title: Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea.
abstract: A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.
authors.affiliation: I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Toffano-Nioche
authors.affiliation: I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
authors.affiliation: I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France fabrice.leclerc@igmors.u-psud.fr.
authors.forename: Fabrice
authors.identifier: http://orcid.org/0000-0002-5641-1525
authors.initials: F
authors.lastname: Leclerc
mesh_terms: D020029:Base Pairing; D019605:Euryarchaeota / Q000235:genetics; D019848:Gene Expression Regulation, Archaeal; D008958:Models, Molecular; D059372:Nucleotide Motifs; D041543:Pyrobaculum / Q000235:genetics*; D043903:Pyrococcus abyssi / Q000235:genetics*; D059370:RNA Folding; D019642:RNA, Archaeal / Q000737:chemistry* / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D013329:Structure-Activity Relationship; D000094704:RNA, Guide, CRISPR-Cas Systems
chemical_list: D019642:RNA, Archaeal; D020537:RNA, Small Nucleolar; D012343:RNA, Transfer; D000094704:RNA, Guide, CRISPR-Cas Systems