title: Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells.
abstract: BACKGROUND
  The 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).
  
  
  RESULTS
  Enhancers 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.
  
  
  CONCLUSIONS
  These 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.
authors.forename: Suhn Kyong
authors.initials: SK
authors.lastname: Rhie
authors.forename: Dennis J
authors.initials: DJ
authors.lastname: Hazelett
authors.forename: Simon G
authors.initials: SG
authors.lastname: Coetzee
authors.forename: Chunli
authors.initials: C
authors.lastname: Yan
authors.forename: Houtan
authors.initials: H
authors.lastname: Noushmehr
authors.affiliation: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. coetzee@usc.edu.
authors.forename: Gerhard A
authors.initials: GA
authors.lastname: Coetzee
mesh_terms: D045744:Cell Line, Tumor; D005260:Female; D006657:Histones / Q000378:metabolism*; D006801:Humans; D042361:Mammary Glands, Human / Q000378:metabolism* / Q000473:pathology; D009707:Nucleosomes; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors