EXPERIMENT_TITLE: GSM5606801: A673-EWS/FLI-KD-HiC 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: AMPure XP bead extraction in situ Hi-C (high throughput chromatin conformation capture)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma.  We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation.  Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines.  These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin. Overall design: in situ Hi-C of A673 Ewing sarcoma cells transduced with shRNA targeting EWS/FLI or Luciferase followed by rescue of EWS/FLI expression with a 3X-FLAG tagged EWS/FLI cDNA construct or empty vector
SAMPLE_TITLE: A673-EWS/FLI-KD-HiC 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A673 Ewing sarcoma cell line"}, {"TAG": "replicate", "VALUE": "2"}, {"TAG": "transduced shrna", "VALUE": "iEF + empty cDNA"}, {"TAG": "condition", "VALUE": "EF-KD"}]
Pool_Member_@attributes_sample_title: A673-EWS/FLI-KD-HiC 2
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