Research resource: The estrogen receptor ? cistrome defined by DamIP.

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)?. In current study, we present the cistrome of hER? determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq-defined hER? 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, hER? binding when reexamined by conventional ChIP. In contrast, DamIP-seq fails to detect some elements with very transient hER? 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 hER? cistrome to further understand the mechanism of hER?-mediated transcription and a new tool to explore other transcriptional factors and cofactors that is very different from conventional ChIP.

SUBMITTER: Xiao R 

PROVIDER: S-EPMC3384088 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature