Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

Proc Natl Acad Sci U S A. 2014 May 20;111(20):7319-24. doi: 10.1073/pnas.1324151111. Epub 2014 Apr 28.


The androgen receptor (AR) is a key factor that regulates the behavior and fate of prostate cancer cells. The AR-regulated network is activated when AR binds enhancer elements and modulates specific enhancer-promoter looping. Kallikrein-related peptidase 3 (KLK3), which codes for prostate-specific antigen (PSA), is a well-known AR-regulated gene and its upstream enhancers produce bidirectional enhancer RNAs (eRNAs), termed KLK3e. Here, we demonstrate that KLK3e facilitates the spatial interaction of the KLK3 enhancer and the KLK2 promoter and enhances long-distance KLK2 transcriptional activation. KLK3e carries the core enhancer element derived from the androgen response element III (ARE III), which is required for the interaction of AR and Mediator 1 (Med1). Furthermore, we show that KLK3e processes RNA-dependent enhancer activity depending on the integrity of core enhancer elements. The transcription of KLK3e was detectable and its expression is significantly correlated with KLK3 (R(2) = 0.6213, P < 5 × 10(-11)) and KLK2 (R(2) = 0.5893, P < 5 × 10(-10)) in human prostate tissues. Interestingly, RNAi silencing of KLK3e resulted in a modest negative effect on prostate cancer cell proliferation. Accordingly, we report that an androgen-induced eRNA scaffolds the AR-associated protein complex that modulates chromosomal architecture and selectively enhances AR-dependent gene expression.

Keywords: KLK3e/AR/Med1 complex; chromosomal looping.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • COS Cells
  • Cell Line, Tumor
  • Chlorocebus aethiops
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Neoplastic*
  • Gene Silencing
  • Humans
  • Kallikreins / metabolism
  • Male
  • Mediator Complex Subunit 1 / metabolism
  • Promoter Regions, Genetic
  • Prostate / metabolism
  • Prostate-Specific Antigen / metabolism
  • Prostatic Neoplasms / metabolism*
  • RNA Interference
  • Receptors, Androgen / metabolism*
  • Regulatory Sequences, Nucleic Acid
  • Tissue Kallikreins / metabolism
  • Transcription, Genetic
  • Transcriptional Activation


  • AR protein, human
  • MED1 protein, human
  • Mediator Complex Subunit 1
  • Receptors, Androgen
  • Kallikreins
  • kallikrein-related peptidase 3, human
  • Tissue Kallikreins
  • Prostate-Specific Antigen