Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [ChIP-Seq]

We profiled fresh-frozen esophageal tumor and normal samples and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Overall design: Esophageal Cancer and normal cell lines and fresh-frozen tissues were harvested, and ChIPseq was performed using H3K27Ac and transcription factor antibodies.