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Journal articles on the topic 'Box C/D RNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Yang, Zuxiao, Jiayin Wang, Lin Huang, David M. J. Lilley, and Keqiong Ye. "Functional organization of box C/D RNA-guided RNA methyltransferase." Nucleic Acids Research 48, no. 9 (April 16, 2020): 5094–105. http://dx.doi.org/10.1093/nar/gkaa247.

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Abstract Box C/D RNA protein complexes (RNPs) catalyze site-specific 2′-O-methylation of RNA with specificity determined by guide RNAs. In eukaryotic C/D RNP, the paralogous Nop58 and Nop56 proteins specifically associate with terminal C/D and internal C'/D' motifs of guide RNAs, respectively. We have reconstituted active C/D RNPs with recombinant proteins of the thermophilic yeast Chaetomium thermophilum. Nop58 and Nop56 could not distinguish between the two C/D motifs in the reconstituted enzyme, suggesting that the assembly specificity is imposed by trans-acting factors in vivo. The two C/D motifs are functionally independent and halfmer C/D RNAs can also guide site-specific methylation. Extensive pairing between C/D RNA and substrate is inhibitory to modification for both yeast and archaeal C/D RNPs. N6-methylated adenine at box D/D' interferes with the function of the coupled guide. Our data show that all C/D RNPs share the same functional organization and mechanism of action and provide insight into the assembly specificity of eukaryotic C/D RNPs.

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2

Ye, K., R. Jia, J. Lin, M. Ju, J. Peng, A. Xu, and L. Zhang. "Structural organization of box C/D RNA-guided RNA methyltransferase." Proceedings of the National Academy of Sciences 106, no. 33 (August 5, 2009): 13808–13. http://dx.doi.org/10.1073/pnas.0905128106.

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3

Yu, Ge, Yu Zhao, and Hong Li. "The multistructural forms of box C/D ribonucleoprotein particles." RNA 24, no. 12 (September 25, 2018): 1625–33. http://dx.doi.org/10.1261/rna.068312.118.

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4

TRAN, E. "Conserved spacing between the box C/D and C'/D' RNPs of the archaeal box C/D sRNP complex is required for efficient 2'-O-methylation of target RNAs." RNA 11, no. 3 (January 20, 2005): 285–93. http://dx.doi.org/10.1261/rna.7223405.

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5

Moore, Terrie, Yanming Zhang, Marcia O. Fenley, and Hong Li. "Molecular Basis of Box C/D RNA-Protein Interactions." Structure 12, no. 5 (May 2004): 807–18. http://dx.doi.org/10.1016/j.str.2004.02.033.

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6

Deryusheva, Svetlana, and Joseph G. Gall. "Small, Smaller, Smallest: Minimal Structural Requirements for a Fully Functional Box C/D Modification Guide RNA." Biomolecules 9, no. 9 (September 7, 2019): 457. http://dx.doi.org/10.3390/biom9090457.

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Site-specific 2’-O-ribose methylation is an abundant post-transcriptional modification mediated by small non-coding nuclear RNAs known as box C/D modification guide RNAs. The minimal structural requirements for these guide RNAs to function in higher eukaryotes are still unclear. To address this question, we generated a series of mutant variants of Drosophila box C/D scaRNA:MeU2-C28 and tested their modification guide activities in the Xenopus oocyte system. Our data suggest that box C/D guide RNA function requires either a terminal or an internal consensus kink-turn structure. We identified the minimal functional box C/D guide RNA. It consists of a single-domain molecule with (i) a terminal stem with a consensus kink-turn domain, (ii) one box C and box D connected by a 14-nucleotide antisense element and (iii) a one-nucleotide spacer between the box C and the antisense element. In this single domain RNA, the sequence of the spacer is more important than its length. We suggest that the secondary structure of box C/D RNAs, essential for guide RNA function, is more complex than generally supposed. At the same time, the expression of functional extremely short single-domain box C/D RNAs is possible in higher eukaryotes.

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7

Bower-Phipps, K. R., D. W. Taylor, H. W. Wang, and S. J. Baserga. "The box C/D sRNP dimeric architecture is conserved across domain Archaea." RNA 18, no. 8 (June 29, 2012): 1527–40. http://dx.doi.org/10.1261/rna.033134.112.

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8

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.

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9

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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10

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.

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11

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.

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12

Omer, A. D. "Probing the structure and function of an archaeal C/D-box methylation guide sRNA." RNA 12, no. 9 (July 7, 2006): 1708–20. http://dx.doi.org/10.1261/rna.31506.

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13

Graziadei, Andrea, Pawel Masiewicz, Audrone Lapinaite, and Teresa Carlomagno. "Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency." RNA 22, no. 5 (February 29, 2016): 764–72. http://dx.doi.org/10.1261/rna.054320.115.

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14

Ashraf, Saira, Lin Huang, and David M. J. Lilley. "Sequence determinants of the folding properties of box C/D kink-turns in RNA." RNA 23, no. 12 (September 27, 2017): 1927–35. http://dx.doi.org/10.1261/rna.063453.117.

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15

Colley, Alan, Jean D. Beggs, David Tollervey, and Denis L. J. Lafontaine. "Dhr1p, a Putative DEAH-Box RNA Helicase, Is Associated with the Box C+D snoRNP U3." Molecular and Cellular Biology 20, no. 19 (October 1, 2000): 7238–46. http://dx.doi.org/10.1128/mcb.20.19.7238-7246.2000.

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ABSTRACT Putative RNA helicases are involved in most aspects of gene expression. All previously characterized members of the DEAH-box family of putative RNA helicases are involved in pre-mRNA splicing. Here we report the analysis of two novel DEAH-box RNA helicases, Dhr1p and Dhr2p, that were found to be predominantly nucleolar. Both genes are essential for viability, and MET-regulated alleles were therefore created. Depletion of Dhr1p or Dhr2p had no detectable effect on pre-mRNA splicing in vivo or in vitro. Both Dhr1p and Dhr2p were, however, required for 18S rRNA synthesis. Depletion of Dhr2p inhibited pre-rRNA cleavage at sites A0, A1, and A2, while Dhr1p depletion inhibited cleavage at sites A1 and A2. No coprecipitation of snoRNAs was detected with ProtA-Dhr2p, but Dhr1p-ProtA was stably associated with the U3 snoRNA. Depletion of Dhr1p inhibited processing steps that require base pairing of U3 to the 5′ end of the 18S rRNA. We speculate that Dhr1p is targeted to the preribosomal particles by the U3-18S rRNA interaction and is required for the structural reorganization of the rRNA during formation of the central pseudoknot.

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16

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.

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17

Paul, Arnaud, Decebal Tiotiu, Benoît Bragantini, Hélène Marty, Bruno Charpentier, Séverine Massenet, and Stéphane Labialle. "Bcd1p controls RNA loading of the core protein Nop58 during C/D box snoRNP biogenesis." RNA 25, no. 4 (January 30, 2019): 496–506. http://dx.doi.org/10.1261/rna.067967.118.

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18

Richter, Hagen, Sabine Mohr, and Lennart Randau. "C/D box sRNA, CRISPR RNA and tRNA processing in an archaeon with a minimal fragmented genome." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 411–15. http://dx.doi.org/10.1042/bst20120276.

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The analysis of deep sequencing data allows for a genome-wide overview of all the small RNA molecules (the ‘sRNome’) that are present in a single organism. In the present paper, we review the processing of CRISPR (clustered regularly interspaced short palindromic repeats) RNA, C/D box sRNA (small non-coding RNA) and tRNA in Nanoarchaeum equitans. The minimal and fragmented genome of this tiny archaeon permits a sequencing depth that enables the identification of processing intermediates in the study of RNA processing pathways. These intermediates include circular C/D box sRNA molecules and tRNA half precursors.

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19

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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20

Ghalei, H., H. H. Hsiao, H. Urlaub, M. C. Wahl, and N. J. Watkins. "A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation." RNA 16, no. 12 (October 20, 2010): 2341–48. http://dx.doi.org/10.1261/rna.2380410.

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21

Diao, Li-Ting, Zhen-Dong Xiao, Xiao-Min Leng, Bin Li, Jun-Hao Li, Yu-Ping Luo, Si-Guang Li, Chuan-He Yu, Hui Zhou, and Liang-Hu Qu. "Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes inAscomycota." RNA 20, no. 9 (July 7, 2014): 1376–85. http://dx.doi.org/10.1261/rna.042309.113.

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22

Tran, E. J. "Efficient RNA 2'-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs." EMBO Journal 22, no. 15 (August 1, 2003): 3930–40. http://dx.doi.org/10.1093/emboj/cdg368.

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23

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.

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24

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.

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25

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.

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26

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.

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27

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.

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28

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.

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29

Lapinaite, Audrone, Bernd Simon, Lars Skjaerven, Magdalena Rakwalska-Bange, Frank Gabel, and Teresa Carlomagno. "The structure of the box C/D enzyme reveals regulation of RNA methylation." Nature 502, no. 7472 (October 2013): 519–23. http://dx.doi.org/10.1038/nature12581.

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30

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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31

Yang, Zuxiao, Jinzhong Lin, and Keqiong Ye. "Box C/D guide RNAs recognize a maximum of 10 nt of substrates." Proceedings of the National Academy of Sciences 113, no. 39 (September 13, 2016): 10878–83. http://dx.doi.org/10.1073/pnas.1604872113.

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Box C/D RNAs guide site-specific 2′-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D′ and boxes C′ to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide–substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C′ side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.

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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.

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Joardar, Archi, Priyatansh Gurha, Geena Skariah, and Ramesh Gupta. "Box C/D RNA-Guided 2′-O Methylations and the Intron of tRNATrp Are Not Essential for the Viability of Haloferax volcanii." Journal of Bacteriology 190, no. 21 (August 29, 2008): 7308–13. http://dx.doi.org/10.1128/jb.00820-08.

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ABSTRACT Deleting the box C/D RNA-containing intron in the Haloferax volcanii tRNATrp gene abolishes RNA-guided 2′-O methylations of C34 and U39 residues of tRNATrp. However, this deletion does not affect growth under standard conditions.

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Richard, Patricia, Arnold M. Kiss, Xavier Darzacq, and Tamás Kiss. "Cotranscriptional Recognition of Human Intronic Box H/ACA snoRNAs Occurs in a Splicing-Independent Manner." Molecular and Cellular Biology 26, no. 7 (April 1, 2006): 2540–49. http://dx.doi.org/10.1128/mcb.26.7.2540-2549.2006.

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ABSTRACT Processing from pre-mRNA introns is a widespread mechanism to generate human box C/D and H/ACA snoRNAs. Recent studies revealed that an optimal position relative to the 3′ splice site is important for efficient processing of most box C/D snoRNAs and that assembly of box C/D snoRNPs is stimulated by splicing factors likely bound to the branch point region. Here we have investigated the processing of another major class of human intron-encoded RNAs, the box H/ACA snoRNAs. Analysis of 80 H/ACA RNA genes revealed that human H/ACA RNAs possess no preferential localization close to the 3′ or 5′ splice site. In vivo processing experiments confirmed that H/ACA intronic snoRNAs are processed in a position-independent manner, indicating that there is no synergy between H/ACA RNA processing and splicing. We also showed that recognition of intronic H/ACA snoRNAs and assembly of pre-snoRNPs is an early event that occurs during transcription elongation parallel with pre-mRNA splice site selection. Finally, we found that efficient processing and correct nucleolar localization of the human U64 H/ACA snoRNA requires RNA polymerase II-mediated synthesis of the U64 precursor. This suggests that polymerase II-associated factors direct the efficient assembly and determine the correct subnuclear trafficking of human H/ACA snoRNPs.

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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.

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Appel, C. D., and E. S. Maxwell. "Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2'-O-methylation." RNA 13, no. 6 (April 24, 2007): 899–911. http://dx.doi.org/10.1261/rna.517307.

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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.

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Lin, Jinzhong, Shaomei Lai, Ru Jia, Anbi Xu, Liman Zhang, Jing Lu, and Keqiong Ye. "Structural basis for site-specific ribose methylation by box C/D RNA protein complexes." Nature 469, no. 7331 (January 2011): 559–63. http://dx.doi.org/10.1038/nature09688.

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Sharma, Sunny, Jun Yang, Rob van Nues, Peter Watzinger, Peter Kötter, Denis L. J. Lafontaine, Sander Granneman, and Karl-Dieter Entian. "Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation." PLOS Genetics 13, no. 5 (May 24, 2017): e1006804. http://dx.doi.org/10.1371/journal.pgen.1006804.

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Tomkuvienė, Miglė, Béatrice Clouet-d’Orval, Ignas Černiauskas, Elmar Weinhold, and Saulius Klimašauskas. "Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases." Nucleic Acids Research 40, no. 14 (May 7, 2012): 6765–73. http://dx.doi.org/10.1093/nar/gks381.

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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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Singh, S. K., P. Gurha, and R. Gupta. "Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP." RNA 14, no. 7 (May 29, 2008): 1411–23. http://dx.doi.org/10.1261/rna.1003308.

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LEE, C. Y. "The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5'-end processing of S. cerevisiae box C/D snoRNAs." RNA 9, no. 11 (November 1, 2003): 1362–70. http://dx.doi.org/10.1261/rna.5126203.

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Watkins, Nicholas J., Ira Lemm, and Reinhard Lührmann. "Involvement of Nuclear Import and Export Factors in U8 Box C/D snoRNP Biogenesis." Molecular and Cellular Biology 27, no. 20 (August 20, 2007): 7018–27. http://dx.doi.org/10.1128/mcb.00516-07.

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ABSTRACT Box C/D snoRNPs, factors essential for ribosome biogenesis, are proposed to be assembled in the nucleoplasm before localizing to the nucleolus. However, recent work demonstrated the involvement of nuclear export factors in this process, suggesting that export may take place. Here we show that there are distinct distributions of U8 pre-snoRNAs and pre-snoRNP complexes in HeLa cell nuclear and cytoplasmic extracts. We observed differential association of nuclear export (PHAX, CRM1, and Ran) factors with complexes in the two extracts, consistent with nucleocytoplasmic transport. Furthermore, we show that the U8 pre-snoRNA in one of the cytoplasmic complexes contains an m3G cap and is associated with the nuclear import factor Snurportin1. Using RNA interference, we show that loss of either PHAX or Snurportin1 results in the incorrect localization of the U8 snoRNA. Our data therefore show that nuclear export and import factors are directly involved in U8 box C/D snoRNP biogenesis. The distinct distribution of U8 pre-snoRNP complexes between the two cellular compartments together with the association of both nuclear import and export factors with the precursor complex suggests that the mammalian U8 snoRNP is exported during biogenesis.

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Wu, Songlin, Yuqiu Wang, Jiayin Wang, Xilong Li, Jiayang Li, and Keqiong Ye. "Profiling of RNA ribose methylation in Arabidopsis thaliana." Nucleic Acids Research 49, no. 7 (March 30, 2021): 4104–19. http://dx.doi.org/10.1093/nar/gkab196.

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Abstract Eukaryotic rRNAs and snRNAs are decorated with abundant 2′-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2′-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.

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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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Stamm, Stefan, and J. Stephen Lodmell. "C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks." Non-coding RNA Research 4, no. 2 (June 2019): 46–53. http://dx.doi.org/10.1016/j.ncrna.2019.02.001.

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D'Souza, Michelle Ninochka, Naveen Kumar Chandappa Gowda, Vishal Tiwari, Rosana Ottakandathil Babu, Praveen Anand, Sudhriti Ghosh Dastidar, Randhir Singh, et al. "FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation." iScience 9 (November 2018): 399–411. http://dx.doi.org/10.1016/j.isci.2018.11.007.

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D'Souza, Michelle Ninochka, Naveen Kumar Chandappa Gowda, Vishal Tiwari, Rosana Ottakandathil Babu, Praveen Anand, Sudhriti Ghosh Dastidar, Randhir Singh, et al. "FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation." iScience 12 (February 2019): 368. http://dx.doi.org/10.1016/j.isci.2019.01.026.

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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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