Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

Abstract

Recent advances in genomic research have revealed the existence of a large number of transcripts devoid of protein-coding potential in multiple organisms 1-8. While the functional role for long non-coding RNAs (lncRNAs) has been best defined in epigenetic phenomena such as X inactivation and imprinting, different classes of lncRNAs may have varied biological functions 8-13. We and others have identified a class of lncRNAs, termed ncRNA-activating (ncRNA-a), that function to activate their neighboring genes using a cis-mediated mechanism 5,14-16. To define the precise mode by which such enhancer-like RNAs function, we depleted factors with known roles in transcriptional activation and assessed their role in RNA-dependent activation. Here we report that depletion of the components of the co-activator complex, Mediator, specifically and potently diminished the ncRNA-induced activation of transcription in such a heterologous reporter assay. In vivo, Mediator is recruited to ncRNA-as target genes, and regulates their expression. We show that ncRNA-as interact with Mediator to regulate its chromatin localization and kinase activity toward histone H3 serine 10. Mediator complex harboring disease causing MED12 mutations 17,18 displays diminished ability to associate with activating ncRNAs. Chromosome conformation capture (3C) confirmed the presence of DNA looping between the ncRNA-a loci and its targets. Importantly, depletion of Mediator subunits or ncRNA-as reduced the chromatin looping between the two loci. Our results identify the human Mediator complex as the transducer of activating ncRNAs and highlight the importance of Mediator and activating ncRNAs association in human disease.

Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation

“…It was recently reported that Mediator associates with ncRNAs to enhance transcriptional activation 43 and likewise ncRNAs contribute to gene repression via PRC1. 57,58 Given the close interplay between Med12 and PRC1 in gene regulation, we focused on one common target gene, Hoxd11, to assess ncRNA-mediated activation.…”

“…Mediator and Med12 were previously shown to play a role in transcriptional activation by ncRNA-mediated mechanisms. 43,54 To assess a potential function of ncRNAs in the activation of Hoxd11 we analyzed a 2Mb region encompassing the HoxD locus (Fig. 5B) for the expression of ncRNAs.…”

“…37 Mediator is also known to act in concert with transcriptionally activating ncRNAs. 42,43 These ncRNAs are transcribed in close proximity to the target gene promoter and they associate with Med12 to promote DNA looping from the ncRNA locus to the target gene enhancing transcription. However, how Mediator and Med12 operate in both transcriptional activation and silencing is still poorly understood.…”

MED12 mutations in human diseases

“…The Mediator complex containing mutant MED12 proteins found in the FG syndrome fails to interact with ncRNA-a. These results suggest that the loss of Mediator-ncRNA-a interactions may contribute to FG syndrome (Lai et al, 2013).…”

The Yin and Yang of enhancer-like RNAs

“…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.…”