COUP-TFII is a modulator of cell-type-specific genetic programs based on genomic localization maps

Chicken ovalbumin upstream promoter transcription factor II (COUP-TFII) is a member of the steroid/thyroid hormone receptor superfamily, but its ligand has not yet been identified. Little is known about the role of the COUP-TFII nuclear receptor in cancer cells. In this study, we mapped the cistrome of COUP-TFII in three different cancer cells, namely breast cancer cells (MCF-7), myelogenous leukaemia cells (K562) and liver cancer cells (HepG2) using publicly available ChIP-seq data. Our results show that COUP-TFII co-localises with master transcription factors (TFs) in a cell-specific manner such as estrogen receptor alpha in MCF-7, hepatocyte nuclear factor alpha in HepG2, and GATA-binding factor in K562, while the shared, non-specific COUP-TFII binding sites are co-occupied by CTCF. We identified chromatin environments for these COUP-TFII and master TF co-bound sites together with COUP-TFII and CTCF co-bound sites. Our results show that COUP-TFII and master TF co-bound sites are marked with active enhancer specific histone modifications (H3K27ac and H3K4me1), while COUP-TFII and CTCF co-bound sites reveal active promoter specific histone marks (H3K27ac and H3K4me3). These results describe the genomic context and role of COUP-TFII in the cell-type specific transcriptional programs. Furthermore, we report that the VEGFA gene regulated by shared COUP-TFII and CTCF co-bound regulatory elements is involved in long-range looping in a cell-type-independent manner. These findings provide a genomic insight into the regulation and angiogenic role of COUP-TFII.