Project description:BackgroundAndrogen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10-100× more binding sites than differentially expressed genes. It is unclear how or if these excess binding sites impact gene transcription.ResultsTo characterize the regulatory logic of AR-mediated transcription, we generated a locus-specific map of enhancer activity by functionally testing all common clinical AR binding sites with Self-Transcribing Active Regulatory Regions sequencing (STARRseq). Only 7% of AR binding sites displayed androgen-dependent enhancer activity. Instead, the vast majority of AR binding sites were either inactive or constitutively active enhancers. These annotations strongly correlated with enhancer-associated features of both in vitro cell lines and clinical prostate cancer samples. Evaluating the effect of each enhancer class on transcription, we found that AR-regulated enhancers frequently interact with promoters and form central chromosomal loops that are required for transcription. Somatic mutations of these critical AR-regulated enhancers often impact enhancer activity.ConclusionsUsing a functional map of AR enhancer activity, we demonstrated that AR-regulated enhancers act as a regulatory hub that increases interactions with other AR binding sites and gene promoters.
Project description:In this study we functionally quantified the enhancer activity of all clinical ARBS. We demonstrated that only 7% of ARBS demonstrate androgen-dependent enhancer activation, while 11% have enhancer activity independent of AR binding. Almost all of these AR enhancers have not been previously studied. Surprisingly the vast majority of ARBS (81%) do not have significant enhancer activity. This in vitro annotation strongly correlated to clinical PCa samples. Integrating long-range chromatin interactome and transcriptomic data, we found androgen inducible enhancers were significantly more enriched to serve as anchors for gene looping and acted as a ?hub? to activate AR-regulated genes. To characterize the mechanism of AR enhancers we developed a deep neural network that can successfully predict active enhancers and identify key features for active enhancers. Finally, combining these results with whole genome sequencing of primary and metastatic PCa, we identified and characterized non-coding somatic SNVs that significantly impacted AR enhancer activity of a critical tumour suppressor.
Project description:In this study we functionally quantified the enhancer activity of all clinical ARBS. We demonstrated that only 7% of ARBS demonstrate androgen-dependent enhancer activation, while 11% have enhancer activity independent of AR binding. Almost all of these AR enhancers have not been previously studied. Surprisingly the vast majority of ARBS (81%) do not have significant enhancer activity. This in vitro annotation strongly correlated to clinical PCa samples. Integrating long-range chromatin interactome and transcriptomic data, we found androgen inducible enhancers were significantly more enriched to serve as anchors for gene looping and acted as a ‘hub’ to activate AR-regulated genes. To characterize the mechanism of AR enhancers we developed a deep neural network that can successfully predict active enhancers and identify key features for active enhancers. Finally, combining these results with whole genome sequencing of primary and metastatic PCa, we identified and characterized non-coding somatic SNVs that significantly impacted AR enhancer activity of a critical tumour suppressor.
