Comparative analysis of eukaryotic U3 snoRNA

The U3 snoRNA is an exceptional box C/D snoRNA, which is involved in pre-rRNA processing without directing chemical modifications. We report here on a comprehensive computational survey resulting in U3 sequences for more than 90 additional eukaryotes. This extended data basis is used to improve the secondary structure models. The detailed investigation of the structural variation of U3 snoRNAs turns out to be much more extensive than previously thought. Many fungal U3 genes, in addition, contain introns. U3 promoters are snRNA-like but show substantial variations even between related species.

[1]  A. Weiner,et al.  Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family , 1980, Cell.

[2]  J. Steitz,et al.  U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. , 1989, The EMBO journal.

[3]  S. Bell,et al.  tRNAs of Trypanosoma brucei. Unusual gene organization and mitochondrial importation. , 1991, The Journal of biological chemistry.

[4]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[5]  T. Hartshorne,et al.  Characterization of putative small nuclear RNAs from Giardia lamblia. , 1994, Molecular and biochemical parasitology.

[6]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[7]  F. Brulé,et al.  Secondary structure of the yeast Saccharomyces cerevisiae pre-U3A snoRNA and its implication for splicing efficiency. , 1996, RNA.

[8]  D. Tollervey,et al.  The yeast Hansenula wingei U3 snoRNA gene contains an intron and its coding sequence co-evolved with the 5' ETS region of the pre-ribosomal RNA. , 1996, RNA: A publication of the RNA Society.

[9]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[10]  Phylogenetic analysis of heterothallic Neurospora species. , 1997, Fungal genetics and biology : FG & B.

[11]  F. Brulé,et al.  U3 snoRNA genes with and without intron in the Kluyveromyces genus: yeasts can accommodate great variations of the U3 snoRNA 3'-terminal domain. , 1998, RNA.

[12]  G. Steger,et al.  Molecular characterization at the RNA and gene levels of U3 snoRNA from a unicellular green alga, Chlamydomonas reinhardtii. , 2000, Nucleic acids research.

[13]  P. Das,et al.  Expression and purification of recombinant Giardia fibrillarin and its interaction with small nuclear RNAs. , 2001, Protein expression and purification.

[14]  D. Lafontaine,et al.  Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments , 2002, The EMBO journal.

[15]  C. Paul,et al.  PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. , 2004, Molecular cell.

[16]  W. Filipowicz,et al.  Characterization of the U3 and U6 snRNA genes from wheat: U3 snRNA genes in monocot plants are transcribed by RNa polymerase III , 1992, Plant Molecular Biology.

[17]  S. Gerbi,et al.  Xenopus U3 snoRNA docks on pre-rRNA through a novel base-pairing interaction. , 2004, RNA.

[18]  T. Kiss,et al.  U17/snR30 Is a Ubiquitous snoRNA with Two Conserved Sequence Motifs Essential for 18S rRNA Production , 2004, Molecular and Cellular Biology.

[19]  Hui Zhou,et al.  Identification of 20 snoRNA-like RNAs from the primitive eukaryote, Giardia lamblia. , 2005, Biochemical and biophysical research communications.

[20]  Sam Griffiths-Jones,et al.  RALEE--RNA ALignment Editor in Emacs , 2005, Bioinform..

[21]  Lun Cai,et al.  Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans , 2007, BMC Molecular Biology.

[22]  P. Stadler,et al.  Invertebrate 7SK snRNAs , 2008, Journal of Molecular Evolution.

[23]  Michael Weiss,et al.  A higher-level phylogenetic classification of the Fungi. , 2007, Mycological research.

[24]  Rolf Backofen,et al.  Structural Local Multiple Alignment of RNA , 2008, German Conference on Bioinformatics.

[25]  R. Nazar,et al.  U3 snoRNA promoter reflects the RNA’s function in ribosome biogenesis , 2008, Current Genetics.

[26]  H. Daniel,et al.  Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. , 2008, FEMS yeast research.

[27]  Toralf Kirsten,et al.  Evolution of Spliceosomal snRNA Genes in Metazoan Animals , 2008, Journal of Molecular Evolution.

[28]  Axel Mosig,et al.  Structure and Function of the Smallest Vertebrate Telomerase RNA from Teleost Fish* , 2008, Journal of Biological Chemistry.

[29]  Kunio Inoue,et al.  Distribution of U3 small nucleolar RNA and fibrillarin during early embryogenesis in Caenorhabditis elegans. , 2008, Biochimie.

[30]  Peter F. Stadler,et al.  Non-coding RNA annotation of the genome of Trichoplax adhaerens , 2009, Nucleic acids research.

[31]  Robert D. Finn,et al.  Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..

[32]  Marcela Dávila López,et al.  Conserved and variable domains of RNase MRP RNA , 2009, RNA biology.