Статті в журналах: "Box C/D small nucleolar RNA"

1

Speckmann, Wayne, Aarthi Narayanan, Rebecca Terns, and Michael P. Terns. "Nuclear Retention Elements of U3 Small Nucleolar RNA." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 8412–21. http://dx.doi.org/10.1128/mcb.19.12.8412.

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ABSTRACT The processing and methylation of precursor rRNA is mediated by the box C/D small nucleolar RNAs (snoRNAs). These snoRNAs differ from most cellular RNAs in that they are not exported to the cytoplasm. Instead, these RNAs are actively retained in the nucleus where they assemble with proteins into mature small nucleolar ribonucleoprotein particles and are targeted to their intranuclear site of action, the nucleolus. In this study, we have identified the cis-acting sequences responsible for the nuclear retention of U3 box C/D snoRNA by analyzing the nucleocytoplasmic distributions of an extensive panel of U3 RNA variants after injection of the RNAs into Xenopus oocyte nuclei. Our data indicate the importance of two conserved sequence motifs in retaining U3 RNA in the nucleus. The first motif is comprised of the conserved box C′ and box D sequences that characterize the box C/D family. The second motif contains conserved box sequences B and C. Either motif is sufficient for nuclear retention, but disruption of both motifs leads to mislocalization of the RNAs to the cytoplasm. Variant RNAs that are not retained also lack 5′ cap hypermethylation and fail to associate with fibrillarin. Furthermore, our results indicate that nuclear retention of U3 RNA does not simply reflect its nucleolar localization. A fragment of U3 containing the box B/C motif is not localized to nucleoli but retained in coiled bodies. Thus, nuclear retention and nucleolar localization are distinct processes with differing sequence requirements.

2

Lange, Thilo Sascha, Michael Ezrokhi, Anton V. Borovjagin, Rafael Rivera-León, Melanie T. North, and Susan A. Gerbi. "Nucleolar Localization Elements of Xenopus laevis U3 Small Nucleolar RNA." Molecular Biology of the Cell 9, no. 10 (October 1998): 2973–85. http://dx.doi.org/10.1091/mbc.9.10.2973.

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The Nucleolar Localization Elements (NoLEs) of Xenopus laevis U3 small nucleolar RNA (snoRNA) have been defined. Fluorescein-labeled wild-type U3 snoRNA injected intoXenopus oocyte nuclei localized specifically to nucleoli as shown by fluorescence microscopy. Injection of mutated U3 snoRNA revealed that the 5′ region containing Boxes A and A′, known to be important for rRNA processing, is not essential for nucleolar localization. Nucleolar localization of U3 snoRNA was independent of the presence and nature of the 5′ cap and the terminal stem. In contrast, Boxes C and D, common to the Box C/D snoRNA family, are critical elements for U3 localization. Mutation of the hinge region, Box B, or Box C′ led to reduced U3 nucleolar localization. Results of competition experiments suggested that Boxes C and D act in a cooperative manner. It is proposed that Box B facilitates U3 snoRNA nucleolar localization by the primary NoLEs (Boxes C and D), with the hinge region of U3 subsequently base pairing to the external transcribed spacer of pre-rRNA, thus positioning U3 snoRNA for its roles in rRNA processing.

3

Narayanan, Aarthi, Wayne Speckmann, Rebecca Terns, and Michael P. Terns. "Role of the Box C/D Motif in Localization of Small Nucleolar RNAs to Coiled Bodies and Nucleoli." Molecular Biology of the Cell 10, no. 7 (July 1999): 2131–47. http://dx.doi.org/10.1091/mbc.10.7.2131.

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Small nucleolar RNAs (snoRNAs) are a large family of eukaryotic RNAs that function within the nucleolus in the biogenesis of ribosomes. One major class of snoRNAs is the box C/D snoRNAs named for their conserved box C and box D sequence elements. We have investigated the involvement of cis-acting sequences and intranuclear structures in the localization of box C/D snoRNAs to the nucleolus by assaying the intranuclear distribution of fluorescently labeled U3, U8, and U14 snoRNAs injected into Xenopus oocyte nuclei. Analysis of an extensive panel of U3 RNA variants showed that the box C/D motif, comprised of box C′, box D, and the 3′ terminal stem of U3, is necessary and sufficient for the nucleolar localization of U3 snoRNA. Disruption of the elements of the box C/D motif of U8 and U14 snoRNAs also prevented nucleolar localization, indicating that all box C/D snoRNAs use a common nucleolar-targeting mechanism. Finally, we found that wild-type box C/D snoRNAs transiently associate with coiled bodies before they localize to nucleoli and that variant RNAs that lack an intact box C/D motif are detained within coiled bodies. These results suggest that coiled bodies play a role in the biogenesis and/or intranuclear transport of box C/D snoRNAs.

4

Nicoloso, M., M. Caizergues-Ferrer, B. Michot, M. C. Azum, and J. P. Bachellerie. "U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals." Molecular and Cellular Biology 14, no. 9 (September 1994): 5766–76. http://dx.doi.org/10.1128/mcb.14.9.5766.

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We have found that intron 11 of the nucleolin gene in humans and rodents encodes a previously unidentified small nucleolar RNA, termed U20. The single-copy U20 sequence is located on the same DNA strand as the nucleolin mRNA. U20 RNA, which does not possess a trimethyl cap, appears to result from intronic RNA processing and not from transcription of an independent gene. In mammals, U20 RNA is an 80-nucleotide-long, metabolically stable species, present at about 7 x 10(3) molecules per exponentially growing HeLa cell. It has a nucleolar localization, as indicated by fluorescence microscopy following in situ hybridization with digoxigenin-labeled oligonucleotides. U20 RNA contains the box C and box D sequence motifs, hallmarks of most small nucleolar RNAs reported to date, and is immunoprecipitated by antifibrillarin antibodies. It also exhibits a 5'-3' terminal stem bracketing the box C-box D motifs like U14, U15, U16, or Y RNA. A U20 homolog of similar size has been detected in all vertebrate classes by Northern (RNA) hybridization with mammalian oligonucleotide probes. U20 RNA contains an extended region (21 nucleotides) of perfect complementarity with a phylogenetically conserved sequence in 18S rRNA. This complementarity is strongly preserved among distant vertebrates, suggesting that U20 RNA may be involved in the formation of the small ribosomal subunit like nucleolin, the product of its host gene.

5

Nicoloso, M., M. Caizergues-Ferrer, B. Michot, M. C. Azum, and J. P. Bachellerie. "U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals." Molecular and Cellular Biology 14, no. 9 (September 1994): 5766–76. http://dx.doi.org/10.1128/mcb.14.9.5766-5776.1994.

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We have found that intron 11 of the nucleolin gene in humans and rodents encodes a previously unidentified small nucleolar RNA, termed U20. The single-copy U20 sequence is located on the same DNA strand as the nucleolin mRNA. U20 RNA, which does not possess a trimethyl cap, appears to result from intronic RNA processing and not from transcription of an independent gene. In mammals, U20 RNA is an 80-nucleotide-long, metabolically stable species, present at about 7 x 10(3) molecules per exponentially growing HeLa cell. It has a nucleolar localization, as indicated by fluorescence microscopy following in situ hybridization with digoxigenin-labeled oligonucleotides. U20 RNA contains the box C and box D sequence motifs, hallmarks of most small nucleolar RNAs reported to date, and is immunoprecipitated by antifibrillarin antibodies. It also exhibits a 5'-3' terminal stem bracketing the box C-box D motifs like U14, U15, U16, or Y RNA. A U20 homolog of similar size has been detected in all vertebrate classes by Northern (RNA) hybridization with mammalian oligonucleotide probes. U20 RNA contains an extended region (21 nucleotides) of perfect complementarity with a phylogenetically conserved sequence in 18S rRNA. This complementarity is strongly preserved among distant vertebrates, suggesting that U20 RNA may be involved in the formation of the small ribosomal subunit like nucleolin, the product of its host gene.

6

Lange, Thilo Sascha, Michael Ezrokhi, Francesco Amaldi, and Susan A. Gerbi. "Box H and Box ACA Are Nucleolar Localization Elements of U17 Small Nucleolar RNA." Molecular Biology of the Cell 10, no. 11 (November 1999): 3877–90. http://dx.doi.org/10.1091/mbc.10.11.3877.

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The nucleolar localization elements (NoLEs) of U17 small nucleolar RNA (snoRNA), which is essential for rRNA processing and belongs to the box H/ACA snoRNA family, were analyzed by fluorescence microscopy. Injection of mutant U17 transcripts into Xenopus laevisoocyte nuclei revealed that deletion of stems 1, 2, and 4 of U17 snoRNA reduced but did not prevent nucleolar localization. The deletion of stem 3 had no adverse effect. Therefore, the hairpins of the hairpin–hinge–hairpin–tail structure formed by these stems are not absolutely critical for nucleolar localization of U17, nor are sequences within stems 1, 3, and 4, which may tether U17 to the rRNA precursor by base pairing. In contrast, box H and box ACA are major NoLEs; their combined substitution or deletion abolished nucleolar localization of U17 snoRNA. Mutation of just box H or just the box ACA region alone did not fully abolish the nucleolar localization of U17. This indicates that the NoLEs of the box H/ACA snoRNA family function differently from the bipartite NoLEs (conserved boxes C and D) of box C/D snoRNAs, where mutation of either box alone prevents nucleolar localization.

7

Gogolevskaya, Irina K., Julia A. Makarova, Larisa N. Gause, Valentina A. Kulichkova, Irina M. Konstantinova, and Dmitri A. Kramerov. "U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells." Gene 292, no. 1-2 (June 2002): 199–204. http://dx.doi.org/10.1016/s0378-1119(02)00678-9.

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8

Westendorf, Joanne M., Konstantin N. Konstantinov, Steven Wormsley, Mei-Di Shu, Naoko Matsumoto-Taniura, Fabienne Pirollet, F. George Klier, Larry Gerace, and Susan J. Baserga. "M Phase Phosphoprotein 10 Is a Human U3 Small Nucleolar Ribonucleoprotein Component." Molecular Biology of the Cell 9, no. 2 (February 1998): 437–49. http://dx.doi.org/10.1091/mbc.9.2.437.

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We have previously developed a novel technique for isolation of cDNAs encoding M phase phosphoproteins (MPPs). In the work described herein, we further characterize MPP10, one of 10 novel proteins that we identified, with regard to its potential nucleolar function. We show that by cell fractionation, almost all MPP10 was found in isolated nucleoli. By immunofluorescence, MPP10 colocalized with nucleolar fibrillarin and other known nucleolar proteins in interphase cells but was not detected in the coiled bodies stained for either fibrillarin or p80 coilin, a protein found only in the coiled body. When nucleoli were separated into fibrillar and granular domains by treatment with actinomycin D, almost all the MPP10 was found in the fibrillar caps, which contain proteins involved in rRNA processing. In early to middle M phase of the cell cycle, MPP10 colocalized with fibrillarin to chromosome surfaces. At telophase, MPP10 was found in cellular structures that resembled nucleolus-derived bodies and prenucleolar bodies. Some of these bodies lacked fibrillarin, a previously described component of nucleolus-derived bodies and prenucleolar bodies, however, and the bulk of MPP10 arrived at the nucleolus later than fibrillarin. To further examine the properties of MPP10, we immunoprecipitated it from cell sonicates. The resulting precipitates contained U3 small nucleolar RNA (snoRNA) but no significant amounts of other box C/D snoRNAs. This association of MPP10 with U3 snoRNA was stable to 400 mM salt and suggested that MPP10 is a component of the human U3 small nucleolar ribonucleoprotein.

9

Verheggen, C. "Box C/D small nucleolar RNA trafficking involves small nucleolar RNP proteins, nucleolar factors and a novel nuclear domain." EMBO Journal 20, no. 19 (October 1, 2001): 5480–90. http://dx.doi.org/10.1093/emboj/20.19.5480.

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10

Brandis, Katrina A., Sarah Gale, Sarah Jinn, Stephen J. Langmade, Nicole Dudley-Rucker, Hui Jiang, Rohini Sidhu, et al. "Box C/D Small Nucleolar RNA (snoRNA) U60 Regulates Intracellular Cholesterol Trafficking." Journal of Biological Chemistry 288, no. 50 (October 30, 2013): 35703–13. http://dx.doi.org/10.1074/jbc.m113.488577.

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11

Yang, Yunfeng, Cynthia Isaac, Chen Wang, François Dragon, Vanda Pogac̆ić, and U. Thomas Meier. "Conserved Composition of Mammalian Box H/ACA and Box C/D Small Nucleolar Ribonucleoprotein Particles and Their Interaction with the Common Factor Nopp140." Molecular Biology of the Cell 11, no. 2 (February 2000): 567–77. http://dx.doi.org/10.1091/mbc.11.2.567.

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Small nucleolar ribonucleoprotein particles (snoRNPs) mainly catalyze the modification of rRNA. The two major classes of snoRNPs, box H/ACA and box C/D, function in the pseudouridylation and 2′-O-methylation, respectively, of specific nucleotides. The emerging view based on studies in yeast is that each class of snoRNPs is composed of a unique set of proteins. Here we present a characterization of mammalian snoRNPs. We show that the previously characterized NAP57 is specific for box H/ACA snoRNPs, whereas the newly identified NAP65, the rat homologue of yeast Nop5/58p, is a component of the box C/D class. Using coimmunoprecipitation experiments, we show that the nucleolar and coiled-body protein Nopp140 interacts with both classes of snoRNPs. This interaction is corroborated in vivo by the exclusive depletion of snoRNP proteins from nucleoli in cells transfected with a dominant negative Nopp140 construct. Interestingly, RNA polymerase I transcription is arrested in nucleoli depleted of snoRNPs, raising the possibility of a feedback mechanism between rRNA modification and transcription. Moreover, the Nopp140-snoRNP interaction appears to be conserved in yeast, because depletion of Srp40p, the yeast Nopp140 homologue, in a conditional lethal strain induces the loss of box H/ACA small nucleolar RNAs. We propose that Nopp140 functions as a chaperone of snoRNPs in yeast and vertebrate cells.

12

Yu, Yi-Tao, Mei-Di Shu, Aarthi Narayanan, Rebecca M. Terns, Michael P. Terns, and Joan A. Steitz. "Internal Modification of U2 Small Nuclear (Snrna) Occurs in Nucleoli of Xenopus Oocytes." Journal of Cell Biology 152, no. 6 (March 19, 2001): 1279–88. http://dx.doi.org/10.1083/jcb.152.6.1279.

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U2 small nuclear (sn)RNA contains a large number of posttranscriptionally modified nucleotides, including a 5′ trimethylated guanosine cap, 13 pseudouridines, and 10 2′-O-methylated residues. Using Xenopus oocytes, we demonstrated previously that at least some of these modified nucleotides are essential for biogenesis of a functional snRNP. Here we address the subcellular site of U2 internal modification. Upon injection into the cytoplasm of oocytes, G-capped U2 that is transported to the nucleus becomes modified, whereas A-capped U2 that remains in the cytoplasm is not modified. Furthermore, by injecting U2 RNA into isolated nuclei or enucleated oocytes, we observe that U2 internal modifications occur exclusively in the nucleus. Analysis of the intranuclear localization of fluorescently labeled RNAs shows that injected wild-type U2 becomes localized to nucleoli and Cajal bodies. Both internal modification and nucleolar localization of U2 are dependent on the Sm binding site. An Sm-mutant U2 is targeted only to Cajal bodies. The Sm binding site can be replaced by a nucleolar localization signal derived from small nucleolar RNAs (the box C/D motif), resulting in rescue of internal modification as well as nucleolar localization. Analysis of additional chimeric U2 RNAs reveals a correlation between internal modification and nucleolar localization. Together, our results suggest that U2 internal modification occurs within the nucleolus.

13

Huang, G. M., A. Jarmolowski, J. C. Struck, and M. J. Fournier. "Accumulation of U14 small nuclear RNA in Saccharomyces cerevisiae requires box C, box D, and a 5', 3' terminal stem." Molecular and Cellular Biology 12, no. 10 (October 1992): 4456–63. http://dx.doi.org/10.1128/mcb.12.10.4456.

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U14 is one of several nucleolar small nuclear RNAs required for normal processing of rRNA. Functional mapping of U14 from Saccharomyces cerevisiae has yielded a number of mutants defective in U14 accumulation or function. In this study, we have further defined three structural elements required for U14 accumulation. The essential elements include the U14-conserved box C and box D sequences and a 5', 3' terminal stem. The box elements are coconserved among several nucleolar small nuclear RNAs and have been implicated in binding of the protein fibrillarin. New mutational results show that the first GA bases of the box C sequence UGAUGA are essential, and two vital bases in box D have also been identified. An intragenic suppressor of a lethal box C mutant has been isolated and shown to contain a new box C-like PyGAUG sequence two bases upstream of normal box C. The importance of the terminal stem was confirmed from new compensatory base changes and the finding that accumulation defects in the box elements can be complemented by extending the terminal stem. The results suggest that the observed defects in accumulation reflect U14 instability and that protein binding to one or more of these elements is required for metabolic stability.

14

Huang, G. M., A. Jarmolowski, J. C. Struck, and M. J. Fournier. "Accumulation of U14 small nuclear RNA in Saccharomyces cerevisiae requires box C, box D, and a 5', 3' terminal stem." Molecular and Cellular Biology 12, no. 10 (October 1992): 4456–63. http://dx.doi.org/10.1128/mcb.12.10.4456-4463.1992.

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U14 is one of several nucleolar small nuclear RNAs required for normal processing of rRNA. Functional mapping of U14 from Saccharomyces cerevisiae has yielded a number of mutants defective in U14 accumulation or function. In this study, we have further defined three structural elements required for U14 accumulation. The essential elements include the U14-conserved box C and box D sequences and a 5', 3' terminal stem. The box elements are coconserved among several nucleolar small nuclear RNAs and have been implicated in binding of the protein fibrillarin. New mutational results show that the first GA bases of the box C sequence UGAUGA are essential, and two vital bases in box D have also been identified. An intragenic suppressor of a lethal box C mutant has been isolated and shown to contain a new box C-like PyGAUG sequence two bases upstream of normal box C. The importance of the terminal stem was confirmed from new compensatory base changes and the finding that accumulation defects in the box elements can be complemented by extending the terminal stem. The results suggest that the observed defects in accumulation reflect U14 instability and that protein binding to one or more of these elements is required for metabolic stability.

15

Galardi, Silvia, Alessandro Fatica, Angela Bachi, Andrea Scaloni, Carlo Presutti, and Irene Bozzoni. "Purified Box C/D snoRNPs Are Able To Reproduce Site-Specific 2′-O-Methylation of Target RNA In Vitro." Molecular and Cellular Biology 22, no. 19 (October 1, 2002): 6663–68. http://dx.doi.org/10.1128/mcb.22.19.6663-6668.2002.

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ABSTRACT Small nucleolar RNAs (snoRNAs) are associated in ribonucleoprotein particles localized to the nucleolus (snoRNPs). Most of the members of the box C/D family function in directing site-specific 2′-O-methylation of substrate RNAs. Although the selection of the target nucleotide requires the antisense element and the conserved box D or D′ of the snoRNA, the methyltransferase activity is supposed to reside in one of the protein components. Through protein tagging of a snoRNP-specific factor, we purified to homogeneity box C/D snoRNPs from the yeast Saccharomyces cerevisiae. Mass spectrometric analysis demonstrated the presence of Nop1p, Nop58p, Nop56p, and Snu13p as integral components of the particle. We show that purified snoRNPs are able to reproduce the site-specific methylation pattern on target RNA and that the predicted S-adenosyl-l-methionine-binding region of Nop1p is responsible for the catalytic activity.

16

Caffarelli, Elisa, Massimo Losito, Corinna Giorgi, Alessandro Fatica, and Irene Bozzoni. "In Vivo Identification of Nuclear Factors Interacting with the Conserved Elements of Box C/D Small Nucleolar RNAs." Molecular and Cellular Biology 18, no. 2 (February 1, 1998): 1023–28. http://dx.doi.org/10.1128/mcb.18.2.1023.

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ABSTRACT The U16 small nucleolar RNA (snoRNA) is encoded by the third intron of the L1 (L4, according to the novel nomenclature) ribosomal protein gene of Xenopus laevis and originates from processing of the pre-mRNA in which it resides. The U16 snoRNA belongs to the box C/D snoRNA family, whose members are known to assemble in ribonucleoprotein particles (snoRNPs) containing the protein fibrillarin. We have utilized U16 snoRNA in order to characterize the factors that interact with the conserved elements common to the other members of the box C/D class. In this study, we have analyzed the in vivo assembly of U16 snoRNP particles in X. laevis oocytes and identified the proteins which interact with the RNA by label transfer after UV cross-linking. This analysis revealed two proteins, of 40- and 68-kDa apparent molecular size, which require intact boxes C and D together with the conserved 5′,3′-terminal stem for binding. Immunoprecipitation experiments showed that the p40 protein corresponds to fibrillarin, indicating that this protein is intimately associated with the RNA. We propose that fibrillarin and p68 represent the RNA-binding factors common to box C/D snoRNPs and that both proteins are essential for the assembly of snoRNP particles and the stabilization of the snoRNA.

17

Zhao, Rongmin, Yoshito Kakihara, Anna Gribun, Jennifer Huen, Guocheng Yang, May Khanna, Michael Costanzo, et al. "Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation." Journal of Cell Biology 180, no. 3 (February 11, 2008): 563–78. http://dx.doi.org/10.1083/jcb.200709061.

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Hsp90 is a highly conserved molecular chaperone that is involved in modulating a multitude of cellular processes. In this study, we identify a function for the chaperone in RNA processing and maintenance. This functionality of Hsp90 involves two recently identified interactors of the chaperone: Tah1 and Pih1/Nop17. Tah1 is a small protein containing tetratricopeptide repeats, whereas Pih1 is found to be an unstable protein. Tah1 and Pih1 bind to the essential helicases Rvb1 and Rvb2 to form the R2TP complex, which we demonstrate is required for the correct accumulation of box C/D small nucleolar ribonucleoproteins. Together with the Tah1 cofactor, Hsp90 functions to stabilize Pih1. As a consequence, the chaperone is shown to affect box C/D accumulation and maintenance, especially under stress conditions. Hsp90 and R2TP proteins are also involved in the proper accumulation of box H/ACA small nucleolar RNAs.

18

Stepanov, Grigoriy A., Dmitry V. Semenov, Anna V. Savelyeva, Elena V. Kuligina, Olga A. Koval, Igor V. Rabinov, and Vladimir A. Richter. "Artificial Box C/D RNAs Affect Pre-mRNA Maturation in Human Cells." BioMed Research International 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/656158.

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Box C/D small nucleolar RNAs (snoRNAs) are known to guide the2′-O-ribose methylation of nucleotides in eukaryotic ribosomal RNAs and small nuclear RNAs. Recently snoRNAs are predicted to regulate posttranscriptional modifications of pre-mRNA. To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. We found that transfection of artificial box C/D snoRNA analogues directed toHSPA8pre-mRNAs into human cells induced suppression of the target mRNA expression in a time- and dose-dependent manner. The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of theHSPA8pre-mRNA caused the most prominent influence on the level ofHSPA8mRNAs. Neither box D nor the ability to direct2′-O-methylation of nucleotides in target RNA was essential for the knockdown activity of artificial snoRNAs. Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes.

19

Deschamps-Francoeur, Gabrielle, Daniel Garneau, Fabien Dupuis-Sandoval, Audrey Roy, Marie Frappier, Mathieu Catala, Sonia Couture, Mélissa Barbe-Marcoux, Sherif Abou-Elela, and Michelle S. Scott. "Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency." Nucleic Acids Research 42, no. 15 (July 29, 2014): 10073–85. http://dx.doi.org/10.1093/nar/gku664.

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Abstract Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and cancer cell lines independent of their functions. The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length. Both forms are overexpressed in cancer cell lines but display a conserved end distribution. Surprisingly, the long forms are more dependent than the short forms on the expression of the core snoRNP protein NOP58, thought to be essential for C/D snoRNA production. In contrast, a subset of short forms are dependent on the splicing factor RBFOX2. Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP. Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.

20

Darzacq, Xavier, and Tamás Kiss. "Processing of Intron-Encoded Box C/D Small Nucleolar RNAs Lacking a 5′,3′-Terminal Stem Structure." Molecular and Cellular Biology 20, no. 13 (July 1, 2000): 4522–31. http://dx.doi.org/10.1128/mcb.20.13.4522-4531.2000.

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ABSTRACT The C and D box-containing (box C/D) small nucleolar RNAs (snoRNAs) function in the nucleolytic processing and 2′-O-methylation of precursor rRNA. In vertebrates, most box C/D snoRNAs are processed from debranched pre-mRNA introns by exonucleolytic activities. Elements directing accurate snoRNA excision are located within the snoRNA itself; they comprise the conserved C and D boxes and an adjoining 5′,3′-terminal stem. Although the terminal stem has been demonstrated to be essential for snoRNA accumulation, many snoRNAs lack a terminal helix. To identify thecis-acting elements supporting the accumulation of intron-encoded box C/D snoRNAs devoid of a terminal stem, we have investigated the in vivo processing of the human U46 snoRNA and an artificial snoRNA from the human β-globin pre-mRNA. We demonstrate that internal and/or external stem structures located within the snoRNA or in the intronic flanking sequences support the accumulation of mammalian box C/D snoRNAs lacking a canonical terminal stem. In the intronic precursor RNA, transiently formed external and/or stable internal base-pairing interactions fold the C and D boxes together and therefore facilitate the binding of snoRNP proteins. Since the external intronic stems are degraded during snoRNA processing, we propose that the C and D boxes alone can provide metabolic stability for the mature snoRNA.

21

Cavaillé, Jérôme. "Box C/D small nucleolar RNA genes and the Prader-Willi syndrome: a complex interplay." Wiley Interdisciplinary Reviews: RNA 8, no. 4 (March 13, 2017): e1417. http://dx.doi.org/10.1002/wrna.1417.

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22

Dudnakova, Tatiana, Hywel Dunn-Davies, Rosie Peters, and David Tollervey. "Mapping targets for small nucleolar RNAs in yeast." Wellcome Open Research 3 (September 19, 2018): 120. http://dx.doi.org/10.12688/wellcomeopenres.14735.1.

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Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.

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Dudnakova, Tatiana, Hywel Dunn-Davies, Rosie Peters, and David Tollervey. "Mapping targets for small nucleolar RNAs in yeast." Wellcome Open Research 3 (November 22, 2018): 120. http://dx.doi.org/10.12688/wellcomeopenres.14735.2.

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Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.

24

Stepanov, G. A., D. V. Semenov, E. V. Kuligina, O. A. Koval, I. V. Rabinov, Yu Ya Kit, and V. A. Richter. "Analogues of Artificial Human Box C/D Small Nucleolar RNA As Regulators of Alternative Splicing of a pre-mRNA Target." Acta Naturae 4, no. 1 (March 15, 2012): 32–41. http://dx.doi.org/10.32607/20758251-2012-4-1-32-41.

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Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA (rRNA) biogenesis. Box C/D snoRNAs guide the site-specific 2-O-ribose methylation of nucleotides in rRNAs and small nuclear RNAs (snRNAs). A number of box C/D snoRNAs and their fragments have recently been reported to regulate post-transcriptional modifications and the alternative splicing of pre-mRNA. Artificial analogues of U24 snoRNAs directed to nucleotides in 28S and 18S rRNAs, as well as pre-mRNAs and mature mRNAs of human heat shock cognate protein (hsc70), were designed and synthesized in this study. It was found that after the transfection of MCF-7 human cells with artificial box C/D RNAs in complex with lipofectamine, snoRNA analogues penetrated into cells and accumulated in the cytoplasm and nucleus. It was demonstrated that the transfection of cultured human cells with artificial box C/D snoRNA targeted to pre-mRNAs induce partial splicing impairments. It was found that transfection with artificial snoRNAs directed to 18S and 28S rRNA nucleotides, significant for ribosome functioning, induce a decrease in MCF-7 cell viability.

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Roberts, T. Guy, Nancy R. Sturm, Billy K. Yee, Michael C. Yu, Toinette Hartshorne, Nina Agabian, and David A. Campbell. "Three Small Nucleolar RNAs Identified from the Spliced Leader-Associated RNA Locus in Kinetoplastid Protozoans." Molecular and Cellular Biology 18, no. 8 (August 1, 1998): 4409–17. http://dx.doi.org/10.1128/mcb.18.8.4409.

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ABSTRACT First characterized in Trypanosoma brucei, the spliced leader-associated (SLA) RNA gene locus has now been isolated from the kinetoplastids Leishmania tarentolae and Trypanosoma cruzi. In addition to the T. brucei SLA RNA, bothL. tarentolae and T. cruzi SLA RNA repeat units also yield RNAs of 75 or 76 nucleotides (nt), 92 or 94 nt, and ∼450 or ∼350 nt, respectively, each with significant sequence identity to transcripts previously described from the T. brucei SLA RNA locus. Cell fractionation studies localize the three additional RNAs to the nucleolus; the presence of box C/D-like elements in two of the transcripts suggests that they are members of a class of small nucleolar RNAs (snoRNAs) that guide modification and cleavage of rRNAs. Candidate rRNA-snoRNA interactions can be found for one domain in each of the C/D element-containing RNAs. The putative target site for the 75/76-nt RNA is a highly conserved portion of the small subunit rRNA that contains 2′-O-ribose methylation at a conserved position (Gm1830) in L. tarentolae and in vertebrates. The 92/94-nt RNA has the potential to form base pairs near a conserved methylation site in the large subunit rRNA, which corresponds to position Gm4141 of small rRNA 2 in T. brucei. These data suggest that trypanosomatids do not obey the general 5-bp rule for snoRNA-mediated methylation.

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Baldini, Laeya, Bruno Charpentier, and Stéphane Labialle. "Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs." Non-Coding RNA 7, no. 2 (May 6, 2021): 30. http://dx.doi.org/10.3390/ncrna7020030.

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Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.

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Falaleeva, Marina, Amadis Pages, Zaneta Matuszek, Sana Hidmi, Lily Agranat-Tamir, Konstantin Korotkov, Yuval Nevo, Eduardo Eyras, Ruth Sperling, and Stefan Stamm. "Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing." Proceedings of the National Academy of Sciences 113, no. 12 (March 8, 2016): E1625—E1634. http://dx.doi.org/10.1073/pnas.1519292113.

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C/D box small nucleolar RNAs (SNORDs) are small noncoding RNAs, and their best-understood function is to target the methyltransferase fibrillarin to rRNA (for example,SNORD27performs 2′-O-methylation of A27 in 18S rRNA). Unexpectedly, we found a subset of SNORDs, includingSNORD27, in soluble nuclear extract made under native conditions, where fibrillarin was not detected, indicating that a fraction of theSNORD27RNA likely forms a protein complex different from canonical snoRNAs found in the insoluble nuclear fraction. As part of this previously unidentified complex,SNORD27regulates the alternative splicing of the transcription factorE2F7pre-mRNA through direct RNA–RNA interaction without methylating the RNA, likely by competing withU1small nuclear ribonucleoprotein (snRNP). Furthermore, knockdown ofSNORD27activates previously “silent” exons in several other genes through base complementarity across the entireSNORD27sequence, not just the antisense boxes. Thus, some SNORDs likely function in both rRNA and pre-mRNA processing, which increases the repertoire of splicing regulators and links both processes.

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Li, Cuicui, Long Wu, Pengpeng Liu, Kun Li, Zhonglin Zhang, Yueming He, Quanyan Liu, et al. "The C/D box small nucleolar RNA SNORD52 regulated by Upf1 facilitates Hepatocarcinogenesis by stabilizing CDK1." Theranostics 10, no. 20 (2020): 9348–63. http://dx.doi.org/10.7150/thno.47677.

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29

He, Jun-yan, Xin Liu, Zhen-hua Qi, Qi Wang, Wen-qing Lu, Qing-tong Zhang, Shu-ya He, and Zhi-dong Wang. "Small Nucleolar RNA, C/D Box 16 (SNORD16) Acts as a Potential Prognostic Biomarker in Colon Cancer." Dose-Response 18, no. 2 (April 1, 2020): 155932582091782. http://dx.doi.org/10.1177/1559325820917829.

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Colon cancer (CC) is considered one of the most common and lethal malignancies occurring both in male and female. Its widespread prevalence demonstrates the need for novel diagnostic and prognostic biomarkers for CC. Emerging evidence has shown that small nucleolar RNAs play critical roles in tumor development. In this study, we investigated the expression profile and functions of SNORD16 in CC. Our data showed that SNORD16, rather than its host gene (RPL4), was upregulated in CC cell lines. Compared to matched adjacent normal tissues, CC tissues showed higher SNORD16 expression levels, and no correlation was found between SNORD16 and RPL4. Patients with high SNORD16 expression levels had a worse prognosis, and multivariate analysis showed the high SNORD16 expression was an independent prognostic factor for CC. In vitro gain- and loss-of-function studies revealed that SNORD16 can promote cell growth, proliferation, migration, and invasion of CC cells by inhibiting apoptosis. These results suggested that SNORD16 has an oncogenic role in CC and might be a novel diagnostic and prognostic biomarker for CC.

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Zhu, Pan, Yuqiu Wang, Nanxun Qin, Feng Wang, Jia Wang, Xing Wang Deng, and Danmeng Zhu. "Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis." Proceedings of the National Academy of Sciences 113, no. 42 (October 5, 2016): 11967–72. http://dx.doi.org/10.1073/pnas.1614852113.

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Ribosome production in eukaryotes requires the complex and precise coordination of several hundred assembly factors, including many small nucleolar RNAs (snoRNAs). However, at present, the distinct role of key snoRNAs in ribosome biogenesis remains poorly understood in higher plants. Here we report that a previously uncharacterized C (RUGAUGA)/D (CUGA) type snoRNA, HIDDEN TREASURE 2 (HID2), acts as an important regulator of ribosome biogenesis through a snoRNA–rRNA interaction. Nucleolus-localized HID2 is actively expressed in Arabidopsis proliferative tissues, whereas defects in HID2 cause a series of developmental defects reminiscent of ribosomal protein mutants. HID2 associates with the precursor 45S rRNA and promotes the efficiency and accuracy of pre-rRNA processing. Intriguingly, disrupting HID2 in Arabidopsis appears to impair the integrity of 27SB, a key pre-rRNA intermediate that generates 25S and 5.8S rRNA and is known to be vital for the synthesis of the 60S large ribosomal subunit and also produces an imbalanced ribosome profile. Finally, we demonstrate that the antisense-box of HID2 is both functionally essential and highly conserved in eukaryotes. Overall, our study reveals the vital and possibly conserved role of a snoRNA in monitoring the efficiency of pre-rRNA processing during ribosome biogenesis.

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Li, Si-Guang, Hui Zhou, Yu-Ping Luo, Peng Zhang, and Liang-Hu Qu. "Identification and Functional Analysis of 20 Box H/ACA Small Nucleolar RNAs (snoRNAs) fromSchizosaccharomyces pombe." Journal of Biological Chemistry 280, no. 16 (February 16, 2005): 16446–55. http://dx.doi.org/10.1074/jbc.m500326200.

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Considering all small nucleolar RNAs (snoRNAs) enriched in the nucleolus, we generated a specialized cDNA library of small nuclear RNAs fromSchizosaccharomyces pombeand isolated, for the first time, 20 novel box H/ACA snoRNAs. Thirteen of these were characterized as novel guides that were predicted to direct 19 pseudouridylations in 18 S and 25 S rRNAs. The remaining seven snoRNAs were considered as orphan guides that lack sequence complementarity to either rRNAs or snRNAs. We have experimentally demonstrated the function of the 10 novel snoRNAs by gene deletion in the fission yeast. The snoRNAs were shown to be dispensable for the viability ofS. pombe, although an impact of snR94 depletion on yeast growth, especially at 23 °C, was revealed. A total of 30 pseudouridylation sites were precisely mapped in theS. pomberRNAs, showing a distinctive pseudouridylation pattern in the budding yeast. Interestingly, the absence of pseudouridylation on U2347 inS. pombe25 S rRNA pointed out a critical role for Ψ2345 in conferring a growth advantage for yeast. In contrast to the intron-encoded box C/D sno-RNAs in yeast, all box H/ACA snoRNAs appeared to be transcribed independently from intergenic regions between two protein-coding genes, except for snR35, which was nested in an open reading frame encoding for a hypothetical protein, although expressed from the opposite strand. Remarkably, snR90 was cotranscribed with an intron-encoded box C/D snoRNA, and this is the first demonstration of a non-coding RNA gene that encodes two different types of snoRNAs by its exon and intron. A detailed comparison of theS. pombesnoRNAs, with their functional homologues in diverse organisms, suggests a mechanism by which the snoRNAs have evolved in coordination with rRNAs to preserve the post-transcriptional modification sites among distant eukaryotes.

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Sahoo, Trilochan, Daniela del Gaudio, Jennifer R. German, Marwan Shinawi, Sarika U. Peters, Richard E. Person, Adolfo Garnica, Sau Wai Cheung, and Arthur L. Beaudet. "Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster." Nature Genetics 40, no. 6 (May 25, 2008): 719–21. http://dx.doi.org/10.1038/ng.158.

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33

Leary, Daniel J., Michael P. Terns, and Sui Huang. "Components of U3 snoRNA-containing Complexes Shuttle between Nuclei and the Cytoplasm and Differentially Localize in Nucleoli: Implications for Assembly and Function." Molecular Biology of the Cell 15, no. 1 (January 2004): 281–93. http://dx.doi.org/10.1091/mbc.e03-06-0363.

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U3 small nucleolar RNA (snoRNA) and associated proteins are required for the processing of preribosomal RNA (pre-rRNA) and assembly of preribosomes. There are two major U3 snoRNA-containing complexes. The monoparticle contains U3 snoRNA and the core Box C/D snoRNA-associated proteins and an early preribosome-associated complex contains the monoparticle and additional factors that we refer to as preribosome-associated proteins. To address how and where the U3 snoRNA-containing preribosome assembles and how these processes are temporally and spatially regulated, we have examined the dynamics and distribution of human U3 complex-associated components in cells with active or inactive transcription of rDNA. We found that U3 complex-associated proteins shuttle between the nucleus and the cytoplasm independent of the synthesis and export of preribosomal particles, suggesting that the shuttling of these proteins may either provide opportunities for their regulation, or contribute to or modulate ribosome export. In addition, monoparticle and preribosome associated components predominantly localize to different nucleolar substructures, fibrillar components, and granular components, respectively, in active nucleoli, and partition separately into the two components during nucleolar segregation induced by inhibition of pol I transcription. Although the predominant localizations of these two sets of factors differ, there are significant areas of overlap that may represent the sites where they reside as a single complex. These results are consistent with a model in which U3 monoparticles associate with the fibrillar components of nucleoli and bind pre-rRNA during transcription, triggering recruitment of preribosome-associated proteins to assemble the complex necessary for pre-rRNA processing.

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Cavaillé, Jérôme, Patrice Vitali, Eugenia Basyuk, Alexander Hüttenhofer, and Jean-Pierre Bachellerie. "A Novel Brain-specific Box C/D Small Nucleolar RNA Processed from Tandemly Repeated Introns of a Noncoding RNA Gene in Rats." Journal of Biological Chemistry 276, no. 28 (May 9, 2001): 26374–83. http://dx.doi.org/10.1074/jbc.m103544200.

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35

Motorin, Yuri, and Virginie Marchand. "Detection and Analysis of RNA Ribose 2′-O-Methylations: Challenges and Solutions." Genes 9, no. 12 (December 18, 2018): 642. http://dx.doi.org/10.3390/genes9120642.

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Ribose 2′-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2′-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2′-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2′-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2′-O-methylations.

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Filippova, Ju A., G. A. Stepanov, D. V. Semenov, O. A. Koval, E. V. Kuligina, I. V. Rabinov, and V. A. Richter. "Modified Method of rRNA Structure Analysis Reveals Novel Characteristics of Box C/D RNA Analogues." Acta Naturae 7, no. 2 (June 15, 2015): 64–73. http://dx.doi.org/10.32607/20758251-2015-7-2-64-73.

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Ribosomal RNA (rRNA) maturation is a complex process that involves chemical modifications of the bases or sugar residues of specific nucleotides. One of the most abundant types of rRNA modifications, ribose 2-O-methylation, is guided by ribonucleoprotein complexes containing small nucleolar box C/D RNAs. Since the majority of 2-O-methylated nucleotides are located in the most conserved regions of rRNA that comprise functionally important centers of the ribosome, an alteration in a 2-O-methylation profile can affect ribosome assembly and function. One of the key approaches for localization of 2-O-methylated nucleotides in long RNAs is a method based on the termination of reverse transcription. The current study presents an adaptation of this method for the use of fluorescently labeled primers and analysis of termination products by capillary gel electrophoresis on an automated genetic analyzer. The developed approach allowed us to analyze the influence of the synthetic analogues of box C/D RNAs on post-transcriptional modifications of human 28S rRNA in MCF-7 cells. It has been established that the transfection of MCF-7 cells with a box C/D RNA analogue leads to an enhanced modification level of certain native sites of 2-O-methylation in the target rRNA. The observed effect of synthetic RNAs on the 2-O-methylation of rRNA in human cells demonstrates a path towards targeted regulation of rRNA post-transcriptional maturation. The described approach can be applied in the development of novel diagnostic methods for detecting diseases in humans.

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Costello, Joe L., Jonathan A. Stead, Monika Feigenbutz, Rebecca M. Jones, and Phil Mitchell. "The C-terminal Region of the Exosome-associated Protein Rrp47 Is Specifically Required for Box C/D Small Nucleolar RNA 3′-Maturation." Journal of Biological Chemistry 286, no. 6 (December 6, 2010): 4535–43. http://dx.doi.org/10.1074/jbc.m110.162826.

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38

Pauli, Cornelius, Yi Liu, Christian Rohde, Chunhong Cui, Daria Fijalkowska, Dennis Gerloff, Carolin Walter, et al. "Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acute myeloid leukemia cell proliferation." Blood 135, no. 23 (June 4, 2020): 2059–70. http://dx.doi.org/10.1182/blood.2019004121.

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Abstract Noncoding RNAs, including small nucleolar RNAs (snoRNAs), play important roles in leukemogenesis, but the relevant mechanisms remain incompletely understood. We performed snoRNA-focused CRISPR-Cas9 knockout library screenings that targeted the entire snoRNAnome and corresponding host genes. The C/D box containing SNORD42A was identified as an essential modulator for acute myeloid leukemia (AML) cell survival and proliferation in multiple human leukemia cell lines. In line, SNORD42A was consistently expressed at higher levels in primary AML patient samples than in CD34+ progenitors, monocytes, and granulocytes. Functionally, knockout of SNORD42A reduced colony formation capability and inhibited proliferation. The SNORD42A acts as a C/D box snoRNA and directs 2′-O-methylation at uridine 116 of 18S ribosomal RNA (rRNA). Deletion of SNORD42A decreased 18S-U116 2′-O-methylation, which was associated with a specific decrease in the translation of ribosomal proteins. In line, the cell size of SNORD42A deletion carrying leukemia cells was decreased. Taken together, these findings establish that high-level expression of SNORD42A with concomitant U116 18S rRNA 2′-O-methylation is essential for leukemia cell growth and survival.

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Newton, Kathryn, Elisabeth Petfalski, David Tollervey, and Javier F. Cáceres. "Fibrillarin Is Essential for Early Development and Required for Accumulation of an Intron-Encoded Small Nucleolar RNA in the Mouse." Molecular and Cellular Biology 23, no. 23 (December 1, 2003): 8519–27. http://dx.doi.org/10.1128/mcb.23.23.8519-8527.2003.

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ABSTRACT Fibrillarin, a protein component of C/D box small nucleolar ribonucleoproteins (snoRNPs), directs 2′-O-methylation of rRNA and is also involved in other aspects of rRNA processing. A gene trap screen in embryonic stem (ES) cells resulted in an insertion mutation in the fibrillarin gene. This insertion generated a fusion protein that contained the N-terminal 132 amino acids of fibrillarin fused to a β-galactosidase-neomycin phosphotransferase reporter. As a result, the N-terminal GAR domain was present in the fusion protein but the methyltransferase-like domain was missing. The ES cell line with the targeted fibrillarin allele was transmitted through the mouse germ line, creating heterozygous animals. Western blot analyses showed a reduction in fibrillarin protein levels in the heterozygous knockout animals. Animals homozygous for the mutation were inviable, and massive apoptosis was observed in early Fibrillarin−/− embryos, showing that fibrillarin is essential for development. Fibrillarin+/− live-born mice displayed no obvious growth defect, but heterozygous intercrosses revealed a reduced ratio of +/− to +/+ mice, showing that some of the Fibrillarin heterozygous embryos die in utero. Analyses of tissue samples and cultured embryonic fibroblasts showed no discernible alteration in pre-rRNA processing or the level of the U3 snoRNA. However, the level of the intron-encoded box C/D snoRNA U76 was clearly reduced. This suggests a high requirement for snoRNA synthesis during an early stage in development.

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Wu, Long, Lei Chang, Haitao Wang, Weijie Ma, Qin Peng, and Yufeng Yuan. "Clinical significance of C/D box small nucleolar RNA U76 as an oncogene and a prognostic biomarker in hepatocellular carcinoma." Clinics and Research in Hepatology and Gastroenterology 42, no. 1 (February 2018): 82–91. http://dx.doi.org/10.1016/j.clinre.2017.04.018.

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41

King, Thomas H., Wayne A. Decatur, Edouard Bertrand, E. Stuart Maxwell, and Maurille J. Fournier. "A Well-Connected and Conserved Nucleoplasmic Helicase Is Required for Production of Box C/D and H/ACA snoRNAs and Localization of snoRNP Proteins." Molecular and Cellular Biology 21, no. 22 (November 15, 2001): 7731–46. http://dx.doi.org/10.1128/mcb.21.22.7731-7746.2001.

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ABSTRACT Biogenesis of small nucleolar RNA-protein complexes (snoRNPs) consists of synthesis of the snoRNA and protein components, snoRNP assembly, and localization to the nucleolus. Recently, two nucleoplasmic proteins from mice were observed to bind to a model box C/D snoRNA in vitro, suggesting that they function at an early stage in snoRNP biogenesis. Both proteins have been described in other contexts. The proteins, called p50 and p55 in the snoRNA binding study, are highly conserved and related to each other. Both have Walker A and B motifs characteristic of ATP- and GTP-binding and nucleoside triphosphate-hydrolyzing domains, and the mammalian orthologs have DNA helicase activity in vitro. Here, we report that theSaccharomyces cerevisiae ortholog of p50 (Rvb2, Tih2p, and other names) is required for production of C/D snoRNAs in vivo and, surprisingly, H/ACA snoRNAs as well. Point mutations in the Walker A and B motifs cause temperature-sensitive or lethal growth phenotypes and severe defects in snoRNA accumulation. Notably, depletion of p50 (called Rvb2 in this study) also impairs localization of C/D and H/ACA core snoRNP proteins Nop1p and Gar1p, suggesting a defect(s) in snoRNP assembly or trafficking to the nucleolus. Findings from other studies link Rvb2 orthologs with chromatin remodeling and transcription. Taken together, the present results indicate that Rvb2 is involved in an early stage of snoRNP biogenesis and may play a role in coupling snoRNA synthesis with snoRNP assembly and localization.

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Chamberlain, Stormy J. "Comment on “Do repeated arrays of box C/D small nucleolar RNA and microRNA genes elicit genomic imprinting?” DOI 10.1002/bies201100032." BioEssays 33, no. 8 (July 19, 2011): 563–64. http://dx.doi.org/10.1002/bies.201100081.

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43

Roychowdhury, Amlan, Clément Joret, Gabrielle Bourgeois, Valérie Heurgué-Hamard, Denis L. J. Lafontaine, and Marc Graille. "The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis." Nucleic Acids Research 47, no. 14 (June 12, 2019): 7548–63. http://dx.doi.org/10.1093/nar/gkz529.

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Abstract Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.

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Bouchard-Bourelle, Philia, Clément Desjardins-Henri, Darren Mathurin-St-Pierre, Gabrielle Deschamps-Francoeur, Étienne Fafard-Couture, Jean-Michel Garant, Sherif Abou Elela, and Michelle S. Scott. "snoDB: an interactive database of human snoRNA sequences, abundance and interactions." Nucleic Acids Research 48, no. D1 (October 10, 2019): D220—D225. http://dx.doi.org/10.1093/nar/gkz884.

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Abstract Small nucleolar RNAs (snoRNAs) are an abundant type of non-coding RNA with conserved functions in all known eukaryotes. Classified into two main families, the box C/D and H/ACA snoRNAs, they enact their most well characterized role of guiding site specific modifications in ribosomal RNA, through the formation of specific ribonucleoprotein complexes, with fundamental implications in ribosome biogenesis. However, it is becoming increasingly clear that the landscape of snoRNA cellular functionality is much broader than it once seemed with novel members, non-uniform expression patterns, new and diverse targets as well as several emerging non-canonical functions ranging from the modulation of alternative splicing to the regulation of chromatin architecture. In order to facilitate the further characterization of human snoRNAs in a holistic manner, we introduce an online interactive database tool: snoDB. Its purpose is to consolidate information on human snoRNAs from different sources such as sequence databases, target information, both canonical and non-canonical from the literature and from high-throughput RNA–RNA interaction datasets, as well as high-throughput sequencing data that can be visualized interactively.

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de los Santos, Tala, Johannes Schweizer, Christian A. Rees, and Uta Francke. "Small Evolutionarily Conserved RNA, Resembling C/D Box Small Nucleolar RNA, Is Transcribed from PWCR1, a Novel Imprinted Gene in the Prader-Willi Deletion Region, Which Is Highly Expressed in Brain." American Journal of Human Genetics 67, no. 5 (November 2000): 1067–82. http://dx.doi.org/10.1086/303106.

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46

Smith, Christine M., and Joan A. Steitz. "Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes." Molecular and Cellular Biology 18, no. 12 (December 1, 1998): 6897–909. http://dx.doi.org/10.1128/mcb.18.12.6897.

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ABSTRACT We have identified gas5 (growth arrest-specific transcript 5) as a non-protein-coding multiple small nucleolar RNA (snoRNA) host gene similar to UHG (U22 host gene). Encoded within the 11 introns of the mouse gas5 gene are nine (10 in human) box C/D snoRNAs predicted to function in the 2′-O-methylation of rRNA. The only regions of conservation between mouse and humangas5 genes are their snoRNAs and 5′-end sequences. Mapping the 5′ end of the mouse gas5 transcript demonstrates that it possesses an oligopyrimidine tract characteristic of the 5′-terminal oligopyrimidine (5′TOP) class of genes. Arrest of cell growth or inhibition of translation by cycloheximide, pactamycin, or rapamycin—which specifically inhibits the translation of 5′TOP mRNAs—results in accumulation of the gas5 spliced RNA. Classification of gas5 as a 5′TOP gene provides an explanation for why it is a growth arrest specific transcript: while the spliced gas5 RNA is normally associated with ribosomes and rapidly degraded, during arrested cell growth it accumulates in mRNP particles, as has been reported for other 5′TOP messages. Strikingly, inspection of the 5′-end sequences of currently known snoRNA host gene transcripts reveals that they all exhibit features of the 5′TOP gene family.

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Boulon, Séverine, Nathalie Marmier-Gourrier, Bérengère Pradet-Balade, Laurence Wurth, Céline Verheggen, Beáta E. Jády, Benjamin Rothé, et al. "The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery." Journal of Cell Biology 180, no. 3 (February 11, 2008): 579–95. http://dx.doi.org/10.1083/jcb.200708110.

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RNA-binding proteins of the L7Ae family are at the heart of many essential ribonucleoproteins (RNPs), including box C/D and H/ACA small nucleolar RNPs, U4 small nuclear RNP, telomerase, and messenger RNPs coding for selenoproteins. In this study, we show that Nufip and its yeast homologue Rsa1 are key components of the machinery that assembles these RNPs. We observed that Rsa1 and Nufip bind several L7Ae proteins and tether them to other core proteins in the immature particles. Surprisingly, Rsa1 and Nufip also link assembling RNPs with the AAA + adenosine triphosphatases hRvb1 and hRvb2 and with the Hsp90 chaperone through two conserved adaptors, Tah1/hSpagh and Pih1. Inhibition of Hsp90 in human cells prevents the accumulation of U3, U4, and telomerase RNAs and decreases the levels of newly synthesized hNop58, hNHP2, 15.5K, and SBP2. Thus, Hsp90 may control the folding of these proteins during the formation of new RNPs. This suggests that Hsp90 functions as a master regulator of cell proliferation by allowing simultaneous control of cell signaling and cell growth.

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Shukla, Vijaya, Tahira Fatima, Ravinder K. Goyal, Avtar K. Handa, and Autar K. Mattoo. "Engineered Ripening-Specific Accumulation of Polyamines Spermidine and Spermine in Tomato Fruit Upregulates Clustered C/D Box snoRNA Gene Transcripts in Concert with Ribosomal RNA Biogenesis in the Red Ripe Fruit." Plants 9, no. 12 (December 4, 2020): 1710. http://dx.doi.org/10.3390/plants9121710.

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Ripening of tomato fruit leads, in general, to a sequential decrease in the endogenous levels of polyamines spermidine (SPD) and spermine (SPM), while the trend for the diamine putrescine (PUT) levels is generally an initial decrease, followed by a substantial increase, and thereafter reaching high levels at the red ripe fruit stage. However, genetic engineering fruit-specific expression of heterologous yeast S-adenosylmethionine (SAM) decarboxylase in tomato has been found to result in a high accumulation of SPD and SPM at the cost of PUT. This system enabled a genetic approach to determine the impact of increased endogenous levels of biogenic amines SPD and SPM in tomato (579HO transgenic line) and on the biogenesis, transcription, processing, and stability of ribosomal RNA (rRNA) genes in tomato fruit as compared with the non-transgenic 556AZ line. One major biogenetic process regulating transcription and processing of pre-mRNA complexes in the nucleus involves small nucleolar RNAs (snoRNAs). To determine the effect of high levels of SPD and SPM on these latter processes, we cloned, sequenced, and identified a box C/D snoRNA cluster in tomato, namely, SlSnoR12, SlU24a, Slz44a, and Slz132b. Similar to this snoRNA cluster housed on chromosome (Chr.) 6, two other noncoding C/D box genes, SlsnoR12.2 and SlU24b, with a 94% identity to those on Chr. 6 were found located on Chr. 3. We also found that other snoRNAs divisible into snoRNA subclusters A and B, separated by a uridine rich spacer, were decorated with other C/D box snoRNAs, namely, J10.3, Z131a/b, J10.1, and Z44a, followed by z132a, J11.3, z132b, U24, Z20, U24a, and J11. Several of these, for example, SlZ44a, Slz132b, and SlU24a share conserved sequences similar to those in Arabidopsis and rice. RNAseq analysis of high SPD/SPM transgenic tomatoes (579HO line) showed significant enrichment of RNA polymerases, ribosomal, and translational protein genes at the breaker+8 ripening stage as compared with the 556AZ control. Thus, these results indicate that SPD/SPM regulates snoRNA and rRNA expression directly or indirectly, in turn, affecting protein synthesis, metabolism, and other cellular activities in a positive manner.

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Warner, Wayne A., David Spencer, Maria Trissal, Nichole Helton, Timothy J. Ley, and Daniel C. Link. "Characterization of snoRNA Expression in Acute Myeloid Leukemia." Blood 126, no. 23 (December 3, 2015): 3649. http://dx.doi.org/10.1182/blood.v126.23.3649.3649.

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Abstract Small nucleolar RNAs (snoRNAs) are small (90-300nt) non-coding guide RNAs found in all multicellular organisms. H/ACA and CD box snoRNAs localize to the nucleolar region and are part of a catalytic multicomponent protein complex selecting target RNAs based on complementarity. They are responsible for the site-specific pseudouridylation and 2' O methylation of ribosomal RNAs, respectively. ScaRNAs localize to the Cajal body and are responsible for the methylation and pseudouridylation of splicesomal RNAs U1, U2, U4, U5, and U12. There are also orphan snoRNAs without any known RNA targets. Recent studies have suggested an expanded role for snoRNAs outside of ribosomal biogenesis, including the regulation of RNA splicing and chromatin remodeling. Moreover, emerging data suggest that aberrantly expressed snoRNAs may contribute to neoplastic transformation. Here, we characterize snoRNA expression in normal human hematopoiesis and in AML. We first developed a novel strategy to identify and quantify properly processed snoRNAs. This is important, since standard RNA sequencing or array-based analyses cannot distinguish between processed snoRNAs and primary mRNA transcripts of the host genes (most snoRNAs are contained in the introns of coding genes). In brief, we take advantage of the fact that, like miRNAs, snoRNAs contain a free 3'-hydroxyl group, which allows for efficient ligation to sequencing adaptors. Following size selection (20-200 nt) to enrich for small non-coding RNAs, the libraries are sequenced on the Illumina next generation sequencing platform. We also have developed a novel analysis pipeline that maps areas of contiguous alignment in the genome, forming ab initio "clusters" representing snoRNAs. Using this sequencing assay, we first interrogated snoRNA expression in hematopoietic cells from healthy individuals. Specifically, we sequenced small RNA libraries derived from CD34+ cells, promyelocytes, neutrophils, monocytes, T-cells, and B-cells. Of the 269 known snoRNAs, 132 (49%) were expressed in one or more hematopoietic cell population. Likewise, 80 of 112 (71%) of known H/ACA box snoRNAs, and all 21 scaRNAs were expressed. In addition, we identified (and computationally validated using SnoReport, snoGPS, and an in-house snoFinder script) 8 putative novel snoRNAs (1 H/ACA box and 7 CD box snoRNAs). Most snoRNAs were stably expressed across all hematopoietic lineages. However, there were numerous examples of snoRNAs that were specifically enriched in a specific hematopoietic cell population (e.g., CD34+ cells). We also identified several snoRNAs that were up- or down-regulated during granulocytic differentiation. For example, many of the orphan C/D box snoRNAs contained in the imprinted DLK/DIO3 locus on chromosome 14q32 are significantly down-regulated during granulocytic differentiation. To determine whether snoRNAs are frequently dysregulated in AML, we next sequenced small non-coding RNAs isolated from the bone marrow of 33 patients with de novo acute myeloid leukemia (all with a normal karyotype). Using a strict 5% false discovery rate, only 9.3% of CD box snoRNAs and 0.9% of H/ACA box snoRNAs were found to have significantly increased or decreased expression compared with normal CD34+ cells (including some of the putative novel snoRNAs). Of note, no differentially expressed snoRNAs were detected comparing AML with or without DNMT3A mutations or with or without IDH1/2 mutations. We next interrogated published whole genome sequencing data to determine whether there were any cytogenetically silent genetic alterations in snoRNAs. No recurring point mutations or small insertions/deletions were detected in snoRNA genes in 50 cases of AML. In summary, we developed a new next-generation sequencing approach and analysis pipeline to quantify snoRNAs. We show that, compared with coding genes, snoRNA expression is more stable across different hematopoietic lineages, consistent with a housekeeping function. However, examples of developmentally-regulated and lineage-restricted snoRNA expression were identified. Finally, we show that a small subset of snoRNAs appear to be dysregulated in AML, although genetic alterations the specifically target snoRNAs appear to be rare in AML. Disclosures No relevant conflicts of interest to declare.

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Rasmussen, Theodore P., and Michael R. Culbertson. "The Putative Nucleic Acid Helicase Sen1p Is Required for Formation and Stability of Termini and for Maximal Rates of Synthesis and Levels of Accumulation of Small Nucleolar RNAs inSaccharomyces cerevisiae." Molecular and Cellular Biology 18, no. 12 (December 1, 1998): 6885–96. http://dx.doi.org/10.1128/mcb.18.12.6885.

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ABSTRACT Sen1p from Saccharomyces cerevisiae is a nucleic acid helicase related to DEAD box RNA helicases and type I DNA helicases. The temperature-sensitive sen1-1 mutation located in the helicase motif alters the accumulation of pre-tRNAs, pre-rRNAs, and some small nuclear RNAs. In this report, we show that cells carryingsen1-1 exhibit altered accumulation of several small nucleolar RNAs (snoRNAs) immediately upon temperature shift. Using Northern blotting, RNase H cleavage, primer extension, and base compositional analysis, we detected three forms of the snoRNA snR13 in wild-type cells: an abundant TMG-capped 124-nucleotide (nt) mature form (snR13F) and two less abundant RNAs, including a heterogeneous population of ∼1,400-nt 3′-extended forms (snR13R) and a 108-nt 5′-truncated form (snR13T) that is missing 16 nt at the 5′ end. A subpopulation of snR13R contains the same 5′ truncation. Newly synthesized snR13R RNA accumulates with time at the expense of snR13F following temperature shift of sen1-1 cells, suggesting a possible precursor-product relationship. snR13R and snR13T both increase in abundance at the restrictive temperature, indicating that Sen1p stabilizes the 5′ end and promotes maturation of the 3′ end. snR13F contains canonical C and D boxes common to many snoRNAs. The 5′ end of snR13T and the 3′ end of snR13F reside within C2U4 sequences that immediately flank the C and D boxes. A mutation in the 5′ C2U4 repeat causes underaccumulation of snR13F, whereas mutations in the 3′ C2U4 repeat cause the accumulation of two novel RNAs that migrate in the 500-nt range. At the restrictive temperature, double mutants carrying sen1-1 and mutations in the 3′ C2U4 repeat show reduced accumulation of the novel RNAs and increased accumulation of snR13R RNA, indicating that Sen1p and the 3′ C2U4 sequence act in a common pathway to facilitate 3′ end formation. Based on these findings, we propose that Sen1p and the C2U4 repeats that flank the C and D boxes promote maturation of the 3′ terminus and stability of the 5′ terminus and are required for maximal rates of synthesis and levels of accumulation of mature snR13F.

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