Functional mapping of androgen receptor enhancer activity

Chia Chi Flora Huang ,Simon Linder,Henk Van Der Poel,Martin Gleave ,Doğancan Özturan ,Stéphane Le Bihan ,Umut Berkay Altıntaş ,Tunç Morova ,Colin C Collins ,Mohammadali Saffarzadeh,Wilbert Zwart,Funda Sar,Suzan Stelloo,Faraz Hach,Eldon Emberly,Andries M Bergman,Shreyas Lingadahalli,Felix Y Feng,Brian Mcconeghy,Eugene Hu,Ivan Pak Lok Yu,Bengul Gokbayrak,Marlous Hoogstraat,Nathan A Lack

doi:10.1186/s13059-021-02339-6

Abstract

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.

Highlights

Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer
We demonstrated that only 7% of AR binding sites (ARBS) have androgen-dependent enhancer activation, while 11% had enhancer activity that was independent of AR binding
By quantifying the relative rate of self-transcribed RNA with nextgeneration sequencing, the enhancer activity can be directly measured. During optimization of this method, we found that similar to published work [24], smaller ARBS inserts (< 250 bp) had lower STARRseq activity, suggesting that the flanking sequences contribute to AR enhancer activity (Additional file 1: Fig. S1)

Summary

Introduction

Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. The AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Androgen receptor (AR)-mediated transcription is the primary driver of prostate cancer (PCa) growth and proliferation [1] Activation of this critical signaling pathway occurs when AR binds to androgens such as testosterone or dihydrotestosterone (DHT). This induces the translocation of the AR into the nucleus, where it interacts with DNA at AR binding sites (ARBS). Once bound to DNA, the AR recruit numerous co-activators (CBP/p300, SRC/ p160), chromatin modifiers (SWI/SNF-BRG1), and co-repressors (HDAC, NCoR) in a highly coordinated manner [6] This protein complex physically interacts with gene promoters via chromosomal loops, activating basal transcriptional machinery to drive transcription. Characterization of ARBS enhancer activity is critical to interpret the underlying regulatory logic of this transcription factor

Methods

Results

Conclusion