title: Evolution of vault RNAs.
abstract: Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received little attention compared with most other noncoding RNA (ncRNA) families. Their poor sequence conservation makes homology search a complex and tedious task even within vertebrates. Here we report on a systematic and comprehensive analysis of this rapidly evolving class of ncRNAs in deuterostomes, providing a comprehensive collection of computationally predicted vtRNA genes. We find that all previously described vtRNAs are located at a conserved genomic locus linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. Lineage-specific expansions to small vtRNA gene clusters are frequently observed in this region. A second vtRNA locus is syntenically conserved across eutherian mammals. The vtRNAs at the two eutherian loci exhibit substantial differences in their promoter structures, explaining their differential expression patterns in several human cancer cell lines. In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction.
authors.affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Julian J-L
authors.initials: JJ
authors.lastname: Chen
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Friedemann
authors.initials: F
authors.lastname: Horn
authors.forename: Phillip
authors.initials: P
authors.lastname: Khaitovich
authors.forename: Antje K
authors.initials: AK
authors.lastname: Kretzschmar
authors.forename: Axel
authors.initials: A
authors.lastname: Mosig
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Qi
authors.forename: Katharina
authors.initials: K
authors.lastname: Schutt
authors.forename: Kerstin
authors.initials: K
authors.lastname: Ullmann
mesh_terms: D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D020394:Vault Ribonucleoprotein Particles / Q000235:genetics* / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D020394:Vault Ribonucleoprotein Particles; D012313:RNA