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Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
BACKGROUND: An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in respon...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599885/ https://www.ncbi.nlm.nih.gov/pubmed/23368971 http://dx.doi.org/10.1186/1471-2164-14-70 |
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author | Wang, Junbai Lan, Xun Hsu, Pei-Yin Hsu, Hang-Kai Huang, Kun Parvin, Jeffrey Huang, Tim H-M Jin, Victor X |
author_facet | Wang, Junbai Lan, Xun Hsu, Pei-Yin Hsu, Hang-Kai Huang, Kun Parvin, Jeffrey Huang, Tim H-M Jin, Victor X |
author_sort | Wang, Junbai |
collection | PubMed |
description | BACKGROUND: An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in response to stimulation of environmental chemicals or hormones. RESULTS: In this study, using MCF7 cells as a model system, we found estrogen stimulation significantly impact chromatin interactions, leading to alteration of gene regulation and the associated histone modification states. Many chromosomal interaction regions at different levels of interaction frequency were identified. In particular, the top 10 hot regions with the highest interaction frequency are enriched with breast cancer specific genes. Furthermore, four types of E2-mediated strong differential (gain- or loss-) chromosomal (intra- or inter-) interactions were classified, in which the number of gain-chromosomal interactions is less than the number of loss-chromosomal interactions upon E2 stimulation. Finally, by integrating with eight histone modification marks, DNA methylation, regulatory elements regions, ERα and Pol-II binding activities, associations between epigenetic patterns and high chromosomal interaction frequency were revealed in E2-mediated gene regulation. CONCLUSIONS: The work provides insight into the effect of chromatin interaction on E2/ERα regulated downstream genes in breast cancer cells. |
format | Online Article Text |
id | pubmed-3599885 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35998852013-03-17 Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation Wang, Junbai Lan, Xun Hsu, Pei-Yin Hsu, Hang-Kai Huang, Kun Parvin, Jeffrey Huang, Tim H-M Jin, Victor X BMC Genomics Research Article BACKGROUND: An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in response to stimulation of environmental chemicals or hormones. RESULTS: In this study, using MCF7 cells as a model system, we found estrogen stimulation significantly impact chromatin interactions, leading to alteration of gene regulation and the associated histone modification states. Many chromosomal interaction regions at different levels of interaction frequency were identified. In particular, the top 10 hot regions with the highest interaction frequency are enriched with breast cancer specific genes. Furthermore, four types of E2-mediated strong differential (gain- or loss-) chromosomal (intra- or inter-) interactions were classified, in which the number of gain-chromosomal interactions is less than the number of loss-chromosomal interactions upon E2 stimulation. Finally, by integrating with eight histone modification marks, DNA methylation, regulatory elements regions, ERα and Pol-II binding activities, associations between epigenetic patterns and high chromosomal interaction frequency were revealed in E2-mediated gene regulation. CONCLUSIONS: The work provides insight into the effect of chromatin interaction on E2/ERα regulated downstream genes in breast cancer cells. BioMed Central 2013-01-31 /pmc/articles/PMC3599885/ /pubmed/23368971 http://dx.doi.org/10.1186/1471-2164-14-70 Text en Copyright ©2013 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wang, Junbai Lan, Xun Hsu, Pei-Yin Hsu, Hang-Kai Huang, Kun Parvin, Jeffrey Huang, Tim H-M Jin, Victor X Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title | Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title_full | Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title_fullStr | Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title_full_unstemmed | Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title_short | Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation |
title_sort | genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in e2-mediated gene regulation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599885/ https://www.ncbi.nlm.nih.gov/pubmed/23368971 http://dx.doi.org/10.1186/1471-2164-14-70 |
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