The Evf2 long non-coding RNA (lncRNA) assembles ribonucleoprotein (RNP) complexes. These complexes regulate gene expression by directing intrachromosomal interactions through Dlx5/6 ultraconserved enhancers (Dlx5/6UCE). The transcription factor Sox2 is an Evf2-RNP complex component, but its role in lncRNA-mediated gene regulation has been unclear. Now, Jhumku Kohtz and colleagues use a combination of chromatin immunoprecipitation approaches and RNA-protein-binding assays to reveal that Sox2 directly interacts with Evf2 as well as other components of the Evf2-RNP complex, such as Dlx1. Loss of Sox2 reduces the expression of genes that are repressed by Evf2 and CUT&RUN profiling shows that the 5′ end of Evf2 is required for Sox2 recruitment to an adjacent shadow enhancer, but not for Sox2 binding to Dlx5/6UCE. Using circular chromosome conformation capture (4C), the researchers show distinct changes in the long-range repression of target genes: Evf2-Sox2 interactions promote Rbm28 gene repression at the expense of Akr1b8 where Sox2 is absent. Finally, through fluorescence imaging, they show that Evf2 organises Sox2 to form ‘protein pools’ at target loci. Together, these data provide a detailed analysis of the spatial and functional interplay between Evf2 and Sox2 during development, and indicate a role for Evf2 in directing Sox2 distribution and activity.
