Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

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.

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

“…Because recent studies have shown that a nucleosome-depleted region (NDR) flanked on each side by a nucleosome having the active enhancer histone mark H3K27Ac is where TFs actually bind [5, 13], we used public and newly generated Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), DNaseI-seq, and FAIRE-seq datasets to further narrow enhancer regions (see Additional file 1: Supplementary Methods for a detailed description of the creation of the enhancer file and Additional file 2: Table S1 for a list of datasets). These narrowed regions represent the functional (TF binding) compartment of the larger regions defined by ChIP-seq data.…”

“…In C42B, RWPE1, MCF7, and MCF10A cells, H3K27Ac ChIP assays were performed using H3K27Ac antibody (Cat # 39133 Lot # 21311004, Active Motif, Carlsbad, CA, USA or ab4729 Abcam, Cambridge, MA, USA), as previously described [5, 35]. Each ChIP-seq experiment was performed in duplicate, and ChIP-seq libraries were sequenced on either Illumina Hiseq 2000 or Nextseq 500 machines.…”

“…Of note, the state most consistently linked to cellular identity is the ‘active enhancer’ state [2, 3]. In addition, previous studies have shown that epigenetic changes at enhancers are significantly better than those at promoters for predicting expression changes of target genes in cancer [4, 5]. …”

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

“…Unlike enhancers, which are located far from a TSS, are cell-type specific, and are closely linked to cellular identity (Rhie et al 2014(Rhie et al , 2016, promoter elements are crucial for basal transcription of genes. The majority of human promoters are classified as CpG island promoters; these promoters are generally active in most cell types (Deaton and Bird 2011).…”

Disturbing the histone code in leukemia: translocations and mutations affecting histone methyl transferases

“…The eventual outcome of different methyl marks not only depends on the modified residue itself, but also on the context of other posttranslational histone modifications on the same and neighboring nucleosomes (histone code) (15,16). To add a layer of complexity, recent research indicates that histone methylation may function in regulating gene expression by affecting nucleosome positioning (17,18). Furthermore, histone methylation is important for X inactivation, cell fate determination, and terminal differentiation (19,20).…”