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Cited by 88Genetic Syndromes and ImprintingRNA modifications and cancerRNA Research and Splicing

The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader-Willi locus generate canonical box C/D snoRNAs

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Bortolin-Cavaille, M.-L., Cavaille, J.·2012·Nucleic Acids Research
DOI 10.1093/nar/gks321PMC PMC3413130
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Abstract

The imprinted Snurf-Snrpn chromosomal domain contains two large arrays of tandemly repeated, paternally expressed box C/D small-nucleolar RNA (snoRNA) genes: the SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters believed to play key roles in the fine-tuning of serotonin receptor (5-HT2C) pre-mRNA processing and in the etiology of the Prader-Willi Syndrome (PWS), respectively. SNORD115 and SNORD116 were recently proposed to undergo significant conversion into shorter RNA species, the so-called psnoRNAs. Here, we provide evidence that argues against the existence of abundant psnoRNAs in human or mouse brain. Instead, we characterize a previously unsuspected low-abundance, fibrillarin-associated SNORD115-derived smaller RNA species. Based on these findings, we strongly recommend that PWS-encoded SNORD115 and SNORD116 be considered as bona fide box C/D snoRNAs.

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  • SNORD115 is expressed exclusively in brain and specifically in neurons.

    “this cluster of ncRNAs is expressed exclusively in brain and specifically in neurons (Bortolin-Cavaille and Cavaille, 2012; Cavaillé, 2017; Chamberlain, 2013; Chamberlain and Lalande, 2010b; Chung et al., 2020; Keshavarz et al., 2020; Wevrick et al., 1994).”

    From Small nucleolar RNAs in plasma extracellular vesicles and their discriminatory power as diagnostic biomarkers of Alzheimer's disease (2021) · cites this paper as Bortolin-Cavaille and Cavaille, 2012

    In Results and Discussion (Figure 2; page unavailable), the paper detects SNORD115 in brain RNA and uses liver as a negative control. It does not establish expression exclusively in the brain. The Conclusion only speculates that production of SNORD115 derivatives may be restricted to neuronal tissues; it does not show that SNORD115 itself is expressed specifically in neurons. (LLM, conf=0.83)

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Research works printed but not linked: 48

  1. [1]Henras AK Dez C Henry Y RNA structure and function in C/D and H/ACA s(no)RNPs Curr. Opin. Struct. Biol. 2004 14 335 343 15193314
  2. [2]Kiss T Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs EMBO J. 2001 20 3617 3622 11447102 PMC125535
  3. [3]Reichow SL Hamma T Ferre-D’Amare AR Varani G The structure and function of small nucleolar ribonucleoproteins Nucleic Acids Res. 2007 35 1452 1464 17284456 PMC1865073
  4. [4]Cavaille J Nicoloso M Bachellerie JP Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides Nature 1996 383 732 735 8878486
  5. [5]Ganot P Bortolin ML Kiss T Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs Cell 1997 89 799 809 9182768
  6. [6]Kiss-Laszlo 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 1088 8674114
  7. [7]Klein DJ Schmeing TM Moore PB Steitz TA The kink-turn: a new RNA secondary structure motif EMBO J. 2001 20 4214 4221 11483524 PMC149158
  8. [8]Hutzinger R Feederle R Mrazek J Schiefermeier N Balwierz PJ Zavolan M Polacek N Delecluse HJ Huttenhofer A Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome PLoS Pathog. 2009 5 e1000547 19680535 PMC2718842
  9. [9]Ender C Krek A Friedlander MR Beitzinger M Weinmann L Chen W Pfeffer S Rajewsky N Meister G A human snoRNA with microRNA-like functions Mol. Cell 2008 32 519 528 19026782
  10. [10]Kawaji H Nakamura M Takahashi Y Sandelin A Katayama S Fukuda S Daub CO Kai C Kawai J Yasuda J Hidden layers of human small RNAs BMC Genomics 2008 9 157 18402656 PMC2359750
  11. [11]Brameier M Herwig A Reinhardt R Walter L Gruber J Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs Nucleic Acids Res. 2011 39 675 686 20846955 PMC3025573
  12. [12]Taft RJ Glazov EA Lassmann T Hayashizaki Y Carninci P Mattick JS Small RNAs derived from snoRNAs RNA 2009 15 1233 1240 19474147 PMC2704076
  13. [13]Saraiya AA Wang CC snoRNA, a novel precursor of microRNA in Giardia lamblia PLoS Pathog. 2008 4 e1000224 19043559 PMC2583053
  14. [14]Ono M Scott MS Yamada K Avolio F Barton GJ Lamond AI Identification of human miRNA precursors that resemble box C/D snoRNAs Nucleic Acids Res. 2011 39 3879 3891 21247878 PMC3089480
  15. [15]Scott MS Avolio F Ono M Lamond AI Barton GJ Human miRNA precursors with box H/ACA snoRNA features PLoS Comput. Biol. 2009 5 e1000507 19763159 PMC2730528
  16. [16]Rother S Meister G Small RNAs derived from longer non-coding RNAs Biochimie 2011 93 1905 1915 21843590
  17. [17]Tuck AC Tollervey D RNA in pieces Trends Genet. 2011 27 422 432 21741109
  18. [18]Scott MS Ono M From snoRNA to miRNA: dual function regulatory non-coding RNAs Biochimie 2011 93 1987 1992 21664409 PMC3476530
  19. [19]Landers M Bancescu DL Le Meur E Rougeulle C Glatt-Deeley H Brannan C Muscatelli F Lalande M Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn Nucleic Acids Res. 2004 32 3480 3492 15226413 PMC443545
  20. [20]Cavaille J Buiting K Kiefmann M Lalande M Brannan CI Horsthemke B Bachellerie JP Brosius J Huttenhofer A Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization Proc. Natl Acad. Sci. USA 2000 97 14311 14316 11106375 PMC18915
  21. [21]Vitali P Royo H Marty V Bortolin-Cavaille ML Cavaille J Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays J. Cell Sci. 2010 123 70 83 20016068
  22. [22]Runte M Huttenhofer A Gross S Kiefmann M Horsthemke B Buiting K The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A Hum. Mol. Genet. 2001 10 2687 2700 11726556
  23. [23]Kishore S Stamm S The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C Science 2006 311 230 232 16357227
  24. [24]Vitali P Basyuk E Le Meur E Bertrand E Muscatelli F Cavaille J Huttenhofer A ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs J. Cell Biol. 2005 169 745 753 15939761 PMC2171610
  25. [25]Ding F Li HH Zhang S Solomon NM Camper SA Cohen P Francke U SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice PLoS One 2008 3 e1709 18320030 PMC2248623
  26. [26]Skryabin BV Gubar LV Seeger B Pfeiffer J Handel S Robeck T Karpova E Rozhdestvensky TS Brosius J Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation PLoS Genet. 2007 3 e235 18166085 PMC2323313
  27. [27]Sahoo T del Gaudio D German JR Shinawi M Peters SU Person RE Garnica A Cheung SW Beaudet AL Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster Nat. Genet. 2008 40 719 721 18500341 PMC2705197
  28. [28]Duker AL Ballif BC Bawle EV Person RE Mahadevan S Alliman S Thompson R Traylor R Bejjani BA Shaffer LG Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome Eur. J. Hum. Genet. 18 1196 1201 20588305 PMC2987474
  29. [29]de Smith AJ Purmann C Walters RG Ellis RJ Holder SE Van Haelst MM Brady AF Fairbrother UL Dattani M Keogh JM A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism Hum. Mol. Genet. 2009 18 3257 3265 19498035 PMC2722987
  30. [30]Shen M Eyras E Wu J Khanna A Josiah S Rederstorff M Zhang MQ Stamm S Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression Nucleic Acids Res. 2011 39 9720 9730 21880592 PMC3239178
  31. [31]Kishore S Khanna A Zhang Z Hui J Balwierz PJ Stefan M Beach C Nicholls RD Zavolan M Stamm S The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing (2010) Hum. Mol. Genet. 19 1153 1164 20053671 PMC2838533
  32. [32]Nakatani J Tamada K Hatanaka F Ise S Ohta H Inoue K Tomonaga S Watanabe Y Chung YJ Banerjee R Abnormal behavior in a chromosome-engineered mouse model for human 15q11-13 duplication seen in autism Cell 2009 137 1235 1246 19563756 PMC3710970
  33. [33]Cavaille J Vitali P Basyuk E Huttenhofer A Bachellerie JP A novel brain-specific box C/D small nucleolar RNA processed from tandemly repeated introns of a noncoding RNA gene in rats J. Biol. Chem. 2001 276 26374 26383 11346658
  34. [34]Perumal K Reddy R The 3’ end formation in small RNAs Gene Expr. 2002 10 59 78 11868988 PMC5977532
  35. [35]Li Y Luo J Zhou H Liao JY Ma LM Chen YQ Qu LH Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia Nucleic Acids Res. 2008 36 6048 6055 18820301 PMC2577346
  36. [36]Lee YS Shibata Y Malhotra A Dutta A A novel class of small RNAs: tRNA-derived RNA fragments (tRFs) Genes Dev. 2009 23 2639 2649 19933153 PMC2779758
  37. [37]Haussecker D Huang Y Lau A Parameswaran P Fire AZ Kay MA Human tRNA-derived small RNAs in the global regulation of RNA silencing RNA 2010 16 673 695 20181738 PMC2844617
  38. [38]Hsieh LC Lin SI Kuo HF Chiou TJ Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots Plant Signal. Behav. 2010 5 537 539 PMC7080466 20404547
  39. [39]Cole C Sobala A Lu C Thatcher SR Bowman A Brown JW Green PJ Barton GJ Hutvagner G Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs RNA 2009 15 2147 2160 19850906 PMC2779667
  40. [40]Taft RJ Glazov EA Cloonan N Simons C Stephen S Faulkner GJ Lassmann T Forrest AR Grimmond SM Schroder K Tiny RNAs associated with transcription start sites in animals Nat. Genet. 2009 41 572 578 19377478
  41. [41]Persson H Kvist A Vallon-Christersson J Medstrand P Borg A Rovira C The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs Nat. Cell Biol. 2009 11 1268 1271 19749744
  42. [42]Verhagen AP Pruijn GJ Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity Bioessays 2011 33 674 682 21735459
  43. [43]Darzacq X Kiss T Processing of intron-encoded box C/D small nucleolar RNAs lacking a 5’,3’-terminal stem structure Mol. Cell Biol. 2000 20 4522 4531 10848579 PMC85834
  44. [44]Qu LH Henry Y Nicoloso M Michot B Azum MC Renalier MH Caizergues-Ferrer M Bachellerie JP U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA Nucleic Acids Res. 1995 23 2669 2676 7651828 PMC307091
  45. [45]Qu LH Nicoloso M Michot B Azum MC Caizergues-Ferrer M Renalier MH Bachellerie JP U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and mammals Nucleic Acids Res. 1994 22 4073 4081 7937132 PMC331892
  46. [46]Nicoloso M Caizergues-Ferrer M Michot B Azum MC Bachellerie JP U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals Mol. Cell Biol. 1994 14 5766 5776 8065311 PMC359102
  47. [47]Kiss T Filipowicz W Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns Genes Dev. 1995 9 1411 1424 7797080
  48. [48]Ding F Prints Y Dhar MS Johnson DK Garnacho-Montero C Nicholls RD Francke U Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models Mamm. Genome 2005 16 424 431 16075369

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Authors
Bortolin-Cavaille, M.-L., & Cavaille, J.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2012-04-11
Volume
40
Issue
14
Pages
6800-6807
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gks321
PMC
PMC3413130
OpenAlex
W1981030624
Cited by
88
References
0
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FWCI
5.20
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • European Commission
  • Agence Nationale de la Recherche
  • Centre National de la Recherche Scientifique
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
SNORD116, box C/D snoRNA, Prader-Willi syndrome, genomic imprinting, fibrillarin
MeSH terms
Animals, Base Sequence, Multigene Family, Humans, Molecular Sequence Data, Prader-Willi Syndrome, Genomic Imprinting, RNA, Small Nucleolar, Mice, Genetic Loci

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