Abstract
p53-bound enhancer regions produce noncoding RNAs and interact with distant target genes.
Major finding: p53-bound enhancer regions produce noncoding RNAs and interact with distant target genes.
Concept: p53-induced enhancer RNAs (eRNA) are required for efficient p53-dependent cell-cycle arrest.
Impact: p53 may have additional target genes regulated by long-range interactions and eRNA activity.
Most p53 mutations affect its sequence-specific DNA binding domain, suggesting that p53 tumor suppression activity is largely attributable to regulation of gene expression. However, recent findings suggesting that p53-dependent regulation of known protein-coding target genes is dispensable for some aspects of tumor suppression, such as induction of cellular senescence, prompted Melo and colleagues to analyze genome-wide p53 binding data to identify additional p53 targets. p53 binding levels similar to those at canonical p53 target gene promoters were observed at intergenic regions with histone modifications characteristic of enhancers, which the authors named p53-bound enhancer regions (p53BER). Reporter assays of several p53BERs showed that these sequences had transcriptional enhancing activity that was dependent on p53. Furthermore, chromosome conformation capture combined with next-generation sequencing showed that p53BERs interacted intrachromosomally with multiple neighboring genes, many of which required p53 for full expression even though significant p53 binding was not observed at their promoters. p53 binding at p53BERs was not required for establishment of these long-range interactions but was required for production of enhancer RNAs (eRNA), long noncoding nonpolyadenylated RNAs that are produced bidirectionally by RNA polymerase II at enhancers. Use of siRNAs targeting eRNAs produced at individual p53BERs showed that eRNAs were required for expression of neighboring genes after p53 activation, several of which were required for efficient p53-dependent cell-cycle arrest after ionizing irradiation. Taken together, these findings suggest that p53 may directly regulate target genes through mechanisms other than promoter binding and raise the possibility that p53BERs play key roles in p53-dependent signaling.