title: Visualizing the secondary and tertiary architectural domains of lncRNA RepA.
abstract: Long noncoding RNAs (lncRNAs) are important for gene expression, but little is known about their structures. RepA is a 1.6-kb mouse lncRNA comprising the same sequence as the 5' region of Xist, including A and F repeats. It has been proposed to facilitate the initiation and spread of X-chromosome inactivation, although its exact role is poorly understood. To gain insight into the molecular mechanism of RepA and Xist, we determined a complete phylogenetically validated secondary-structural map of RepA through SHAPE and DMS chemical probing of a homogeneously folded RNA in vitro. We combined UV-cross-linking experiments with RNA modeling methods to produce a three-dimensional model of RepA functional domains demonstrating that tertiary architecture exists within lncRNA molecules and occurs within specific functional modules. This work provides a foundation for understanding of the evolution and functional properties of RepA and Xist and offers a framework for exploring architectural features of other lncRNAs.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.|Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Srinivas
authors.initials: S
authors.lastname: Somarowthu
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.|Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.|Department of Chemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Anna Marie
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D000818:Animals; D051379:Mice; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D062085:RNA, Long Noncoding