title: Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms.
abstract: Non-messenger RNAs (nmRNAs) play a wide and essential role in cellular functions. Computational identification of novel nmRNAs in genomes of model organisms is severely restricted owing to their lack of an open reading frame. Hence, we describe experimental approaches for their identification by generating cDNA libraries derived from nmRNAs for which we coined the term experimental RNomics. Two different procedures are introduced for cDNA library construction. First, we describe the construction of a general purpose cDNA library from sized RNA fractions. Second, we introduce a more specialized RNomics strategy employing this approach to generate a cDNA library from a specific abundant class of nmRNAs. This is illustrated using as a paradigm the two families of small nucleolar RNAs that guide modification of nucleotides in rRNAs or spliceosomal RNAs small nuclear RNAs (snRNAs) by short antisense elements complementary to the modification site. Following the identification of novel members from the class of small nuclear RNAs by experimental RNomics, we demonstrate how their target sequences in rRNAs or snRNAs can be identified.
authors.affiliation: Institut für Molekularbiologie, Abt. Funktionelle Genomik, Universität Innsbruck, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Hüttenhofer
authors.forename: Jérome
authors.initials: J
authors.lastname: Cavaillé
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Bachellerie
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D015723:Gene Library; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D012333:RNA, Messenger; D020537:RNA, Small Nucleolar; D012313:RNA