Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.
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.
Kwon
Young-Soo
YS
Department of Cellular and Molecular Medicine, University of California at San Diego School of Medicine, La Jolla, CA 92093-0651, USA.
Garcia-Bassets
Ivan
I
Hutt
Kasey R
KR
Cheng
Christine S
CS
Jin
Mingjie
M
Liu
Dongyan
D
Benner
Chris
C
Wang
Dong
D
Ye
Zhen
Z
Bibikova
Marina
M
Fan
Jian-Bing
JB
Duan
Lingxun
L
Glass
Christopher K
CK
Rosenfeld
Michael G
MG
Fu
Xiang-Dong
XD
D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004958:Estradiol / Q000494:pharmacology; D047628:Estrogen Receptor alpha / Q000378:metabolism*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D015894:Genome, Human / Q000187:drug effects / Q000235:genetics; D006657:Histones / Q000378:metabolism; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000187:drug effects / Q000235:genetics*; D011485:Protein Binding / Q000187:drug effects
D047628:Estrogen Receptor alpha; D006657:Histones; D004958:Estradiol