The Evf2 enhancer lncRNA links chromosomal interactions and interneuron diversity

Understanding how genes are selectively regulated during development is a major goal in biology. While DNA enhancers selectively regulate genes at a distance, mechanisms regulating long distance enhancer interactions are only beginning to be understood. Our previous work reported transcriptional activity by Evf2 , an enhancer long non‐coding RNA (lncRNA) transcribed from the Dlx5/6 ultraconserved enhancer ( Dlx5/6ei )1. Evf2 regulates adjacent chr6 genes Dlx5/6, recruiting both activators and repressors to Dlx5/6ei, and forms a large ribonucleoprotein complex ( Evf2 ‐RNP, ~79 proteins) that contains the DLX1 homeodomain transcription factor and chromatin remodelers2,3,4. Promiscuous interactions between Evf2 and chromatin remodelers reveal RNA‐mediated direct inhibition of BRG1(SMARCA4) ATPase and remodeling activities4. Thus, enhancer RNAs can regulate enhancer activity by providing a scaffold for multiple promiscuous RNA binding proteins, and directly regulating enzymatic activity. Here, we show evidence supporting that Evf2 controls chromosome‐wide enhancer interactions and histone modifications, selectively regulating genes located in a ~27Mb region of chr6 ( Evf2 ‐ chr6 targets). These data support the idea and that while Evf2 plays a major role in chromosome topology, only a subset of Evf2 ‐dependent enhancer interactions contribute to gene regulation. Evf2 loss, truncation, and rescue distinguish between the roles of the Evf2‐5 ′ ultraconserved enhancer‐containing region and trans/cis mechanisms that regulate Evf2‐chr6 targets. Together, this work identifies a novel network of interneuron subtype gene regulation that links enhancer lncRNA directed chromosomal interactions and interneuron diversity in the embryonic mouse brain. Support or Funding Information NIMH R01MH094653 to J.D.K