chip and chip - seq libraries construction for histone marks h3k4me1/2/3 were performed as previously described 14 , the libraries were sequenced to 35bp with the illumina genome analyzer .
chip experiments for ar , nkx3.1 and oct-1 as well as chip - qpcr were performed as previously described 27 .
data sets of ar ( fdr of 5% ) and foxa1 ( fdr of 1% ) binding sites were from our previous works 16,25 .
nucleosome intervals were defined as the 200bp centered on the center position of the nps identified nucleosomes .
nucleosome pairs with center positions lying in a range between 250 and 450 bp were identified for further analysis . for each nucleosome pair the number of tags in the nucleosomes and in the inter - nucleosomal region was counted .
a tag was considered to belong to a genomic interval if , when shifted 73 bp in a strand directed direction , the entire tag fell within that interval .
these pairs are then given a nsd score ( s ) by the formula that takes into account changes in h3k4me2 chip - seq tag counts falling on the flanking nucleosomes as well as the region lying between them .
tag counts were scaled in proportion to the overall counts in the treatment and control samples . in this formula , n is the tag count , superscript  treat  and  control  refer to dht and vehicle conditions , respectively .
known dna motifs that are enriched relative to the center of model predicted tf binding sites were identified using the following statistic .
motif analysis was conducted on 600bp dna segments , each segment representing one nucleosome pair .
each segment was derived from a 1 kb sequence centered at the midpoint between a nucleosome pair from which 200bp centered on each of the nucleosomes was excluded .
all subsequences within these sequences were scored by a transfac motif 29 and the genomic background sequence composition to identify hits above a probability cutoff .
let xi , be a value between 0 and 1 , which denotes the relative location of motif hit i out of n total motif hits ( where 0 and 1 represent the respective center and edge of the sequence ) .
we define a z score , z=i=1 to n ( xi  0.5)/(n/12 ) that represents the positional bias of a motif toward the centers of the regions .
different integer cutoffs were tested for each motif , and the cutoff resulting in the highest z was selected .
this statistic is based on the assumptions that insignificant dna motifs will be uniformly distributed across the sequences and the null distribution of i = 1 to n xi can be estimated as the n - fold convolution of uniform density functions .
affymetrix u133 plus 2.0 microarray data were analyzed using the rma algorithm 30 using acustom cdf probe ( v11 ) mapping to refseq genes 31 .
differentially expressed genes were identified using the sam algorithm at a local fdr of 10% 32 .
the nearest putative tf binding sites were associated with each non - redundant refseq gene transcription start site .
the statistical significance association between putative tf binding sites was calculated using fisher s exact test where genes were categorized according to whether they were differentially expressed , and whether they had at least one putative tf binding site within 20 kb of the transcription start site .
chip and chip - seq libraries construction for histone marks h3k4me1/2/3 were performed as previously described 14 , the libraries were sequenced to 35bp with the illumina genome analyzer .
chip experiments for ar , nkx3.1 and oct-1 as well as chip - qpcr were performed as previously described 27 .
data sets of ar ( fdr of 5% ) and foxa1 ( fdr of 1% ) binding sites were from our previous works 16,25 .
nucleosome intervals were defined as the 200bp centered on the center position of the nps identified nucleosomes .
nucleosome pairs with center positions lying in a range between 250 and 450 bp were identified for further analysis . for each nucleosome pair the number of tags in the nucleosomes and in the inter - nucleosomal region was counted .
a tag was considered to belong to a genomic interval if , when shifted 73 bp in a strand directed direction , the entire tag fell within that interval .
these pairs are then given a nsd score ( s ) by the formula that takes into account changes in h3k4me2 chip - seq tag counts falling on the flanking nucleosomes as well as the region lying between them .
tag counts were scaled in proportion to the overall counts in the treatment and control samples . in this formula , n is the tag count , superscript  treat  and  control  refer to dht and vehicle conditions , respectively .
known dna motifs that are enriched relative to the center of model predicted tf binding sites were identified using the following statistic .
motif analysis was conducted on 600bp dna segments , each segment representing one nucleosome pair .
each segment was derived from a 1 kb sequence centered at the midpoint between a nucleosome pair from which 200bp centered on each of the nucleosomes was excluded .
all subsequences within these sequences were scored by a transfac motif 29 and the genomic background sequence composition to identify hits above a probability cutoff .
let xi , be a value between 0 and 1 , which denotes the relative location of motif hit i out of n total motif hits ( where 0 and 1 represent the respective center and edge of the sequence ) .
we define a z score , z=i=1 to n ( xi  0.5)/(n/12 ) that represents the positional bias of a motif toward the centers of the regions .
different integer cutoffs were tested for each motif , and the cutoff resulting in the highest z was selected .
this statistic is based on the assumptions that insignificant dna motifs will be uniformly distributed across the sequences and the null distribution of i = 1 to n xi can be estimated as the n - fold convolution of uniform density functions .
affymetrix u133 plus 2.0 microarray data were analyzed using the rma algorithm 30 using acustom cdf probe ( v11 ) mapping to refseq genes 31 .
differentially expressed genes were identified using the sam algorithm at a local fdr of 10% 32 .
the nearest putative tf binding sites were associated with each non - redundant refseq gene transcription start site .
the statistical significance association between putative tf binding sites was calculated using fisher s exact test where genes were categorized according to whether they were differentially expressed , and whether they had at least one putative tf binding site within 20 kb of the transcription start site .
 chromatin plays a central role in eukaryotic gene regulation . 
 we have performed genome - wide mapping of epigenetically - marked nucleosomes to determine their position both near transcription start sites and at distal regulatory elements including enhancers . in prostate cancer cells where androgen receptor ( ar ) binds primarily to enhancers 
 , we found that androgen treatment dismisses a central nucleosome present over ar binding sites that is flanked by a pair of marked nucleosomes . a novel quantitative model built on the behavior of such nucleosome pairs correctly identified regions bound by the regulators of the immediate androgen response including ar and foxa1 . 
 more importantly this model also correctly predicted novel binding sites for other transcription factors present following prolonged androgen stimulation including oct1 and nkx3.1 . 
 thus quantitative modeling of enhancer structure provides a powerful predictive method to infer the identity of transcription factors involved in cellular responses to specific stimuli . 
METHODS
ChIP-seq and ChIP-qPCR
Peak calling
AR and FoxA1 binding sites definition
Model for identifying differential transcription factor binding locations
Motif statistics
Gene expression analysis
Supplementary Material