title: SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.
abstract: The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein-RNA interactions within Xist are poorly understood. We used selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides. The Xist RNA structure modulates protein interactions in cells via multiple mechanisms. For example, repeat-containing elements adopt accessible and dynamic structures that function as landing pads for protein cofactors. Structured RNA motifs create interaction domains for specific proteins and also sequester other motifs, such that only a subset of potential binding sites forms stable interactions. This work creates a broad quantitative framework for understanding structure-function interrelationships for Xist and other lncRNAs in cells.
authors: Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599;
authors: Matthew J
authors: 0000-0002-2123-9681
authors: MJ
authors: Smola
authors: Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599;
authors: Thomas W
authors: TW
authors: Christy
authors: Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599;
authors: Kaoru
authors: K
authors: Inoue
authors: Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708.
authors: Cindo O
authors: CO
authors: Nicholson
authors: Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708.
authors: Matthew
authors: M
authors: Friedersdorf
authors: Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708.
authors: Jack D
authors: JD
authors: Keene
authors: Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599;
authors: David M
authors: DM
authors: Lee
authors: Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599; weeks@unc.edu jmcalabr@med.unc.edu.
authors: J Mauro
authors: JM
authors: Calabrese
authors: Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599; weeks@unc.edu jmcalabr@med.unc.edu.
authors: Kevin M
authors: KM
authors: Weeks
mesh_terms: D000215:Acylation / Q000235:genetics; D000818:Animals; D005260:Female; D051379:Mice; D009154:Mutation; D009690:Nucleic Acid Conformation; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D014960:X Chromosome / Q000235:genetics; D049951:X Chromosome Inactivation / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins; C077885:XIST non-coding RNA
keywords: RNA structure; RNA–protein interaction; SHAPE-MaP; X-inactivation