Abstract
BackgroundThe precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown. Here we identified cell type specific enhancers coupled with gene expression in two different types of breast epithelial cells, HMEC (normal breast epithelial cells) and MDAMB231 (triple negative breast cancer cell line).ResultsEnhancers were defined by modified neighboring histones [using chromatin immunoprecipitation followed by sequencing (ChIP-seq)] and nucleosome depletion [using formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq)]. Histone modifications at enhancers were related to the expression levels of nearby genes up to 750 kb away. These expression levels were correlated with enhancer status (poised or active), defined by surrounding histone marks. Furthermore, about fifty percent of poised and active enhancers contained nucleosome-depleted regions. We also identified response element motifs enriched at these enhancer sites that revealed key transcription factors (e.g. TP63) likely involved in regulating breast epithelial enhancer-mediated gene expression. By utilizing expression data, potential target genes of more than 600 active enhancers were identified. These genes were involved in proteolysis, epidermis development, cell adhesion, mitosis, cell cycle, and DNA replication.ConclusionsThese findings facilitate the understanding of epigenetic regulation specifically, such as the relationships between regulatory elements and gene expression and generally, how breast epithelial cellular phenotypes are determined by cell type specific enhancers.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-331) contains supplementary material, which is available to authorized users.
Highlights
The precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown
In order to verify the method used to identify cell type specific enhancers, we compared our human mammary epithelial cell (HMEC) specific enhancer loci (HSEL) with enhancers classified by using a multivariate Hidden Markov Model in HMEC from ENCODE database [21]
At HMEC specific enhancer loci (HSEL), H3K4me1 marks were highly enriched in HMEC, compared to MDAMB231 with more than 60 fold higher mean density of H3K4me1 Chromatin immunoprecipitation (ChIP)-seq tags (Figure 1A)
Summary
The precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown. The specific mechanism(s), Genomic DNA is organized into chromatin; 147 base pairs of DNA are wrapped around two copies of each of the core histone proteins, namely H2A, H2B, H3, and H4, forming a single octameric nucleosome core particle. By contrast, chromatin is relatively ‘open’ or loosely packaged, forming ‘beads on a string’ structures. In this open form, gene regulatory proteins may bind to the DNA, and nuclear processes such as transcription can be performed and influenced by dynamic nucleosome positioning [3]. Nucleosome position and histone marks play important roles to demarcate regulatory elements such as promoters, enhancers, and repressed regions
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