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Готові списки джерел за темами / D small nucleolar RNA

Добірка наукової літератури з теми "D small nucleolar RNA"

Автор: Grafiati

Опубліковано: 14 вересня 2021

Оновлено: 3 лютого 2022

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Статті в журналах з теми "D small nucleolar RNA":

1

Gerbi, Susan A. "Small nucleolar RNA." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 845–58. http://dx.doi.org/10.1139/o95-092.

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A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3′ terminal stem; the roles of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.Key words: RNA processing, small nucleolar RNAs, nucleolus, ribosome biogenesis, rRNA processing complex.

2

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.

3

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.

4

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.

5

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.

6

Vitali, Patrice, Eugenia Basyuk, Elodie Le Meur, Edouard Bertrand, Françoise Muscatelli, Jérôme Cavaillé, and Alexander Huttenhofer. "ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs." Journal of Cell Biology 169, no. 5 (June 6, 2005): 745–53. http://dx.doi.org/10.1083/jcb.200411129.

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Posttranscriptional, site-specific adenosine to inosine (A-to-I) base conversions, designated as RNA editing, play significant roles in generating diversity of gene expression. However, little is known about how and in which cellular compartments RNA editing is controlled. Interestingly, the two enzymes that catalyze RNA editing, adenosine deaminases that act on RNA (ADAR) 1 and 2, have recently been demonstrated to dynamically associate with the nucleolus. Moreover, we have identified a brain-specific small RNA, termed MBII-52, which was predicted to function as a nucleolar C/D RNA, thereby targeting an A-to-I editing site (C-site) within the 5-HT2C serotonin receptor pre-mRNA for 2′-O-methylation. Through the subcellular targeting of minigenes that contain natural editing sites, we show that ADAR2- but not ADAR1-mediated RNA editing occurs in the nucleolus. We also demonstrate that MBII-52 forms a bona fide small nucleolar ribonucleoprotein particle that specifically decreases the efficiency of RNA editing by ADAR2 at the targeted C-site. Our data are consistent with a model in which C/D small nucleolar RNA might play a role in the regulation of RNA editing.

7

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.

8

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.

9

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.

10

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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Більше джерел

Дисертації з теми "D small nucleolar RNA":

1

Canzler, Sebastian [Verfasser], Peter F. [Akademischer Betreuer] Stadler, Peter F. [Gutachter] Stadler, and Hsien-Da [Gutachter] Huang. "Insights into the Evolution of small nucleolar RNAs : Prediction, Comparison, Annotation / Sebastian Canzler ; Gutachter: Peter F. Stadler, Hsien-Da Huang ; Betreuer: Peter F. Stadler." Leipzig : Universitätsbibliothek Leipzig, 2017. http://d-nb.info/1240696841/34.

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2

Canzler, Sebastian. "Insights into the Evolution of small nucleolar RNAs." Doctoral thesis, Universitätsbibliothek Leipzig, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-217924.

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Over the last decades, the formerly irrevocable believe that proteins are the only key-factors in the complex regulatory machinery of a cell was crushed by a plethora of findings in all major eukaryotic lineages. These suggested a rugged landscape in the eukaryotic genome consist- ing of sequential, overlapping, or even bi-directional transcripts and myriads of regulatory elements. The vast part of the genome is indeed transcribed into an RNA intermediate, but solely a small fraction is finally translated into functional proteins. The sweeping majority, however, is either degraded or functions as a non-protein coding RNA (ncRNA). Due to continuous developments in experimental and computational research, the variety of ncRNA classes grew larger and larger, ranging from key-processes in the cellular lifespan to regulatory processes that are driven and guided by ncRNAs. The bioinformatical part pri- marily concentrates on the prediction, annotation, and extraction of characteristic properties of novel ncRNAs. Due to conservation of sequence and/or structure, this task is often deter- mined by an homology-search that utilizes information about functional, and hence conserved regions, as an indicator. This thesis focuses mainly on a special class of ncRNAs, small nucleolar RNAs (snoRNAs). These abundant molecules are mainly responsible for the guidance of 2’-O-ribose-methylations and pseudouridylations in different types of RNAs, such as ribosomal and spliceosomal RNAs. Although the relevance of single modifications is still rather unclear, the elimination of a bunch of modifications is shown to cause severe effects, including lethality. Several de novo prediction programs have been published over the last years and a substantial amount of publicly available snoRNA databases has originated. Normally, these are restricted to a small amount of species and a collection of experimentally extracted snoRNA. The detection of snoRNAs by means of wet lab experiments and/or de novo prediction tools is generally time consuming (wet lab) and a quite tedious task (identification of snoRNA-specific characteristics). The snoRNA annotation pipeline snoStrip was developed with the intention to circumvent these obstacles. It therefore utilizes a homology-based search procedure to reliably predict snoRNA genes in genomic sequences. In a subsequent step, all candidates are filtered with respect to specific sequence motifs and secondary structures. In a functional analysis, poten- tial target sites are predicted in ribosomal and spliceosomal RNA sequences. In contrast to de novo prediction tools, snoStrip focuses on the extension of the known snoRNA world to uncharted organisms and the mapping and unification of the existing diversity of snoRNAs into functional, homologous families. The pipeline is properly suited to analyze a manifold set of organisms in search for their snoRNAome in short timescales. This offers the opportunity to generate large scale analyses over whole eukaryotic kingdoms to gain insights into the evolutionary history of these spe- cial ncRNA molecules. A set of experimentally validated snoRNA genes in Deuterostomia and Fungi were starting points for highly comprehensive surveys searching and analyzing the snoRNA repertoire in these two major eukaryotic clades. In both cases, the snoStrip pipeline proved itself as a fast and reliable tool and collected thousands of snoRNA genes in nearly 200 organisms. Additionally, the Interaction Conservation Index (ICI), which is am- plified to additionally work on single lineages, provides a convenient measure to analyze and evaluate the conservation of snoRNA-targetRNA interactions across different species. The massive amount of data and the possibility to score the conservation of predicted interactions constitute the main pillars to gain an extraordinary insight into the evolutionary history of snoRNAs on both the sequence and the functional level. A substantial part of the snoR- NAome is traceable down to the root of both eukaryotic lineages and might indicate an even more ancient origin of these snoRNAs. However, a plenitude of lineage specific innovation and deletion events are also discernible. Due to its automated detection of homologous and functionally related snoRNA sequences, snoStrip identified extraordinary target switches in fungi. These unveiled a coupled evolutionary history of several snoRNA families that were previously thought to be independent. Although these findings are exceedingly interesting, the broad majority of snoRNA families is found to show remarkable conservation of the se- quence and the predicted target interactions. On two occasions, this thesis will shift its focus from a genuine snoRNA inspection to an analysis of introns. Both investigations, however, are still conducted under an evolutionary viewpoint. In case of the ubiquitously present U3 snoRNA, functional genes in a notable amount of fungi are found to be disrupted by U2-dependent introns. The set of previously known U3 genes is considerably enlarged by an adapted snoStrip-search procedure. Intron- disrupted genes are found in several fungal lineages, while their precise insertion points within the snoRNA-precursor are located in a small and homologous region. A potential targetRNA of snoRNA genes, U6 snRNA, is also found to contain intronic sequences. Within this work, U6 genes are detected and annotated in nearly all fungal organisms. Although a few U6 intron- carrying genes have been known before, the widespread of these findings and the diversity regarding the particular insertion points are surprising. Those U6 genes are commonly found to contain more than just one intron. In both cases of intron-disrupted non-coding RNA genes, the detected RNA molecules seem to be functional and the intronic sequences show remarkable sequence conservation for both their splice sites and the branch site. In summary, the snoStrip pipeline is shown to be a reliable and fast prediction tool that works on homology-based search principles. Large scale analyses on whole eukaryotic lineages become feasible on short notice. Furthermore, the automated detection of functionally related but not yet mapped snoRNA families adds a new layer of information. Based on surveys covering the evolutionary history of Fungi and Deuterostomia, profound insights into the evolutionary history of this ncRNA class are revealed suggesting ancient origin for a main part of the snoRNAome. Lineage specific innovation and deletion events are also found to occur at a large number of distinct timepoints.

3

Hebras, Jade. "Caractérisation moléculaire du petit ARN nucléolaire SNORD115 : un rôle dans la régulation de l'expression et de la fonction du récepteur à la sérotonine 5-HT2C ?" Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30209.

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Le nucléole des mammifères contient des centaines de petits ARN nucléolaires à boîte C/D (SNORD) dont la grande majorité guide une 2'-O-ribose méthylation sur les précurseurs des ARN ribosomiques (pré-ARNr). Certains SNORD facilitent aussi les clivages que subissent le pré-ARNr ou modifient le petit ARN nucléaire U6. Des travaux récents laissent également entrevoir que certains SNORD interagissent avec des ARNm. C'est le cas par exemple pour SNORD115 qui est au cœur de mon travail de thèse. SNORD115 est exprimé uniquement dans le cerveau à partir de nombreux gènes répétés en tandem situés au locus SNURF-SNRPN dont l'expression est contrôlée par l'empreinte génomique parentale. Des défauts génétiques associés à ce locus chromosomique sont associés à une maladie rare: le syndrome de Prader-Willi (SPW). SNORD115 est remarquable car il possède une longue complémentarité conservée avec l'ARNm codant un récepteur à la sérotonine, le variant 5-HT2C. Certains travaux proposent que SNORD115 régule la voie 5-HT2C en modulant l'épissage alternatif ou l'édition A vers I du pré-ARNm 5-HT2C. Un défaut dans l'activité du 5-HT2C pourrait être à l'origine de l'hyperphagie et/ou des anomalies comportementales qui caractérisent le SPW. Mon projet de thèse principal consistait à éprouver cette hypothèse grâce à un nouveau modèle murin CRISPR/Cas9 invalidé pour SNORD115. Mes résultats montrent que la perte d'expression de SNORD115 ne perturbe pas la régulation post-transcriptionnelle du pré-ARNm 5-HT2C in vivo. D'autre part, des études réalisées dans l'équipe n'ont pas permis de révéler des anomalies marquées dans les phénotypes anxio-dépressifs, ni dans le comportement alimentaire. Ma thèse soulève donc des questions importantes quant au rôle régulateur de SNORD115 dans le cerveau et de sa contribution potentielle dans l'étiologie du SPW. En parallèle, j'ai aussi abordé le répertoire des 2'-O-méthylations de l'ARNr dans des tissus murins, notamment le cerveau. Ce travail s'inscrivait dans la thématique émergente de la théorie du "ribosome spécialisé" qui propose qu'une hétérogénéité structurale des composants du ribosome puisse se traduire par des changements dans les capacités fonctionnelles du ribosome. Mes résultats montrent des variations dans la méthylation pour un nombre très limité de sites, et ce principalement au cours du développement. Aussi, les ribosomes des tissus développementaux sont globalement moins méthylés que ceux des tissus adultes. Nous avons concentré nos efforts sur LSU-G4593 dont la méthylation guidée par SNORD78 est retrouvée uniquement au cours du développement. Nous proposons que des évènements d'épissage alternatif du gène-hôte de SNORD78 modulent la production de SNORD78, et de fait le niveau de méthylation LSU-Gm4593. Grâce à l'étude d'une lignée cellulaire humaine (HEK293) invalidée pour SNORD78, j'ai recherché les implications fonctionnelles de LSU-Gm4593. A ce jour, mes travaux ne montrent pas un rôle marqué dans la prolifération cellulaire, ni dans la fidélité de la traduction. La fonction précise de LSU-Gm4593 demeure donc incomprise
The nucleolus of mammalian cells contains hundreds of box C/D small nucleolar RNAs (SNORDs). Majority of them, guide sequence-specific 2'-O ribose methylations into ribosomal RNA (rRNA). Some of them facilitate RNA folding and cleavages of ribosomal RNA precursors or guide ribose methylations into spliceosomal small nuclear RNA U6. Recent studies propose that some SNORD could target other transcripts, possibly messenger RNA as suggested by the brain-specific SNORD115. SNORD115 is processed from tandemly repeated genes embedded in the imprinted SNURF-SNRPN domain. Defects in gene expression at this domain are causally linked to rare disease: the Prader-Willi Syndrome (PWS). Excitingly, SNORD115 displays an extensive region of complementary to a brain-specific mRNA encoding the serotonin receptor 5-HT2C. SNORD115 could influence 5-HT2C signaling by fine-tuning alternative splicing or A to I RNA editing of 5-HT2C pre-mRNA. Reduced 5-HT2C receptor activity could contribute to impaired emotional response and/or compulsive overeating that characterized the syndrome. My work was to test this hypothesis using a CRISPR/Cas9-mediated SNORD115 knockout mouse model. My results show that loss of SNORD115 expression, in vivo, does not alter the post-transcriptional regulation of 5-HT2C pre-mRNA processing. Others results from the team do not reveal any defects in anxio-depressive phenotypes and eating behaviour. Our study questions the regulatory roles of SNORD115 in brain functions and behavioural disturbance associated with PWS. On other hand, I have studied ribose methylation sites in rRNA from mouse tissues. This work was included in emerging field of the specialized ribosome hypothesis which suggests heterogeneity in ribosomes may impact activity of ribosomes. Our results show significant changes at few discrete set of sites, especially in rRNA from developing tissues. Also, rRNA from developing tissues is globally less methylated than rRNA from adult tissues. We focus on LSU-Gm4593 site because this position is specifically methylated only during development and hardly ever detected in adult tissues. Methylation at LSU-G4593 is guided by SNORD78. We propose that the expression levels of SNORD78 during development appeared to be regulated by alternative splicing of the host-gene and to correlate with the methylation level of its target site at LSU-G4593. We've used a human cell line (HEK293T) inactivated for the SNORD78 gene in order to understand the functionally role of the corresponding ribose methylation. Our work did not demonstrate any overt cellular phenotypes, even though translation fidelity and the precise function of LSU-Gm4593 remains unknown

4

Hochschartner, Gerald. "Revealing the past : the potential of a novel small nucleolar RNA (snoRNA) marker system for studying plant evolution." Thesis, University of St Andrews, 2011. http://hdl.handle.net/10023/1695.

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Despite the existence of various molecular marker systems there are still limitations in distinguishing between closely related species based on molecular divergence, especially when hybridization events have occurred in the past. The characterisation of plant small nucleolar RNA (snoRNA) genes and their organisation into multigene clusters provides a potential nuclear marker system which could help in resolving the phylogenetic history of plants and might be applicable in DNA barcoding. Using closely and distantly related Senecio species, I investigated a combination of fragment length and sequence variation of snoRNA genes/snoRNA gene clusters to assess the utility of this marker system for barcoding and resolving species relationships. SnoRNA gene and gene cluster sequences identified in Arabidopsis thaliana were used to find homologues in other species and subsequently used for the design of universal primers. Most of the universal primer pairs designed were successful in amplifying snoRNA fragments in most Senecio species and fragment length variation between and within species could be detected. Furthermore, the combination of some fragment length datasets produced by different primer pairs enabled the separation of species and the detection of reticulate evolution indicating a high potential of snoRNA gene/gene cluster fragment length polymorphisms (SRFLPs) for phylogenetic reconstructions in Senecio and other plant genera. Most of the examined gene clusters showed a similar gene order in Senecio and Arabidopsis. However, the majority of these clusters appeared to exhibit more copies in Senecio, some of which were distinguishable by a combined sequencing/fragment profiling approach, and shown to be putative single copy regions with the potential to be used as co-dominant markers. However, a high number of paralogues and possible differences in copy number between species excludes these regions from being used in DNA barcoding. This is because specific primers would have to be developed for specific copies which would preclude development of a universal application for barcoding. None of the regions showed enough sequence variation to delimit distinctly closely related Senecio species and were therefore also considered to be unsuitable for DNA barcoding. Although most snoRNA genes and gene clusters might be inapplicable for DNA barcoding, they are likely to be valuable for phylogenetic studies of species groups, genera and families. On this scale, specific primers might act universally and the number of paralogous copies is likely to be equal across the species group of interest.

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Fremerey, Julia [Verfasser], Arndt [Gutachter] Borkhardt, and Holger [Gutachter] Schwender. "Nucleolin: a nucleolar rna-binding protein involved in ribosome biogenesis / Julia Fremerey ; Gutachter: Arndt Borkhardt, Holger Schwender." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2017. http://d-nb.info/1123197792/34.

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Detzer, Anke [Verfasser]. "Small interfering RNA (siRNA) : zelluläre Einschleusung und Wirkmechanismen / Anke Detzer." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2011. http://d-nb.info/1010454587/34.

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Pfeuffer, Natalia [Verfasser]. "Therapeutische small interfering RNA zur Wachstumsreduktion von Hautkrebs / Natalia Pfeuffer." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1239663749/34.

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Fesser, Stephanie Marion [Verfasser], and Klaus [Akademischer Betreuer] Förstemann. "Contribution of RNA binding proteins to substrate specificity in small RNA biogenesis / Stephanie Marion Fesser. Betreuer: Klaus Förstemann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2013. http://d-nb.info/1055907793/34.

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Cui, Chunhong [Verfasser], Mike [Gutachter] Schutkowski, Carsten [Gutachter] Müller-Tidow, Christoph [Gutachter] Schliemann, and Stefan [Gutachter] Hüttelmaier. "The role of small nucleolar Ribonucleoprotein complexes in lung cancer / Chunhong Cui ; Gutachter: Mike Schutkowski, Carsten Müller-Tidow, Christoph Schliemann, Stefan Hüttelmaier." Halle (Saale) : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2019. http://d-nb.info/1210732114/34.

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Czech, Benjamin [Verfasser], and Gregory [Akademischer Betreuer] Hannon. "Mechanisms of Small RNA Biogenesis in Drosophila / Benjamin Czech ; Betreuer: Gregory Hannon." Tübingen : Universitätsbibliothek Tübingen, 2013. http://d-nb.info/1162843756/34.

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Книги з теми "D small nucleolar RNA":

1

Weck, Edward. RNA Interference (D & MD Reports). D&md Publications, 2003.

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Частини книг з теми "D small nucleolar RNA":

1

Peffers, Mandy J., Andy Cremers, and Tim J. M. Welting. "Small Nucleolar RNA Expression Profiling in." In Methods in Molecular Biology, 135–49. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1119-7_10.

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Filipowicz, Witold, Pawel Pelczar, Vanda Pogacic, and François Dragon. "Biogenesis, Structure and Function of Small Nucleolar RNAs." In RNA Biochemistry and Biotechnology, 291–302. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4485-8_21.

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Costa-Nunes, Pedro, and Olga Pontes. "Chromatin and Small RNA Regulation of Nucleolar Dominance." In Polyploid and Hybrid Genomics, 291–311. Oxford, UK: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118552872.ch18.

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Bachellerie, Jean-Pierre, and Jérôme Cavaillé. "Small Nucleolar RNAs Guide the Ribose Methylations of Eukaryotic rRNAs." In Modification and Editing of RNA, 255–72. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818296.ch13.

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Bai, Baoyan, and Marikki Laiho. "Deep Sequencing Analysis of Nucleolar Small RNAs: RNA Isolation and Library Preparation." In The Nucleolus, 231–41. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3792-9_18.

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Bachellerie, Jean-Pierre, Jérôme Cavaillé, and Liang-Hu Qu. "Nucleotide Modifications of Eukaryotic rRNAs: the World of Small Nucleolar RNA Guides Revisited." In The Ribosome, 191–203. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818142.ch17.

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"snoRNA (small nucleolar RNA)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1837. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_15814.

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Krämer, Angela. "Purification of small nuclear ribonucleoprotein particles active in RNA processing." In RNA Processing Part B: Specific Methods, 215–32. Elsevier, 1990. http://dx.doi.org/10.1016/0076-6879(90)81124-d.

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Keefer, Robert F. "Macronutrients—Phosphorus and Potassium." In Handbook of Soils for Landscape Architects. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195121025.003.0014.

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Plants have a P concentration between 0.03 and 0.70%, but the usual amount is between 0.1 and 0.4%. Phosphorus is found in every living cell of a plant and is involved in genetic transfer and energy relationships. The actively growing parts, that is, stem tips, new leaves, and new roots, need much P. Seeds, especially at maturity, also have a rich supply of P acting as reserve food. Phosphorus is used in plants for (a) root development—especially the lateral and fibrous roots; (b) cell division—energy for metabolism; (c) reproduction—flowering, fruiting, seed formation all controlled by nucleic acids; (d) maturation—counteracts the ill effects of excessive N fertilization; arid (e) disease resistance— especially important in root rots of seedlings. Plant P is a major constituent of chromosomes present as DNA (deoxyribonucleic acid) used in reproduction and RNA (ribonucleic acid) used in growth processes. Plant P is also a constituent of adenosine triphosphate (ATP) that stores energy for plant use, along with many other phosphate compounds, such as phytin (inositol hexaphosphate) stored in seeds, phospholipids in the chloroplasts, and complexes of sugars, sugar amines, aldehydes, amides, and acids—all involved in plant metabolism. Deficiency of P is not striking or characteristic and is difficult to diagnose. The older leaves may be dark bluish-green, bronze, or purple. The stalks are thin, leaves small, limited lateral growth, delayed maturity, and defoliate prematurely. Probably the most obvious symptom would be the purple coloration, but this is exhibited by only a limited number of plants. The best way to determine if a plant is deficient in P would be to conduct a plant tissue test. If the P level is lower than 0.2% P, then P probably is deficient and the soil in which the plant is growing would benefit from P fertilization. . . . Phosphorus Toxicity? . . . Phosphorus toxicity has not been observed in the field and has only been evident in greenhouse culture solutions when P was present at extremely high concentrations.

Тези доповідей конференцій з теми "D small nucleolar RNA":

1

Yamamura, Soichiro, Yozo Mitsui, Shahana Majid, Hannah Nip, Nathan Bucay, Sharanjot Saini, Guoren Deng, Varahram Shahryary, Rajvir Dahiya, and Yuichiro Tanaka. "Abstract 956: Anticancer effects of silibinin-induced small nucleolar RNA 11B on bladder cancer cells." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-956.

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2

Jensen-McMullin, Cynthia, Mark Bachman, and Guann-Pyng Li. "Universal Microcarriers for Microfluidic Assays." In ASME 2007 5th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2007. http://dx.doi.org/10.1115/icnmm2007-30226.

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Bead and cell suspension based flow-through assays are popular for high throughput biological analysis. Several technologies incorporate a tagging scheme with beads to enable multiplexing. Modern flow-through systems such as flow cytometers and cell sorters are large, bulky and expensive; consequently, much research has been performed using microfluidics to miniaturize these systems. However, several problems remain with these systems, notably it remains difficult to perform manipulations on the beads (or cells), and in the case of multiplexed systems, it remains difficult to read the tags quickly. In this paper, we present a micromachined micro-carrier, referred to as a ‘micropallet’, designed to move through a microfluidic device, which helps to solve several of these problems. Micropallets are small carrier structures, micromachined out of plastic or other materials, that are used to carry attached biological or chemical samples through a microfluidic system (e.g., DNA, RNA, proteins, antibodies, adherent cells, organisms). Similar to conventional factory pallets that carry a product through an automated manufacturing line, micropallets are engineered to carry their cargo through a micro-scale system. Thus micropallets may contain shapes, structures and materials designed to interact with and work in a microfluidic system, such as for docking, sorting, manipulation and readout. Additionally, micropallets may include bar codes or other markings, and be engineered to optimally suit the cargo they carry (for example, a micropallet might contain 3-D structures and treated sections for cells, molecules or organisms to attach). Results are presented for the use of micropallets in cell assays, DNA assays and antibody assays. Micropallets may be designed to carry a sample through a microfluidic system or for use in a static assay system, enabling versatile customisation of the micropallets and flow system for design of a programmable system that interacts with the micropallets for detection, control and manipulation.