title: Structural imprints in vivo decode RNA regulatory mechanisms.
abstract: Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Robert C
authors: RC
authors: Spitale
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Ryan A
authors: RA
authors: Flynn
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Qiangfeng Cliff
authors: QC
authors: Zhang
authors: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors: Pete
authors: P
authors: Crisalli
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Byron
authors: B
authors: Lee
authors: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors: Jong-Wha
authors: JW
authors: Jung
authors: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors: Hannes Y
authors: HY
authors: Kuchelmeister
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Pedro J
authors: PJ
authors: Batista
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Eduardo A
authors: EA
authors: Torre
authors: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors: Eric T
authors: ET
authors: Kool
authors: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors: Howard Y
authors: HY
authors: Chang
mesh_terms: D000215:Acylation; D000241:Adenosine / Q000031:analogs & derivatives; D000818:Animals; D001665:Binding Sites; D002470:Cell Survival; D057930:Click Chemistry; D019295:Computational Biology; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics; D016678:Genome / Q000235:genetics; D051379:Mice; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D016601:RNA-Binding Proteins; D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA; C010223:N-methyladenosine; D000241:Adenosine