Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

Abstract

p53 binds enhancers to regulate key target genes. Here, we globally mapped p53-regulated enhancers by looking at enhancer RNA (eRNA) production. Intriguingly, while many p53-induced enhancers contained p53-binding sites, most did not. As long non-coding RNAs (lncRNAs) are prominent regulators of chromatin dynamics, we hypothesized that p53-induced lncRNAs contribute to the activation of enhancers by p53. Among p53-induced lncRNAs, we identified LED and demonstrate that its suppression attenuates p53 function. Chromatin-binding and eRNA expression analyses show that LED associates with and activates strong enhancers. One prominent target of LED was located at an enhancer region within CDKN1A gene, a potent p53-responsive cell cycle inhibitor. LED knockdown reduces CDKN1A enhancer induction and activity, and cell cycle arrest following p53 activation. Finally, promoter-associated hypermethylation analysis shows silencing of LED in human tumours. Thus, our study identifies a new layer of complexity in the p53 pathway and suggests its dysregulation in cancer.

Expanding the p53 regulatory network: LncRNAs take up the challenge

“…Surprisingly, a consistent number of p53-induced eRNAs were not bound by p53, suggesting that an indirect mediator of p53 activation should be involved [77].…”

“…Notably, LED depletion can affect p53 response and impair cell cycle arrest since one of the enhancer regions bound and activated by LED is located within the p21-coding gene. In this context, LED knockdown fails to activate its target enhancer locus in the p21 gene, leading to a reduction in p21 expression and, consequently, a decrease in p53-mediated proliferation arrest [77].…”

Neat1 is a p53-inducible lincRNA essential for transformation suppression

“…These findings have raised the question of which p53 target genes are therefore the most essential for suppressing tumorigenesis. Recent genomic approaches, including ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing), have helped to identify new p53-regulated genes whose biological functions in the p53 tumor suppression pathway could be explored (Kenzelmann Broz et al 2013;Sánchez et al 2014;Léveillé et al 2015;Younger et al 2015).…”

The bright side of dark matter: lncRNAs in cancer

“…CTBP1-AS directly inhibits CTBP1 transcription via recruitment ing network (30). Consistent with this, the lncRNA LED is a p53 target gene that activates strong enhancers including in cyclindependent kinase 1A (CDKN1A), thus providing a mechanism for p53-activated enhancers that do not have a p53-binding site (31). The lncRNA MEG3 selectively enhances transcriptional activation by p53 and downregulates MDM2, resulting in cell-cycle arrest and apoptosis in vitro as well as modulation of autophagy (32,33).…”