Base-pair resolution around androgen receptor motif matches reveals a unique pattern of protection by the androgen receptor. (a) Aggregate plot of DNase-seq signal around AR motif matches within poised DHS sites that also bind the AR. The pattern of DNase I cuts within the motif closely follows the known structure of the AR dimer as well as the information content of the AR DNA recognition motif determined de novo from ChIP-seq sequences that overlap DHS sites. (b) Aggregate DNase-seq signal centered around CTCF motif and (c) neuron-restrictive silencer factor (NRSF) matches genome-wide displaying a structurally different footprint from that of the AR. (d) Aggregate plot of DNase-seq signal around AR motif matches within DHS sites unique to LNCaP-induced cells that also bind the AR. (e) Aggregate plot of DNase-seq signal around the centers of 10,000 randomly sampled DHS sites shared between LNCaP and LNCaP-induced cells. Note that overall the aggregate signal is higher in LNCaP as compared to LNCaP-induced cells within all DHS sites. AR: androgen receptor; CTCF: CCCTC-binding factor; DHS: DNase I hypersensitive; DNase-seq: DNase I hypersensitivity analysis coupled with high-throughput sequencing; NRSF: neuron-restrictive silencer factor.
Tewari et al. Genome Biology 2012 13:R88 doi:10.1186/gb-2012-13-10-r88