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 sta

SUBMITTER: Rhie SK 

PROVIDER: S-EPMC4035062 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature