Genomics

Dataset Information

240

The Estrogen receptor alpha cistrome defined by DamIP


ABSTRACT: We have developed a new method to study DNA-protein interaction in vivo called DamIP, which is based on fusing a protein of interest to a mutant form of DNA adenine methylatransferase (Dam) from E. coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor alpha (hERα). In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq defined hERα cistrome overlaps significantly with those determined by ChIP-chip or ChIP-seq, but identifies many new binding regions. As shown by conventional ChIP assay, many DamIP-seq unique hERα binding regions show relatively stable hERα binding, whereas DamIP-seq misses some regions with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 days. 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. MCF7 cells were transfected with DamK9A or DamK9A-hERalpha. DamIP were performed from each sample and subjected to solexa sequencing

ORGANISM(S): Homo sapiens  

SUBMITTER: Yuanxin Xi   David D Moore  Rui Xiao  Deqiang Sun  Stephen Ayers 

PROVIDER: E-GEOD-33804 | ArrayExpress | 2011-11-19

SECONDARY ACCESSION(S): SRP009416GSE33804PRJNA148121

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Xiao Rui R   Sun Deqiang D   Ayers Stephen S   Xi Yuanxin Y   Li Wei W   Baxter John D JD   Moore David D DD  

Molecular endocrinology (Baltimore, Md.) 20111229 2


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 previ  ...[more]

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