TOP1 Activity Facilitates Ligand-Dependent Enhancer Activation

Enhancers regulate transcription of associated coding target genes via chromatin looping and expression of noncoding enhancer RNAs (eRNA) that stabilize enhancer–promoter interactions. Several features of transcription and enhancer activation, including nucleosome depletion, eRNA synthesis, and RNA polymerase movement, have been hypothesized to generate supercoiled DNA, a topological strain that can impede transcription. DNA topoisomerase 1 (TOP1) relaxes supercoils during DNA replication by generating single-strand DNA (ssDNA) nicks, prompting Puc and colleagues to examine whether TOP1 plays a similar role in transcription and enhancer activation. Genome-wide localization studies performed in androgen-dependent prostate adenocarcinoma cells revealed rapid TOP1 recruitment to multiple androgen receptor (AR)–associated enhancers following androgen stimulation. Binding of TOP1 to AR enhancers was dependent on the androgen-regulated transcription factor NKX3.1, which has previously been shown to bind and enhance TOP1 activity. Silencing of either TOP1 or NKX3.1 reduced ligand-induced eRNA synthesis and mRNA production from corresponding target genes, including KLK3, KLK2, and TMPRSS2, without affecting AR recruitment to enhancers. Consistent with a role for TOP1-mediated cleavage in enhancer activation, ssDNA nicks were generated near the KLK3 enhancer region upon androgen stimulation, and expression of the catalytically inactive TOP1 Y723F mutant was unable to rescue the inhibitory effects of TOP1 depletion on AR-regulated enhancers. Ligand treatment also stimulated recruitment of the DNA damage repair protein meiotic recombination 11 (MRE11), which was required for induction of eRNAs and the AR transcription program. Furthermore, In line with ssDNA formation, multiple additional DNA damage repair proteins, including ATR, XRCC1, and DNA ligase I, were also recruited to AR-regulated enhancers, suggesting that the base excision DNA repair pathway may be recruited to ensure proper re-ligation of TOP1-induced ssDNA breaks. Together, this work highlights a previously underappreciated role for TOP1 activity in androgen-dependent enhancer activation and suggests a link between transcription and DNA damage repair.

Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, et al. Ligand-dependent enhancer activation regulated by topoisomerase-I activity. Cell 2015;160:367–80.