Journal Article

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

Shiekhattar, Ramin, Beringer, Malte, Lai, Fan, Taatjes, Dylan J., Cesaroni, Matteo, Orom, Ulf A., Blobel, Gerd A.

2013

Overview

A class of long non-coding RNA (lncRNA) with enhancer-like activity is found to associate with the co-activator complex Mediator and promote its genomic association and enzymatic activity; together with Mediator, the lncRNAs also help to maintain the chromosomal architecture of active regulatory elements. Mediator acts with ncRNA-a in gene regulation Long non-coding RNAs (lncRNAs) can both repress and activate gene expression. Here, a class of lncRNAs with enhancer-like activity is found to associate with the translational co-activator complex Mediator. Termed ncRNA-activating (ncRNA-a), these molecules promote the genomic association and enzymatic activity of Mediator, and acting together with Mediator, they also help to maintain the chromosomal architecture of active regulatory elements. Importantly, Mediator complexes containing disease-linked mutant MED12 proteins fail to associate with ncRNA-a. The MED12 gene encodes a Mediator complex subunit, and MED12 mutations have been linked to FG syndrome, a rare genetic disorder with symptoms including intellectual disability. This work suggests that the loss of Mediator–ncRNA-a interactions might be a possible contributing factor in such developmental diseases. Recent advances in genomic research have revealed the existence of a large number of transcripts devoid of protein-coding potential in multiple organisms 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 . Although the functional role for long non-coding RNAs (lncRNAs) has been best defined in epigenetic phenomena such as X-chromosome inactivation and imprinting, different classes of lncRNAs may have varied biological functions 8 , 9 , 10 , 11 , 12 , 13 . We and others have identified a class of lncRNAs, termed ncRNA-activating (ncRNA-a), that function to activate their neighbouring genes using a cis -mediated mechanism 5 , 14 , 15 , 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 a heterologous reporter assay using human HEK293 cells. In vivo , Mediator is recruited to ncRNA-a target genes and regulates their expression. We show that ncRNA-a interact with Mediator to regulate its chromatin localization and kinase activity towards histone H3 serine 10. The Mediator complex harbouring disease- 17 , 18 displays diminished ability to associate with activating ncRNAs. Chromosome conformation capture confirmed the presence of DNA looping between the ncRNA-a loci and its targets. Importantly, depletion of Mediator subunits or ncRNA-a 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 ncRNA association in human disease.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/337/384/2568 / Agenesis of Corpus Callosum - genetics / Anus, Imperforate - genetics / Architecture / Cellular signal transduction / Chromatin - chemistry / Chromatin - genetics / Chromatin - metabolism / Constipation - genetics / Gene expression / Gene Knockdown Techniques / Genes, Reporter - genetics / Genetic transcription / Humanities and Social Sciences / Humans / Identification and classification / Inactivation / Kinases / letter / Mediator Complex - chemistry / Mediator Complex - deficiency / Mediator Complex - genetics / Mediator Complex - metabolism / Mental Retardation, X-Linked - genetics / Molecular Conformation / multidisciplinary / Muscle Hypotonia - congenital / Muscle Hypotonia - genetics / Observations / Properties / Protein Subunits - genetics / Protein Subunits - metabolism / Proteins / RNA / RNA polymerase / RNA, Long Noncoding - genetics / RNA, Long Noncoding - metabolism / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - genetics / RNA-Binding Proteins - metabolism / Science / Transcription, Genetic - genetics