publishing Group). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ 14 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Chronic myeloid leukaemia
Genome informatics
spellingShingle Chronic myeloid leukaemia
Genome informatics
Cao, Fan
Fang, Yiwen
Tan, Hong Kee
Goh, Yufen
Choy, Jocelyn Yeen Hui
Koh, Bryan Thean Howe
Hao Tan, Jiong
Bertin, Nicolas
Ramadass, Aroul
Hunter, Ewan
Green, Jayne
Salter, Matthew
Akoulitchev, Alexandre
Wang, Wilson
Chng, Wee Joo
Tenen, Daniel G.
Fullwood, Melissa Jane
Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
description Stretched histone regions, such as super-enhancers and broad H3K4me3 domains, are associated with maintenance of cell identity and cancer. We connected super-enhancers and broad H3K4me3 domains in the K562 chronic myelogenous leukemia cell line as well as the MCF-7 breast cancer cell line with chromatin interactions. Super-enhancers and broad H3K4me3 domains showed higher association with chromatin interactions than their typical counterparts. Interestingly, we identified a subset of super-enhancers that overlap with broad H3K4me3 domains and show high association with cancer-associated genes including tumor suppressor genes. Besides cell lines, we could observe chromatin interactions by a Chromosome Conformation Capture (3C)-based method, in primary human samples. Several chromatin interactions involving super-enhancers and broad H3K4me3 domains are constitutive and can be found in both cancer and normal samples. Taken together, these results reveal a new layer of complexity in gene regulation by super-enhancers and broad H3K4me3 domains.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Cao, Fan
Fang, Yiwen
Tan, Hong Kee
Goh, Yufen
Choy, Jocelyn Yeen Hui
Koh, Bryan Thean Howe
Hao Tan, Jiong
Bertin, Nicolas
Ramadass, Aroul
Hunter, Ewan
Green, Jayne
Salter, Matthew
Akoulitchev, Alexandre
Wang, Wilson
Chng, Wee Joo
Tenen, Daniel G.
Fullwood, Melissa Jane
format Article
author Cao, Fan
Fang, Yiwen
Tan, Hong Kee
Goh, Yufen
Choy, Jocelyn Yeen Hui
Koh, Bryan Thean Howe
Hao Tan, Jiong
Bertin, Nicolas
Ramadass, Aroul
Hunter, Ewan
Green, Jayne
Salter, Matthew
Akoulitchev, Alexandre
Wang, Wilson
Chng, Wee Joo
Tenen, Daniel G.
Fullwood, Melissa Jane
author_sort Cao, Fan
title Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
title_short Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
title_full Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
title_fullStr Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
title_full_unstemmed Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
title_sort super-enhancers and broad h3k4me3 domains form complex gene regulatory circuits involving chromatin interactions
publishDate 2017
url https://hdl.handle.net/10356/83768
http://hdl.handle.net/10220/42747
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