Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer

Methods Mol Biol. 2016:1366:79-98. doi: 10.1007/978-1-4939-3127-9_8.

Abstract

Chromatin immunoprecipitation-sequencing (ChIP-Seq) is a powerful tool which combines the established method of ChIP with next-generation sequencing (NGS) to determine DNA-binding sites of a protein of interest on a genome-wide level, importantly, allowing for de novo discovery of binding events. Here we describe ChIP-seq using the well-established example of estrogen receptor-α mapping in the MCF7 breast cancer cell line.

Keywords: Chromatin; Chromatin immunoprecipitation; Enhancers; Estrogen receptor; Next-generation sequencing; Promoters.

MeSH terms

  • Binding Sites
  • Breast Neoplasms / genetics
  • Breast Neoplasms / metabolism*
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation*
  • Computational Biology
  • Databases, Genetic
  • Estrogen Receptor alpha / genetics
  • Estrogen Receptor alpha / metabolism*
  • Female
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • MCF-7 Cells
  • Polymerase Chain Reaction
  • Protein Binding
  • Sequence Analysis, DNA*
  • Workflow

Substances

  • Chromatin
  • ESR1 protein, human
  • Estrogen Receptor alpha