title: Genome-wide profiling of mouse RNA secondary  structures reveals key features of the mammalian  transcriptome.
abstract: BACKGROUND
  The understanding of RNA structure is a key feature toward the comprehension of RNA functions and mechanisms of action. In particular, non-coding RNAs are thought to exert their functions by specific secondary structures, but an efficient annotation on a large scale of these structures is still missing.
  
  
  RESULTS
  By using a novel high-throughput method, named chemical inference of RNA structures, CIRS-seq, that uses dimethyl sulfate, and N-cyclohexyl- N'-(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate to modify RNA residues in single-stranded conformation within native deproteinized RNA secondary structures, we investigate the structural features of mouse embryonic stem cell transcripts. Our analysis reveals an unexpected higher structuring of the 5′ and 3′ untranslated regions compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observe that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we find that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation.
  
  
  CONCLUSIONS
  This work defines for the first time the complete RNA structurome of mouse embryonic stem cells,revealing an extremely distinct RNA structural landscape. These results demonstrate that CIRS-seq constitutes an important tool for the identification of native deproteinized RNA structures.
authors.affiliation: Human Genetics Foundation (HuGeF), via Nizza 52, Torino 10126, Italy.
authors.forename: Danny
authors.initials: D
authors.lastname: Incarnato
authors.forename: Francesco
authors.initials: F
authors.lastname: Neri
authors.forename: Francesca
authors.initials: F
authors.lastname: Anselmi
authors.forename: Salvatore
authors.initials: S
authors.lastname: Oliviero
mesh_terms: D000818:Animals; D053595:Embryonic Stem Cells / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D016678:Genome; D051379:Mice; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D012313:RNA