title: MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures.
abstract: 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.
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Mondal
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Santhilal
authors.initials: S
authors.lastname: Subhash
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Roshan
authors.initials: R
authors.lastname: Vaid
authors.affiliation: Department of Immunology, Genetics and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden.
authors.forename: Stefan
authors.initials: S
authors.lastname: Enroth
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Sireesha
authors.initials: S
authors.lastname: Uday
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Reinius
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Sanhita
authors.initials: S
authors.lastname: Mitra
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Arif
authors.initials: A
authors.lastname: Mohammed
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Alva Rani
authors.initials: AR
authors.lastname: James
authors.affiliation: Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, SE-405 30 Gothenburg, Sweden.
authors.forename: Emily
authors.initials: E
authors.lastname: Hoberg
authors.affiliation: 1] Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, PO Box 582, SE-751 23 Uppsala, Sweden [2] Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, PO Box 595, SE-751 24 Uppsala, Sweden.
authors.forename: Aristidis
authors.initials: A
authors.lastname: Moustakas
authors.affiliation: Department of Immunology, Genetics and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden.
authors.forename: Ulf
authors.initials: U
authors.lastname: Gyllensten
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia BC V5Z 4S6, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, SE-405 30 Gothenburg, Sweden.
authors.forename: Claes M
authors.initials: CM
authors.lastname: Gustafsson
authors.affiliation: Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, Edinburgh EH4 2XR, UK.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Sims
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Westerlund
authors.affiliation: Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo CEP:05508-090, Brazil.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Gorab
authors.affiliation: Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden.
authors.forename: Chandrasekhar
authors.initials: C
authors.lastname: Kanduri
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000378:metabolism; D000071221:Enhancer of Zeste Homolog 2 Protein; D005786:Gene Expression Regulation; D006801:Humans; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000378:metabolism*; D016212:Transforming Growth Factor beta / Q000378:metabolism
chemical_list: C498907:MEG3 non-coding RNA, human; D062085:RNA, Long Noncoding; D016212:Transforming Growth Factor beta; C051802:triplex DNA; D004247:DNA; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D063151:Polycomb Repressive Complex 2