Research resource: The estrogen receptor α cistrome defined by DamIP

Mol Endocrinol. 2012 Feb;26(2):349-57. doi: 10.1210/me.2011-1080. Epub 2011 Dec 29.

Abstract

Gene expression is tightly regulated by transcription factors and cofactors that function by directly or indirectly interacting with DNA of the genome. Understanding how and where these proteins bind provides essential information to uncover genetic regulatory mechanisms. We have developed a new method to study DNA-protein interaction in vivo called DNA adenine methyltransferase (Dam)IP, which is based on fusing a protein of interest to a mutant form of Dam from Escherichia coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor (hER)α. In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq-defined hERα cistrome identifies many new binding regions and overlaps with those determined by chromatin immunoprecipitation (ChIP)-chip or ChIP-seq. Elements uniquely identified by DamIP-seq include a unique class of elements that show low, but persistent, hERα binding when reexamined by conventional ChIP. In contrast, DamIP-seq fails to detect some elements with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 d. In summary, the current study provides both an alternate view of the hERα cistrome to further understand the mechanism of hERα-mediated transcription and a new tool to explore other transcriptional factors and cofactors that is very different from conventional ChIP.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Cell Line, Tumor
  • Chromatin Immunoprecipitation
  • Chromosome Mapping
  • Escherichia coli Proteins / biosynthesis*
  • Escherichia coli Proteins / metabolism
  • Estrogen Receptor alpha / biosynthesis*
  • Estrogen Receptor alpha / metabolism
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Protein Binding
  • Recombinant Fusion Proteins / biosynthesis*
  • Recombinant Fusion Proteins / metabolism
  • Regulatory Elements, Transcriptional
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / biosynthesis*
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / metabolism

Substances

  • Escherichia coli Proteins
  • Estrogen Receptor alpha
  • Recombinant Fusion Proteins
  • estrogen receptor alpha, human
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)
  • dam protein, E coli