title: Coupled nucleotide covariations reveal dynamic RNA interaction patterns.
abstract: Evolutionarily conserved structures in related RNA molecules contain coordinated variations (covariations) of paired nucleotides. Analysis of covariations is a very powerful approach to deduce phylogenetically conserved (i.e., functional) conformations, including tertiary interactions. Here we discuss conserved RNA folding pathways that are revealed by covariation patterns. In such pathways, structural requirements for alternative pairings cause some nucleotides to covary with two different partners. Such "coupled" covariations between three or more nucleotides were found in various types of RNAs. The analysis of coupled covariations can unravel important features of RNA folding dynamics and improve phylogeny reconstruction in some cases. Importantly, it is necessary to distinguish between multiple covariations determined by mutually exclusive structures and those determined by tertiary contacts.
authors: Section Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences of Leiden University, The Netherlands. sgultyaev@rulsfb.leidenuniv.nl
authors: A P
authors: AP
authors: Gultyaev
authors: T
authors: T
authors: Franch
authors: K
authors: K
authors: Gerdes
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001427:Bacterial Toxins; D001483:Base Sequence; D029968:Escherichia coli Proteins; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D001427:Bacterial Toxins; D029968:Escherichia coli Proteins; C087025:Hok protein, E coli; D012333:RNA, Messenger; D012313:RNA