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

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

PROVIDER: PRJEB7307 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR652839.fastq.gz	Fastqsanger.gz
	ERR652840.fastq.gz	Fastqsanger.gz
	ERR652841.fastq.gz	Fastqsanger.gz
	ERR652842.fastq.gz	Fastqsanger.gz
	ERR652843.fastq.gz	Fastqsanger.gz

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

Project description: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.

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Project description:Triple helix is a potential mechanism how lncRNAs interact with the genome. Our in silico method (Triplex Domain Finder) is able to predict the binding sites of lncRNA MEG3 and GATA6-AS in the genome. In order to validate these predictions, we develop DBD-Capture-Seq to capture the DNA loci where the given RNA oligo binds to via triplex. Method: Different RNA oligos are used The biotinylated RNA oligos (MEG3 TFR1, MEG3 TFR2, and GATA6-AS TFR1) were incubated with sheared genomic DNA to allow for triplex formation. After binding to streptavidin-coated beads, RNA-associated DNA was eluted and subjected to deep sequencing. Control experiments were conducted in the absence of biotinylated RNA oligos.

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