title: Consistent global structures of complex RNA states through multidimensional chemical mapping.
abstract: Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, United States.
authors.forename: Clarence Yu
authors.initials: CY
authors.lastname: Cheng
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, United States.
authors.forename: Fang-Chieh
authors.initials: FC
authors.lastname: Chou
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, United States.
authors.forename: Wipapat
authors.initials: W
authors.lastname: Kladwang
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, United States.
authors.forename: Siqi
authors.initials: S
authors.lastname: Tian
authors.affiliation: Biomedical Informatics Program, Stanford University, Stanford, United States.
authors.forename: Pablo
authors.initials: P
authors.lastname: Cordero
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, United States.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
mesh_terms: D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D022661:RNA, Untranslated
keywords: biochemistry; biophysics; high-throughput; next-generation sequencing; non-coding RNA; none; riboswitches; ribozymes; structural biology; structure prediction