EXPERIMENT_TITLE: GSM3417096: T47D E180 1618f57a8_0e24fcc35; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In Situ Hi-C was performed according previously described protocol (Rao et al., 2014) with some modifications (Le Dily et al., 2017). Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which genes transcription is coordinately regulated in response to steroid hormones. Here we further described that responsive TADs contain 20-100 kb-long clusters of intermingled estrogen receptor (ER) and progesterone receptor (PR) binding sites, hereafter called Hormone-Control Regions (HCRs). In T47D cells, we identified more than 200 HCRs, which are frequently bound by unliganded ER and PR. These HCRs establish steady long-distance inter-TAD interactions between them and organize characteristic looping structures with promoters even in the absence of hormones in ER+-PR+ cells. This organization is dependent on the expression of the receptors and is further dynamically modulated in response to steroid hormones. HCRs function as platforms integrating different signals resulting in some cases in opposite transcriptional responses to estrogens or progestins. Altogether, these results suggest that steroid hormone receptors act not only as hormone-regulated sequence-specific transcription factors, but also as local and global genome organizers. Overall design: Three dimensional structural differences between ER+/PR+ and ER-/PR- cells were analysed by in situ Hi-C.
SAMPLE_TITLE: T47D E180 1618f57a8_0e24fcc35
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "T47D"}, {"TAG": "cell type", "VALUE": "ER+/PR+"}, {"TAG": "pre treatment", "VALUE": "Untreated"}, {"TAG": "pre treatment time", "VALUE": "0"}, {"TAG": "treatment", "VALUE": "Estrogen"}, {"TAG": "treatment time", "VALUE": "180"}, {"TAG": "sequencing core", "VALUE": "CNAG"}, {"TAG": "send for sequencing on", "VALUE": "1/18/2016"}, {"TAG": "sequencing index", "VALUE": "GTGAAA"}, {"TAG": "illumina machine", "VALUE": "Illumina HiSeq 2000"}, {"TAG": "application", "VALUE": "INHIC"}, {"TAG": "read length", "VALUE": "76"}, {"TAG": "restriction enzyme", "VALUE": "DpnII"}, {"TAG": "sequencing type", "VALUE": "PE"}, {"TAG": "library type", "VALUE": "hic"}]
Pool_Member_@attributes_sample_title: T47D E180 1618f57a8_0e24fcc35
RUN_SET_RUN_Pool_Member_@attributes_sample_title: T47D E180 1618f57a8_0e24fcc35
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