title: Global analysis of RNA secondary structure in two metazoans.
abstract: The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.
authors: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Fan
authors: F
authors: Li
authors: Qi
authors: Q
authors: Zheng
authors: Paul
authors: P
authors: Ryvkin
authors: Isabelle
authors: I
authors: Dragomir
authors: Yaanik
authors: Y
authors: Desai
authors: Subhadra
authors: S
authors: Aiyer
authors: Otto
authors: O
authors: Valladares
authors: Jamie
authors: J
authors: Yang
authors: Shelly
authors: S
authors: Bambina
authors: Leah R
authors: LR
authors: Sabin
authors: John I
authors: JI
authors: Murray
authors: Todd
authors: T
authors: Lamitina
authors: Arjun
authors: A
authors: Raj
authors: Sara
authors: S
authors: Cherry
authors: Li-San
authors: LS
authors: Wang
authors: Brian D
authors: BD
authors: Gregory
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D044127:Epigenesis, Genetic; D016678:Genome / Q000235:genetics; D035683:MicroRNAs / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012330:RNA, Double-Stranded; D018510:RNA, Helminth; D012333:RNA, Messenger; D012313:RNA