Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics. 2009; 94:83–88.
Article
CAS
PubMed
Google Scholar
Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Genomics. 2007; 8:209–20.
Article
CAS
Google Scholar
Rodor J, Letelier I, Holuigue L, Echeverria M. Nucleolar RNPs: from genes to functional snoRNAs in plants. Biochem Soc Trans. 2010; 38:672–6.
Article
CAS
PubMed
Google Scholar
Bachellerie JP, Cavaillé J, Hüttenhofer A. The expanding snoRNA world. Biochimie. 2002; 84:775–90.
Article
CAS
PubMed
Google Scholar
Darzacq X, Jády BE, Verheggen C, Kiss AM, Bertrand E, Kiss T. Cajal body-specific small nuclear RNAs: a novel class of 2’-O-methylation and pseudouridylation guide RNAs. EMBO J. 2002; 21:2746–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kiss T, Filipowicz W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 1995; 9:1411–24.
Article
CAS
PubMed
Google Scholar
Filipowicz W, Pogacić V. Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol. 2002; 14:319–27. doi:10.1016/S0955-0674(02)00334-4.
Article
CAS
PubMed
Google Scholar
Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD. Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science. 2010; 330:838–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown JW, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 2003; 8:42–9.
Article
CAS
PubMed
Google Scholar
Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH. The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res. 2003; 31:2601–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim S, Spensley M, Choi SK, Calixto CP, Pendle AF, Koroleva O, et al. Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Res. 2010; 38:3054–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Allmang C, Kufel J, Chanfreau G, Mitchell P, Petfalski E, Tollervey D. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 1999; 18:5399–410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leader DJ, Clark GP, Watters J, Beven AF, Shaw PJ, Brown JW. Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs. Plant Mol Biol. 1999; 39:1091–100.
Article
CAS
PubMed
Google Scholar
Caffarelli E, Maggi L, Fatica A, De Gregorio E, Frangapane P, Bozzoni I. Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reaction and the stability of the mature snoRNA. EMBO J. 1996; 15:1121–31.
CAS
PubMed
PubMed Central
Google Scholar
Michaud M, Cognat V, Duchêne AM, Maréchal-Drouard L. A global picture of tRNA genes in plant genomes. Plant J. 2011; 66:80–93.
Article
CAS
PubMed
Google Scholar
Mo D, Raabe CA, Reinhardt R, Brosius J, Rozhdestvensky TS. Alternative processing as evolutionary mechanism for the origin of novel nonprotein coding RNAs. Genome Biol Evol. 2013; 5:2061–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, et al. Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res. 2014; 42:10073–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watkins N, Segault V, Charpentier B, Nottrott S, Fabrizio P, Bachi A, et al. A common core RNP structure shared between the small nucleolar box C/D RNPs and the spliceosomal U4 snRNP. Cell. 2000; 103:457–66.
Article
CAS
PubMed
Google Scholar
Klein D, Schmeing T, Moore P, Steitz T. The kink-turn: A new RNA secondary structure motif. EMBO J. 2001; 20:4214–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuhn J, Tran E, Maxwell ES. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res. 2002; 30:931–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dupuis-Sandoval F, Poirier M, S SM. The emerging landscape of small nucleolar RNAs in cell biology. Wiley Interdiscip Rev RNA. 2015; 6:381–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Torchet C, Badis G, Devaux F, Costanzo G, Werner M, Jacquier A. The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae. RNA. 2005; 11:928–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Balakin AG, Smith L, Fournier MJ. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell. 1996; 86:823–34.
Article
CAS
PubMed
Google Scholar
Venema J, Vos HR, Faber AW, van Venrooij WJ, Raué HA. Yeast Rrp9p is an evolutionarily conserved U3 snoRNP protein essential for early pre-rRNA processing cleavages and requires box C for its association. RNA. 2000; 6:1660–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Venema J, Tollervey D. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet. 1999; 33:261–311.
Article
CAS
PubMed
Google Scholar
Lafontaine DLJ, Tollervey D. The function and synthesis of ribosomes. Nat Rev Mol Cell Biol. 2001; 2:514–20.
Article
CAS
PubMed
Google Scholar
Marz M, Stadler PF. Comparative Analysis of Eukaryotic U3 snoRNAs. RNA Biol. 2009; 6:503–7.
Article
CAS
PubMed
Google Scholar
Scott M, Ono M. From snoRNA to miRNA: dual function regulatory non-coding RNAs. Biochimie. 2011; 93:1987–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu TT, Zhu D, Chen W, Deng W, He H, He G, et al. A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. Mol Plant. 2013; 6:830–486.
Article
CAS
PubMed
Google Scholar
Herter EK, Stauch M, Gallant M, Wolf E, Raabe T, Gallant P. snoRNAs are a novel class of biologically relevant Myc targets. BMC Biology. 2015; 13:25.
Article
PubMed
PubMed Central
Google Scholar
Hoeppner MP, Poole AM. Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evol Biol. 2012; 12:183.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kehr S, Bartschat S, Tafer H Stadler PF, Hertel J. Matching of Soulmates: Coevolution of snoRNAs and Their Targets. Mol Biol Evol. 2014; 31:455–67.
Article
CAS
PubMed
Google Scholar
Bartschat S, Kehr S, Tafer H, Stadler PF, J H. snoStrip: a snoRNA annotation pipeline. Bioinformatics. 2014; 30:115–6.
Article
CAS
PubMed
Google Scholar
Shao P, Yang JH, Zhou H, Guan DG, Qu LH. Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics. 2009; 10:86.
Article
PubMed
PubMed Central
Google Scholar
Liu N, Xiao ZD, Yu CH, Shao P, Liang YT, Guan DG, et al. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics. 2009; 10:515.
Article
PubMed
PubMed Central
Google Scholar
Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, et al. The expansion of the Metazoan MicroRNA Repertoire. BMC Genomics. 2006; 7:15.
Article
Google Scholar
Schmitz J, Zemann A, Churakov G, Kuhl H, Grtzner F, Reinhardt R, et al. Retroposed SNOfall–a mammalian-wide comparison of platypus snoRNAs. Genome Res. 2008; 18(6):1005–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, et al. An updated human snoRNAome. Nucl Acids Res. 2016; 44:5068–82. doi:10.1093/nar/gkw386.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gardner PP, Bateman A, Poole AM. SnoPatrol: how many snoRNA genes are there?J Biol. 2010; 9:4.
Article
PubMed
PubMed Central
Google Scholar
Machyna M, Kehr S, Straube K, Kappei D, Butter F, Ule J, et al. The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Mol Cell. 2014; 56:389–99.
Article
CAS
PubMed
Google Scholar
Angrisani A, Tafer H, Stadler PF, Furia M. Developmentally regulated expression and expression strategies of Drosophila snoRNAs. Insect Biochem Mol Biol. 2015; 61:69–78. doi:10.1016/j.ibmb.2015.01.013.
Article
CAS
PubMed
Google Scholar
Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 2006; 34:D158–62.
Article
CAS
PubMed
Google Scholar
Yoshihama M, Nakao A, Kenmochi N. snOPY: a small nucleolar RNA orthological gene database. BMC Res Notes. 2013; 6:426.
Article
PubMed
PubMed Central
Google Scholar
Lee TH, Tang H, Wang X, Paterson AH. PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res. 2013; 41:D1152–8.
Article
CAS
PubMed
Google Scholar
Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T. Multiple snoRNA gene clusters from Arabidopsis. RNA. 2001; 7:1817–32.
CAS
PubMed
PubMed Central
Google Scholar
Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA. 2012; 5:900–14.
Article
Google Scholar
Hertel J, Stadler PF. The Expansion of Animal MicroRNA Families Revisited. Life (Basel). 2015; 5:905–20. doi:10.3390/life5010905.
Google Scholar
Brown JW, Echeverria M, Qu LH, Lowe TM Bachellerie JP, Hüttenhofer A, et al. Plant snoRNA database. Nucleic Acids Res. 2003; 31:432–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barneche F, Steinmetz F, Echeverria M. Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana. J Biol Chem. 2000; 275:27212–20.
CAS
PubMed
Google Scholar
Barneche F, Gaspin C, Guyot R, Echeverria M. Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2’-O-methylation sites. J Biol Chem. 2001; 311:57–73.
CAS
Google Scholar
Qu LH, Meng Q, Zhou H, Chen YQ. Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res. 2001; 29:1623–30.
Article
CAS
PubMed
Google Scholar
Chen CL, Chen CJ, Vallon O, Huang ZP, Zhou H, Qu LH. Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii, reveals an extensive organization into intronic gene clusters. Genetics. 2008; 179:21–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qu G, Kruszka K, Plewka P, Yang SYCTJ, Jarmolowski A, Szweykowska-Kulinska Z, et al. Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics. 2015; 16:1009. doi:10.1186/s12864-015-2221-x.
Article
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013; 41:D590–6.
Article
CAS
PubMed
Google Scholar
Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. Front Plant Sci. 2014; 5:708. doi:10.3389/fpls.2014.00708.
Article
PubMed
PubMed Central
Google Scholar
Tran E, Zhang X, Lackey L, Maxwell ES. Conserved spacing between the box C/D and C’/D’ RNPs of the archaeal box C/D sRNP complex is required for efficient 2’-O-methylation of target RNAs. RNA. 2005; 11:285–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gaspin C, Cavaillé J, Erauso G, Bachellerie JP. Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol. 2000; 297:895–906.
Article
CAS
PubMed
Google Scholar
Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009; 25:1335–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wuchty S, Fontana W, Hofacker IL, Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers. 1999; 49(2):145–65.
Article
CAS
PubMed
Google Scholar