The Yin and Yang of enhancer-like RNAs.

Long noncoding RNAs are emerging as a critical component of transcriptional activation. Over the past few years, there has been a number of examples where long noncoding RNAs expressed from distal sites exert their activating functions on neighbouring protein-coding genes. A new study in The EMBO Journal (Lu et al, 2013) now extends this paradigm by revealing a role for the transcription factor Yin Yang 1 (YY1) in the regulation of the expression of long noncoding RNAs (termed Yams) during myogenesis. Importantly, the authors demonstrate a functional role for Yam-1 in muscle differentiation through activation of a neighbouring micoRNA-715 leading to downregulation of Wnt7b. There is converging evidence that distal regulatory sites commonly known as ‘enhancers’ are transcribed in a stimulus-dependent manner as long noncoding RNAs (known as enhancer RNAs, eRNAs) and such eRNAs contribute to transcriptional activation of their neighbouring genes (De Santa et al, 2010; Kim et al, 2010; Hah et al, 2013; Lam et al, 2013; Li et al, 2013; Melo et al, 2013). Concomitantly, studies of long noncoding RNAs located in intergenic sites (termed lincRNAs, large intergenic noncoding RNAs) have uncovered a role for a class of lincRNAs (named noncoding RNA-activating, ncRNA-a) having enhancer-like functions (Orom et al, 2010; Wang et al, 2011). These activating lincRNAs are enriched with transcription factor binding sites at their promoters and display responsiveness to differentiating stimuli (Orom et al, 2010). While the degree of overlap between eRNAs and ncRNA-a is not clear at the present, recent studies have suggested a similar mechanism of action for the two classes of long noncoding RNAs through recruitment of Mediator–Cohesin complexes and promoting DNA looping (Kagey et al, 2010; Lai et al, 2013; Li et al, 2013). However, the transcription and chromatin regulatory factors underlying the expression and biogenesis of these activating long noncoding RNAs have not been illustrated. The study by Lu et al (2013) examined the genome-wide occupancy of transcription factor and chromatin regulator, Yin Yang 1 (YY1), in proliferating C2C12 myoblats (MBs) before and following their differentiation into myotubes (MTs) using low mitogen conditions. Interestingly, the authors found no significant overlap in the chromatin residence of YY1 following differentiation of the MBs into MTs. Additionally, while the authors did not find a significant overlap between YY1 and components of the polycomb repressive complex, Ezh2, binding sites, YY1 displayed a substantial (31.9%) co-occupancy with muscle master regulator, MyoD, binding sites. Examination of publically available RNA sequencing data sets corresponding to proliferating MBs versus differentiating MTs indicated that a large number of YY1-regulated genes decreased their expression during MB to MT transition concomitant with diminished levels of YY1. These results suggested a role for YY1 as a positive regulator of these set of genes in MBs. Moreover, detailed analysis of YY1 binding sites revealed that while about 60% of YY1 occupied regions were close to the transcriptional start sites (TSS) of protein-coding genes, about a quarter of the binding sites mapped to intergenic sites distal to annotated TSS. The occurrence of intergenic YY1 binding sites compelled the authors to examine the association of YY1 with lincRNA loci and to assess the possible regulation of lincRNA expression by YY1. Analysis of 475 intergenic YY1 binding sites led to the identification of 13.3% of binding events within 100 kb of previously annotated lincRNAs. The authors validated YY1 binding to four lincRNA loci using chromatin immunoprecipitation followed by real-time PCR. They found an enrichment of YY1 binding to these lincRNAs (named YY1associated muscle lincRNAs or Yams) in MBs but not in MTs. Closer examination of one of these lincRNAs, Yam-1, revealed a YY1 binding site 687 bp upstream of its TSS. Importantly,