Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation

Junbai Wang, Xun Lan, Pei Yin Hsu, Hang Kai Hsu, Kun Huang, Jeffrey Parvin, Hui-ming Huang, Victor X Jin

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number70
JournalBMC Genomics
Volume14
Issue number1
DOIs
StatePublished - Jan 31 2013

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Histone Code
Epigenomics
Chromatin
Genome
Genes
Chemical Stimulation
Breast Neoplasms
Nucleic Acid Regulatory Sequences
Neoplasm Genes
MCF-7 Cells
DNA Methylation
Estrogens
Hormones
Neoplasms

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

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, Hui-ming; Jin, Victor X.

In: BMC Genomics, Vol. 14, No. 1, 70, 31.01.2013.

Research output: Contribution to journalArticle

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AU - Huang, Kun

AU - Parvin, Jeffrey

AU - Huang, Hui-ming

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