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Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control site-specific gene expression of thousands of targets. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases association of transcriptional activators (DLX homeodomain proteins) to key DNA enhancers, but represses gene expression. In this report, mass spectrometry shows that the Evf2/DLX1 ribonucleoprotein (RNP) contains SWI/SNF related chromatin-remodelers, Brahma related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in developing forebrain. Evf2 RNA co-localizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA/BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity is promiscuous, suggesting that context is a critical factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model where RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin-remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers, with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin Siris Syndrome, a human intellectual disability disorder, localize to the BRG1 RNA binding and DLX1 binding domains.

Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition