LAUSR

Introduction The chromatin landscape of mammalian cells underpins their transcriptional profiles, which then dictate fate and function. Mutations within chromatin remodelling genes have been implicated in early oesophageal adenocarcinoma (OAC) development, thus alterations in the chromatin landscape may pose an important molecular step in OAC development. OAC is often lethal, therefore genome-wide, basic research will provide foundations to develop new treatments and patient stratification methods. Material and methods We have used Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to profile the accessible chromatin landscape of normal oesophagus and oesophageal adenocarcinoma tissue samples, in addition to representative cell lines. Downstream analysis has involved bioinformatic de novo motif analysis and ATAC-footprinting, Chromatin immunoprecipitation with sequencing (ChIP-seq) and siRNA-mediated knockdowns. Results and discussions Our results revealed an altered chromatin landscape in cancerous tissue and identified ‘cancer-specific’ regions of accessibility. Using de novo motif discovery methods and footprinting analysis, we have identified enriched transcription factor motifs for GATA6 and HNF4A in differentially accessible regions and footprints. Also, comparison between the chromatin landscape of OAC cell-lines and OAC tissue identified the cell-line that best represents OAC tumours. HNF4A ChIP-seq and GATA6 ChIP-seq data, in oesophageal cancer cells, shows co-occupancy of HNF4A and GATA6 at 90% of sites and confirm motif enrichment and footprint observations. HNF4A and GATA6 knockdown experiments demonstrate overlap of gene regulation and also identify genes that are exclusively regulated by the presence HNF4A and GATA6. Importantly, genes directly regulated by HNF4A or GATA6 are on average overexpressed in OAC, however genes regulated by both factors are more overexpressed by 2-fold. Conclusion Our data demonstrate the power of ATAC-seq in genome-wide discovery methods and we have identified a novel HNF4A-GATA6 transcription network that is active in OAC.