Transcriptional programs establish and maintain cell identities. Regulation of gene expression is mediated by sequence-specific transcription factors (TFs) and cis-regulatory elements present in the genome. More recently, cell identity has been associated with lineage-defining super-enhancers: comprising dense TF platforms. Endothelial cells are key players of vascular integrity. The ETS TF ERG is constitutively expressed in endothelial cells and essential for endothelial lineage specification, vascular homeostasis and angiogenesis. However, the genomic programs that are regulated by ERG in endothelial cells are poorly understood. In this thesis, I show that ERG densely occupies super-enhancers in human umbilical vein endothelial cells (HUVEC), and its high occupancy can identify super-enhancers. I find that variants associated with cardiovascular disease are enriched in ERG-defined super-enhancers providing insight to the endothelial contribution to complex disease. Depletion of ERG causes profound modulation of the active enhancer mark H3K27ac genome-wide and in recruitment of the transcriptional co-activator Mediator complex. Loss of ERG leads to a decrease in 107 endothelial super-enhancers that have reduced co-occupancy of TFs GATA2 and AP-1. This indicates that ERG plays an essential role as a positive regulator of a core set of endothelial super-enhancers. Interestingly, aberrant ERG overexpression in prostate cancer via androgen-responsive TMPRSS2:ERG fusion proteins is oncogenic. Comparison between HUVEC and prostate cancer TMPRSS2:ERG fusion-positive VCaP cells revealed distinct lineage-specific transcriptome and super-enhancer profiles. In endothelial cells, I show that ERG is required at promoters and enhancers yet assembles distinct TF complexes at these two regions. ERG also colocalises with structural chromatin regulator CTCF in HUVEC, implying a role for ERG in coordinating chromatin structural organisation. Finally, I adopt CRISPR-Cas9 gene editing technology to genetically dissect the super-enhancer of adhesion molecular VE-cadherin. The mechanistic exploration of ERG and endothelial super-enhancers provide insight into the regulation of the endothelial-specific gene expression program.