PMID- 22508765
OWN - NLM
STAT- MEDLINE
DCOM- 20121207
LR  - 20211021
IS  - 1549-5469 (Electronic)
IS  - 1088-9051 (Print)
IS  - 1088-9051 (Linking)
VI  - 22
IP  - 6
DP  - 2012 Jun
TI  - Differential DNase I hypersensitivity reveals factor-dependent chromatin 
      dynamics.
PG  - 1015-25
LID - 10.1101/gr.133280.111 [doi]
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 (DeltaDHS) 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, DeltaDHS 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.
FAU - He, Housheng Hansen
AU  - He HH
AD  - Department of Biostatistics and Computational Biology, Dana-Farber Cancer 
      Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA;
FAU - Meyer, Clifford A
AU  - Meyer CA
FAU - Chen, Mei Wei
AU  - Chen MW
FAU - Jordan, V Craig
AU  - Jordan VC
FAU - Brown, Myles
AU  - Brown M
FAU - Liu, X Shirley
AU  - Liu XS
LA  - eng
SI  - GEO/GSE33216
GR  - R01 DK074967/DK/NIDDK NIH HHS/United States
GR  - P50 CA090381/CA/NCI NIH HHS/United States
GR  - 2P50 CA090381-06/CA/NCI NIH HHS/United States
GR  - 1R01 GM099409/GM/NIGMS NIH HHS/United States
GR  - P30 CA051008/CA/NCI NIH HHS/United States
GR  - R01 GM099409/GM/NIGMS NIH HHS/United States
GR  - GM099409/GM/NIGMS NIH HHS/United States
GR  - 2R01 DK074967-06/DK/NIDDK NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20120416
PL  - United States
TA  - Genome Res
JT  - Genome research
JID - 9518021
RN  - 0 (AR protein, human)
RN  - 0 (Chromatin)
RN  - 0 (ESR1 protein, human)
RN  - 0 (Estrogen Receptor alpha)
RN  - 0 (Estrogens)
RN  - 0 (FOXA1 protein, human)
RN  - 0 (Hepatocyte Nuclear Factor 3-alpha)
RN  - 0 (Nucleosomes)
RN  - 0 (Receptors, Androgen)
RN  - 0 (Transcription Factors)
RN  - EC 2.3.1.48 (NCOA3 protein, human)
RN  - EC 2.3.1.48 (Nuclear Receptor Coactivator 3)
RN  - EC 3.1.21.1 (Deoxyribonuclease I)
SB  - IM
MH  - Binding Sites
MH  - Breast Neoplasms/genetics/metabolism
MH  - Cell Line, Tumor
MH  - Chromatin/*metabolism
MH  - Deoxyribonuclease I/*metabolism
MH  - Estrogen Receptor alpha/*metabolism
MH  - Estrogens/metabolism/pharmacology
MH  - Female
MH  - Hepatocyte Nuclear Factor 3-alpha/metabolism
MH  - Humans
MH  - Male
MH  - Nuclear Receptor Coactivator 3/metabolism
MH  - Nucleosomes/metabolism
MH  - Predictive Value of Tests
MH  - Prostatic Neoplasms/drug therapy/genetics/metabolism
MH  - Receptors, Androgen/*metabolism
MH  - Transcription Factors/metabolism
PMC - PMC3371710
EDAT- 2012/04/18 06:00
MHDA- 2012/12/12 06:00
PMCR- 2012/12/01
CRDT- 2012/04/18 06:00
PHST- 2012/04/18 06:00 [entrez]
PHST- 2012/04/18 06:00 [pubmed]
PHST- 2012/12/12 06:00 [medline]
PHST- 2012/12/01 00:00 [pmc-release]
AID - gr.133280.111 [pii]
AID - 10.1101/gr.133280.111 [doi]
PST - ppublish
SO  - Genome Res. 2012 Jun;22(6):1015-25. doi: 10.1101/gr.133280.111. Epub 2012 Apr 16.