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Nat Commun. 2017 May 30;8:15622. doi: 10.1038/ncomms15622.

A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers.

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Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.
IRCCS Multimedica, Milan 20099, Italy.
Laboratory of Cancer Genomics, Fondo Edo Tempia, Biella 13900, Italy.
Molecular Oncology Unit, CIEMAT and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28040, Spain.
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1066, Switzerland.


Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.

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