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Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one of the chromatin-interacting lncRNAs,  MEG3 , we explore the mechanisms by which lncRNAs target chromatin. Here we show that  MEG3  and  EZH2  share common target genes, including the TGF-β pathway genes. Genome-wide mapping of  MEG3  binding sites reveals that  MEG3  modulates the activity of TGF-β genes by binding to distal regulatory elements.  MEG3  binding sites have GA-rich sequences, which guide  MEG3  to the chromatin through RNA–DNA triplex formation. We have found that RNA–DNA triplex structures are widespread and are present over the  MEG3  binding sites associated with the TGF-β pathway genes. Our findings suggest that RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures