RT Journal
A1 He, Housheng Hansen
A1 Meyer, Clifford A.
A1 Chen, Mei Wei
A1 Jordan, V. Craig
A1 Brown, Myles
A1 Liu, X. Shirley
T1 Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics
JF Genome Research 
JO Genome Research 
YR 2012 
FD June 01 
VO 22 
IS 6 
SP 1015 
OP 1025 
DO 10.1101/gr.133280.111 
UL http://genome.cshlp.org/content/22/6/1015.abstract 
AB Transcription factor cistromes are highly cell-type specific. Chromatin accessibility, histone modifications, and nucleosome occupancy have all been found to play a role in defining these binding locations. Here, we show that hormone-induced DNase I hypersensitivity changes (ΔDHS) are highly predictive of androgen receptor (AR) and estrogen receptor 1 (ESR1) binding in prostate cancer and breast cancer cells, respectively. While chromatin structure prior to receptor binding and nucleosome occupancy after binding are strikingly different for ESR1 and AR, ΔDHS is highly predictive for both. AR binding is associated with changes in both local nucleosome occupancy and DNase I hypersensitivity. In contrast, while global ESR1 binding is unrelated to changes in nucleosome occupancy, DNase I hypersensitivity dynamics are also predictive of the ESR1 cistrome. These findings suggest that AR and ESR1 have distinct modes of interaction with chromatin and that DNase I hypersensitivity dynamics provides a general approach for predicting cell-type specific cistromes.