Divergent transcription of the Nkx2-5 locus generates two enhancer RNAs with opposing functions

We described two eRNAs transcribed from the enhancer of NK2 homeobox 5 (Nkx2-5) with antagonistic regulatory effects on the target gene’s transcription. These two eRNAs, which we have called Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs), are encoded on the same strand (SS) and in the divergent direction (div). Of note, IRENE-SS acts as a canonical promoter of Nkx2-5 transcription, whereas IRENE-div, represses the activity of the enhancer by recruiting the histone deacetylase (HDAC) sirtuin 1 (SIRT1). Experiments on human induced pluripotent stem cells (hiPSCs) revealed that the two human homologues are regulated during cardiac differentiation in vitro. Our findings demonstrate the existence of a new epigenetic mechanism involving an autoregulatory loop in which the transcription of a TF is controlled by the balance of eRNAs stemming from its own gene’s enhancer.