Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.
|Title||Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.|
|Publication Type||Journal Article|
|Year of Publication||2007|
|Authors||Kwon Y-S, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan J-B, Duan L, Glass CK, Rosenfeld MG, Fu X-D|
|Journal||Proc Natl Acad Sci U S A|
|Date Published||2007 Mar 20|
|Keywords||Breast Neoplasms, Cell Line, Tumor, Chromatin Immunoprecipitation, Estradiol, Estrogen Receptor alpha, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Histones, Humans, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Protein Binding|
ChIP coupled with microarray provides a powerful tool to determine in vivo binding profiling of transcription factors to deduce regulatory circuitries in mammalian cells. Aiming at improving the specificity and sensitivity of such analysis, we developed a new technology called ChIP-DSL using the DNA selection and ligation (DSL) strategy, permitting robust analysis with much reduced materials compared with standard procedures. We profiled general and sequence-specific DNA binding transcription factors using a full human genome promoter array based on the ChIP-DSL technology, revealing an unprecedented number of the estrogen receptor (ERalpha) target genes in MCF-7 cells. Coupled with gene expression profiling, we found that only a fraction of these direct ERalpha target genes were highly responsive to estrogen and that the expression of those ERalpha-bound, estrogen-inducible genes was associated with breast cancer progression in humans. This study demonstrates the power of the ChIP-DSL technology in revealing regulatory gene expression programs that have been previously invisible in the human genome.
|Alternate Journal||Proc. Natl. Acad. Sci. U.S.A.|