Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8:209–20. https://doi.org/10.1038/nrm2124.
Article
CAS
PubMed
Google Scholar
Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics. 2009;94:83–8.
Article
CAS
Google Scholar
Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. Wiley Interdiscip Rev RNA. 2019;10:e1530. https://doi.org/10.1002/wrna.1530.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bergeron D, Fafard-Couture É, Scott MS. Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans. 2020;48:645–56. https://doi.org/10.1042/BST20191046.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kiss T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 2001;20:3617–22. https://doi.org/10.1093/emboj/20.14.3617.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tyc K, Steitz JA. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 1989;8:3113–9. https://doi.org/10.1002/j.1460-2075.1989.tb08463.x.
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. https://doi.org/10.1093/nar/gku664.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marmier-Gourrier N, Cléry A, Senty-Ségault V, Charpentier B, Schlotter F, Leclerc F, et al. A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA. RNA. 2003;9:821–38. https://doi.org/10.1261/rna.2130503.
Article
CAS
PubMed
PubMed Central
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(Database issue):D158. https://doi.org/10.1093/nar/gkj002.
Article
CAS
PubMed
Google Scholar
Kiss-László Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell. 1996;85:1077–88. https://doi.org/10.1016/S0092-8674(00)81308-2.
Article
PubMed
Google Scholar
Ganot P, Caizergues-Ferrer M, Kiss T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 1997;11:941–56. https://doi.org/10.1101/gad.11.7.941.
Article
CAS
PubMed
Google Scholar
Ganot P, Bortolin ML, Kiss T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell. 1997;89:799–809. https://doi.org/10.1016/S0092-8674(00)80263-9.
Article
CAS
PubMed
Google Scholar
Wright MW, Bruford EA. Naming “junk”: human non-protein coding RNA (ncRNA) gene nomenclature. Human Genomics. 2011;5:90–8. https://doi.org/10.1186/1479-7364-5-2-90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seal RL, Chen L, Griffiths-Jones S, Lowe TM, Mathews MB, O’Reilly D, et al. A guide to naming human non-coding RNA genes. EMBO J. 2020;39. https://doi.org/10.15252/embj.2019103777.
Dupuis-Sandoval F, Poirier M, Scott MS. The emerging landscape of small nucleolar RNAs in cell biology. Wiley Interdiscip Rev RNA. 2015;6:381–97. https://doi.org/10.1002/wrna.1284.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bratkovič T, Bozič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res. 2020;48:1627–51. https://doi.org/10.1093/nar/gkz1140.
Article
CAS
PubMed
Google Scholar
Falaleeva M, Welden JR, Duncan MJ, Stamm S. C/D-box snoRNAs form methylating and non-methylating ribonucleoprotein complexes: old dogs show new tricks. BioEssays. 2017;39. https://doi.org/10.1002/bies.201600264.
Bouchard-Bourelle P, Desjardins-Henri C, Mathurin-St-Pierre D, Deschamps-Francoeur G, Fafard-Couture É, Garant JM, et al. SnoDB: an interactive database of human snoRNA sequences, abundance and interactions. Nucleic Acids Res. 2020;48:D220–5. https://doi.org/10.1093/nar/gkz884.
Article
CAS
PubMed
Google Scholar
Fafard-Couture É, Bergeron D, Couture S, Abou Elela S, Scott MS. Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. bioRxiv. 2021;1. https://doi.org/10.1101/2021.02.11.430834.
Boivin V, Deschamps-Francoeur G, Scott MS. Protein coding genes as hosts for noncoding RNA expression. Semin Cell Dev Biol. 2018;75:3–12.
Article
CAS
Google Scholar
Kazazian HH. Mobile elements: drivers of genome evolution. Science. 2004;303:1626–32. https://doi.org/10.1126/science.1089670.
Article
CAS
PubMed
Google Scholar
Weber MJ. Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet. 2006;2:1984–97. https://doi.org/10.1371/journal.pgen.0020205.
Article
Google Scholar
Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. Genetica. 2003;118:99–115. https://doi.org/10.1023/A:1024141306559.
Article
CAS
PubMed
Google Scholar
Zhang Y, Liu J, Jia C, Li T, Wu R, Wang J, et al. Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genomics. 2010;11:61. https://doi.org/10.1186/1471-2164-11-61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doucet AJ, Droc G, Siol O, Audoux J, Gilbert N. U6 snRNA pseudogenes: markers of retrotransposition dynamics in mammals. Mol Biol Evol. 2015;32:1815–32. https://doi.org/10.1093/molbev/msv062.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmitz J, Zemann A, Churakov G, Kuhl H, Grützner F, Reinhardt R, et al. Retroposed SNOfall - a mammalian-wide comparison of platypus snoRNAs. Genome Res. 2008;18:1005–10. https://doi.org/10.1101/gr.7177908.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo Y, Li S. Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs. Nucleic Acids Res. 2007;35:559–71. https://doi.org/10.1093/nar/gkl1086.
Article
CAS
PubMed
Google Scholar
Zemann A. op de Bekke a, Kiefmann M, Brosius J, Schmitz J. evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 2006;34:2676–85. https://doi.org/10.1093/nar/gkl359.
Article
CAS
PubMed
PubMed Central
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. https://doi.org/10.1186/1471-2164-10-86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hirose T, Ideue T, Nagai M, Hagiwara M, Di Shu M, Steitz JA. A Spliceosomal intron binding protein, IBP160, links position-dependent assembly of intron-encoded box C/D snoRNP to pre-mRNA splicing. Mol Cell. 2006;23:673–84. https://doi.org/10.1016/j.molcel.2006.07.011.
Article
CAS
PubMed
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. https://doi.org/10.1186/1471-2148-12-183.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scott MS, Ono M. From snoRNA to miRNA: dual function regulatory non-coding RNAs. Biochimie. 2011;93:1987–92. https://doi.org/10.1016/j.biochi.2011.05.026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 2021;49:D192–200. https://doi.org/10.1093/nar/gkaa1047.
Article
CAS
PubMed
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. https://doi.org/10.1093/molbev/mst209.
Article
CAS
PubMed
Google Scholar
Lu Z, Gregory MA. Developmental analysis of Spliceosomal snRNA isoform expression. G3 genes, genomes. Genet. 2015;5:103–10. https://doi.org/10.1534/g3.114.015735.
Article
Google Scholar
O’Reilly D, Dienstbier M, Cowley SA, Vazquez P, Drozdz M, Taylor S, et al. Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. Genome Res. 2013;23:281–91. https://doi.org/10.1101/gr.142968.112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, et al. Tissue- and time-specific expression of otherwise identical tRNA genes. PLoS Genet. 2016;12. https://doi.org/10.1371/journal.pgen.1006264.
Isakova A, Fehlmann T, Keller A, Quake SR. A mouse tissue atlas of small noncoding RNA. Proc Natl Acad Sci U S A. 2020;117:25634–45. https://doi.org/10.1073/pnas.2002277117.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, et al. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA. 2018;24:950–65. https://doi.org/10.1261/rna.064493.117.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu H, Yao J, Wu DC, Lambowitz AM. Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction. Sci Rep. 2019;9. https://doi.org/10.1038/s41598-019-44457-z.
Qin Y, Yao J, Wu DC, Nottingham RM, Mohr S, Hunicke-Smith S, et al. High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases. RNA. 2016;22:111–28. https://doi.org/10.1261/rna.054809.115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nottingham RM, Wu DC, Qin Y, Yao J, Hunicke-Smith S, Lambowitz AM. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase. RNA. 2016;22:597–613. https://doi.org/10.1261/rna.055558.115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deschamps-Francoeur G, Boivin V, Abou Elela S, Scott MS. CoCo: RNA-seq read assignment correction for nested genes and multimapped reads. Bioinformatics. 2019;35:5039–47. https://doi.org/10.1093/bioinformatics/btz433.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hirose T, Di Shu M, Steitz JA. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell. 2003;12:113–23. https://doi.org/10.1016/S1097-2765(03)00267-3.
Article
CAS
PubMed
Google Scholar
Capra E, Lazzari B, Frattini S, Chessa S, Coizet B, Talenti A, et al. Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus. BMC Genomics. 2018;19:417. https://doi.org/10.1186/s12864-018-4767-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cavaillé J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B, et al. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci U S A. 2000;97:14311–6. https://doi.org/10.1073/pnas.250426397.
Article
PubMed
PubMed Central
Google Scholar
Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF. Phylogenetic distribution of plant snoRNA families. BMC Genomics. 2016;17:969. https://doi.org/10.1186/s12864-016-3301-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
The contribution of RNAs and retroposition to evolutionary novelties - PubMed. https://pubmed.ncbi.nlm.nih.gov/12868601/. Accessed 9 Mar 2021.
Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM. An evaluation of function of multicopy noncoding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Mol Biol Evol. 2018;35:1451–62. https://doi.org/10.1093/molbev/msy046.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yanshina DD, Bulygin KN, Malygin AA, Karpova GG. Hydroxylated histidine of human ribosomal protein uL2 is involved in maintaining the local structure of 28S rRNA in the ribosomal peptidyl transferase center. FEBS J. 2015;282:1554–66. https://doi.org/10.1111/febs.13241.
Article
CAS
PubMed
Google Scholar
Sharma S, Marchand V, Motorin Y, Lafontaine DLJ. Identification of sites of 2′-O-methylation vulnerability in human ribosomal RNAs by systematic mapping. Sci Rep. 2017;7. https://doi.org/10.1038/s41598-017-09734-9.
Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, et al. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res. 2017;45:2341–53. https://doi.org/10.1093/nar/gkw1321.
Article
CAS
PubMed
Google Scholar
Krogh N, Jansson MD, Häfner SJ, Tehler D, Birkedal U, Christensen-Dalsgaard M, et al. Profiling of 2′-O-me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Res. 2016;44:7884–95. https://doi.org/10.1093/nar/gkw482.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marchand V, Pichot F, Neybecker P, Ayadi L, Bourguignon-Igel V, Wacheul L, et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res. 2020;48:e110. https://doi.org/10.1093/nar/gkaa769.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ketchesin KD, Zong W, Hildebrand MA, Seney ML, Cahill KM, Scott MR, et al. Diurnal rhythms across the human dorsal and ventral striatum. Proc Natl Acad Sci U S A. 2021;118. https://doi.org/10.1073/pnas.2016150118.
Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science. 2006;311:230–2. https://doi.org/10.1126/science.1118265.
Article
CAS
PubMed
Google Scholar
Duan S, Luo X, Zeng H, Zhan X, Yuan C. SNORA71B promotes breast cancer cells across blood–brain barrier by inducing epithelial-mesenchymal transition. Breast Cancer. 2020;27:1072–81. https://doi.org/10.1007/s12282-020-01111-1.
Article
PubMed
PubMed Central
Google Scholar
Lykke-Andersen S, Chen Y, Ardal BR, Lilje B, Waage J, Sandelin A, et al. Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes. Genes Dev. 2014;28:2498–517. https://doi.org/10.1101/gad.246538.114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doucet AJ, Wilusz JE, Miyoshi T, Liu Y, Moran JV. A 3′ poly(a) tract is required for LINE-1 Retrotransposition. Mol Cell. 2015;60:728–41. https://doi.org/10.1016/j.molcel.2015.10.012.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berndt H, Harnisch C, Rammelt C, Stöhr N, Zirkel A, Dohm JC, et al. Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming. RNA. 2012;18:958–72. https://doi.org/10.1261/rna.032292.112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koster J, Rahmann S. Snakemake--a scalable bioinformatics workflow engine. Bioinformatics. 2012;28:2520–2. https://doi.org/10.1093/bioinformatics/bts480.
Article
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dobin A, Gingeras TR. Optimizing RNA-seq mapping with STAR. In: Methods in molecular biology: Humana Press Inc; 2016. p. 245–62. https://doi.org/10.1007/978-1-4939-3572-7_13.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422–3. https://doi.org/10.1093/bioinformatics/btp163.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. https://doi.org/10.1101/gr.229102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034–50. https://doi.org/10.1101/gr.3715005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2. https://doi.org/10.1093/bioinformatics/btq033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. DbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11. https://doi.org/10.1093/nar/29.1.308.
Article
CAS
PubMed
PubMed Central
Google Scholar