Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA

Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell type-specific gene expression programs1-4, but how those enhancers are exploited to institute alternative, signal-dependent transcriptional responses remains poorly understood. Here we present evidence that cell lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), to act on structurally- and functionally-distinct classes of enhancers. Consequently, FoxA1 down-regulation, an unfavorable prognostic sign in certain advanced prostate tumors, triggers dramatic reprogramming of the hormonal response by causing a massive switch in AR binding to a distinct cohort of pre-established enhancers. These enhancers are functional, as evidenced by the production of enhancer-templated non-coding RNA (eRNA5) based on global nuclear-on (GRO-seq) analysis6, with a unique class apparently requiring no nucleosome remodeling to induce specific enhancer-promoter looping and gene activation. GRO-seq data also suggest that liganded AR induces both transcription initiation and elongation. Together, these findings reveal a large repository of active enhancers that can be dynamically tuned to elicit alternative gene expression programs, which may underlie many sequential gene expression events in development, cell differentiation and disease progression.