Увійти

Готові списки джерел за темами / D small nucleolar RNA / Дисертації

Дисертації з теми "D small nucleolar RNA"

Щоб переглянути інші типи публікацій з цієї теми, перейдіть за посиланням: D small nucleolar RNA.

Автор: Grafiati

Опубліковано: 14 вересня 2021

Оновлено: 3 лютого 2022

Оформте джерело за APA, MLA, Chicago, Harvard та іншими стилями

Оберіть тип джерела:

Ознайомтеся з топ-50 дисертацій для дослідження на тему "D small nucleolar RNA".

Біля кожної праці в переліку літератури доступна кнопка «Додати до бібліографії». Скористайтеся нею – і ми автоматично оформимо бібліографічне посилання на обрану працю в потрібному вам стилі цитування: APA, MLA, «Гарвард», «Чикаго», «Ванкувер» тощо.

Також ви можете завантажити повний текст наукової публікації у форматі «.pdf» та прочитати онлайн анотацію до роботи, якщо відповідні параметри наявні в метаданих.

Переглядайте дисертації для різних дисциплін та оформлюйте правильно вашу бібліографію.

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

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.

5

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

6

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

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

7

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

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

8

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

9

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

10

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.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

11

Klesen, Simon Christoph [Verfasser]. "Gating of small RNA mobility in plant stem cell niches / Simon Christoph Klesen." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1225739977/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

12

Klesen, Simon [Verfasser]. "Gating of small RNA mobility in plant stem cell niches / Simon Christoph Klesen." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1225739977/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

13

Wright, Patrick R. [Verfasser], and Rolf [Akademischer Betreuer] Backofen. "Predicting small RNA targets in prokaryotes – a challenge beyond the barriers of thermodynamic models." Freiburg : Universität, 2016. http://d-nb.info/1124004432/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

14

Dueck, Anne Verfasser], and Gunter [Akademischer Betreuer] [Meister. "Analysis of small RNA-Argonaute complexes in different organisms / Anne Dueck. Betreuer: Gunter Meister." Regensburg : Universitätsbibliothek Regensburg, 2015. http://d-nb.info/1072293773/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

15

Siboni, Ruth. "Characterization of Small Molecules that Reduce CUG Repeat RNA in Myotonic Dystrophy." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19260.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Myotonic dystrophy (DM) is an inherited disease characterized by myotonia, insulin resistance, cardiomyopathy, and cognitive deficiencies. DM is a triplet repeat disorder, meaning that affected individuals carry anywhere between 50 and thousands of CTG/CCTG repeats in their genetic makeup. When transcribed into RNA, these repeats become “toxic” in the sense that they serve to bind and sequester important RNA binding proteins. One such family of proteins, the Muscleblind-like (MBNL) family, is important in the regulation of alternative mRNA splicing, and thus the sequestration of MBNL proteins leads to a number of mis-splicing events. Many of these events are directly correlated to DM symptoms. While there is no known cure for DM, the use of small molecules to treat symptoms is a well-characterized therapeutic tactic with immense promise. Pentamidine is a small molecule that was found to reverse mis-splicing in both DM cell and mouse models. Mechanistically, this molecule is particularly unique because unlike many small molecules, which physically displace MBNL from the toxic CUG RNA, pentamidine reduces CUG RNA levels, possibly through inhibition of CTG transcription. Chapter I summarizes alternative splicing mechanisms and regulation, defines MBNL protein structure and function, describes DM pathophysiology and molecular mechanism, and finally provides an overview of pentamidine characterization as a small molecule therapeutic. Chapter II reports the development of an in vitro T7 transcription assay, which allowed us to compare the relative efficacy by which pentamidine is able to inhibit the transcription of various repeat and non-repeat DNA sequences. This chapter further reports the characterization of a series of methylene linker analogues of pentamidine, which were also characterized through the T7 transcription assay. Chapter III details our thorough structure-activity relationship investigation of bisbenzamidine analogues of pentamidine, both in in vivo and in vitro models. Chapter IV describes our characterization of actinomycin D, a known transcription inhibitor and chemotherapeutic, within the DM disease framework. Chapter V summarizes these data, which ultimately serve as a proof of concept for the potential of CTG transcription inhibition in therapeutic contexts and broadly describe their application in other repeat diseases. This dissertation contains previously published and unpublished co-authored material.
10000-01-01

16

Pfeiffer, Verena. "Characterization of small non-coding RNAs regulating outer membrane synthesis in the model pathogen Salmonella Typhimurium." Berlin mbv, Mensch-und-Buch-Verl, 2009. http://d-nb.info/998090034/04.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

17

Ruwe, Hannes [Verfasser], Christian [Akademischer Betreuer] Schmitz-Linneweber, Ian David [Akademischer Betreuer] Small, and Wolfgang [Akademischer Betreuer] Schuster. "PPRs and cpRNPs : RNA-binding proteins required for global RNA stabilization in plant organelles / Hannes Ruwe. Gutachter: Christian Schmitz-Linneweber ; Ian David Small ; Wolfgang Schuster." Berlin : Lebenswissenschaftliche Fakultät, 2015. http://d-nb.info/1074487354/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

18

Ma, Hsiu-Ching. "Discovery and characterisation of new miRNAs during embryogenesis of D. melanogaster." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609448.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

19

Lobentanzer, Sebastian [Verfasser], Jochen [Akademischer Betreuer] Klein, Jochen [Gutachter] Klein, and Hermona [Gutachter] Soreq. "Small RNA dynamics in cholinergic systems / Sebastian Lobentanzer ; Gutachter: Jochen Klein, Hermona Soreq ; Betreuer: Jochen Klein." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2020. http://d-nb.info/1221669087/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

20

Su, Andreas A. H. [Verfasser], and Lennart [Akademischer Betreuer] Randau. "Small RNA-guided processes in the hyperthermophilic methanogen Methanopyrus kandleri / Andreas A. H. Su. Betreuer: Lennart Randau." Marburg : Philipps-Universität Marburg, 2015. http://d-nb.info/1064976034/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

21

Santos, Sara F. C. [Verfasser], Jörg [Gutachter] Vogel, Alexander J. [Gutachter] Westermann, and Jay [Gutachter] Hinton. "Expanding the targetome of Salmonella small RNA PinT using MS2 affinity purification and RNA-Seq (MAPS) / Sara F. C. Santos ; Gutachter: Jörg Vogel, Alexander J. Westermann, Jay Hinton." Würzburg : Universität Würzburg, 2021. http://d-nb.info/1238018351/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

22

Helfer, Stephanie [Verfasser], and Klaus [Akademischer Betreuer] Förstemann. "Interrelation between AU-rich element mediated decay and the small RNA silencing system / Stephanie Helfer. Betreuer: Klaus Förstemann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2012. http://d-nb.info/1031379894/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

23

Jehn, Julia [Verfasser]. "Small RNA Pathways – Exploration of new players, supposedly lost sites of action and an unperceived defense strategy / Julia Jehn." Mainz : Universitätsbibliothek Mainz, 2019. http://d-nb.info/1200556399/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

24

Hirsch, Markus [Verfasser]. "Dynamics of small interfering RNA - FRET based integrity measurements of siRNA in the cuvette & inside cells / Markus Hirsch." Mainz : Universitätsbibliothek Mainz, 2015. http://d-nb.info/1070861790/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

25

Seifert, Felix [Verfasser], and Stefan [Akademischer Betreuer] Scholten. "Analysis of small RNA expression in the context of heterosis formation in Zea mays L. / Felix Seifert. Betreuer: Stefan Scholten." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2014. http://d-nb.info/1061127885/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

26

Wang, Yu [Verfasser], Hans-Werner [Akademischer Betreuer] Mewes, and Heiko [Akademischer Betreuer] Schoof. "Charting Small RNA Landscape – an Exciting Journey in the Postgenomic Era / Yu Wang. Gutachter: Heiko Schoof. Betreuer: Hans-Werner Mewes." München : Universitätsbibliothek der TU München, 2011. http://d-nb.info/1023128608/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

27

Pinzon, Restrepo Natalia. "Characterization of regulatory noncoding RNAs : the U1 small nuclear RNA and Cajal body-specific box C/D guide RNAs." Toulouse 3, 2011. http://thesesups.ups-tlse.fr/2458/.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Les cellules contiennent de nombreux ARNs non-codants qui jouent un rôle essentiel dans toutes les étapes de l'expression génique. Nos travaux concernent la caractérisation de possibles nouvelles fonctions associés à deux classes d'ARNs non-codants : l'ARN U1 et les scaARNs. Le petit ARN nucléaire U1 forme une ribonucléoparticule (snRNP U1) qui joue un rôle clé dans l'épissage des ARN pré-messagers. De plus, l'ARN U1 semble intervenir dans d'autres étapes de la synthèse des ARNm fonctionnels. Nos travaux ont démontré qu'une fraction de l'ARN U1 interagit spécifiquement avec la protéine TAF15, dans un complexe qui diffère dans sa composition protéique de la particule d'épissage canonique Sm snRNP U1. Nous avons constaté qu'à la différence de la particule d'épissage, la snRNP U1-TAF15 est fortement attachée à la chromatine. De plus, suite à l'arrêt de la transcription par l'ARN polymérase II, la particule U1-TAF15 se relocalise dans la coiffe périnucléolaire, à l'opposé de la particule Sm snRNP U1 qui s'accumule alors dans les "speckles". Une étude protéomique de la particule U1-TAF15 nous a permis d'établir des hypothèses quant à sa fonction qui sont actuellement à l'étude dans le laboratoire. Récemment, une protéine essentielle à l'adressage des scaARNs (ARNs spécifiques des Corps de Cajal) dans les Corps de Cajal a été identifiée (Tycowski et al. , 2009; Venteicher et al. , 2009). Une analyse par séquençage à haut-débit de l'ensemble des petits ARNs associés à WDR79 a permis d'identifier de nombreux nouveaux scaARNs putatifs. Parmi eux, l'analyse de deux ARNs à boite C/D a défini des structures essentielles pour leur localisation dans les corps de Cajal. Des études plus approfondies devraient nous permettre de déterminer des éléments spécifiques nécessaires à l'adressage des scaARNs à boite C/D vers les corps de Cajal. Par ailleurs, nous avons commencé la caractérisation d'un nouveau scaARN qui ciblerait la modification d'un ARN de transfert. Alors que les ARN C/D connus chez les Eucaryotes participent à la biogenèse des ARN ribosomiques et des petits ARN nucléaires, nous avons identifié pour la première fois chez les Eucaryotes un ARN C/D qui ciblerait un ARN de transfert
Noncoding regulatory RNAs (ncRNAs) are in the focus of current research, since they participate in nearly all cellular processes. To get further insights into the functional and structural complexity of ncRNAs, we studied human ncRNAs belonging to two classes of ncRNAs, the nucleoplasmic spliceosomal snRNAs and the nucleolar and Cajal body-specific box C/D 2'-O-methylation guide RNAs. The U1 snRNP is an evolutionarily conserved, abundant nucleoplasmic snRNP that plays a central role in pre-mRNA splicing. According to a recently emerging view, besides its constitutive role in splicing, the U1 snRNP has important regulatory functions in different steps of pre-mRNA production. We demonstrated that a fraction of the human U1 snRNA specifically associates with the nuclear RNA-binding protein TAF15 that is known to interact with a subpopulation of TFIID and RNA polymerase II complexes. The U1-TAF15 snRNP is structurally and functionally distinct from the well-characterized U1 spliceosomal snRNP and it tightly associates with chromatin. The function of U1-TAF15 snRNP remains unknown; it might contribute to the coupling of transcription and splicing. WDR79 (also called WRAP53) has been recently identified as an essential factor for targeting a subclass of box C/D and H/ACA modification guide RNAs, as well as telomerase H/ACA RNA, into the Cajal bodies. Accumulation of box C/D and H/ACA RNPs in Cajal bodies is essential for the biogenesis of functional spliceosomal snRNPs and telomere synthesis. Co-immunopurification of WDR79-associated human RNAs, followed by cDNA synthesis and deep sequencing identified a large number of novel Cajal body-specific RNAs. We are currently dissecting the cis-acting RNA element responsible for WDR79-binding and for targeting box C/D 2'-O-methylation guide RNPs into Cajal bodies. We have also identified a novel Cajal body-specific 2'-O-methylation guide RNA that is predicted to direct methylation of cytidine 34 at the Wobble position of tRNA-Met-CAT elongator. Interestingly, tRNA modification is a novel function for vertebrate box C/D scaRNPs

28

Ng, Tsz Wa. "Effect of small interfering RNA specific for N-methyl-D-asparate receptor two B in models of Parkinson's disease." HKBU Institutional Repository, 2011. http://repository.hkbu.edu.hk/etd_ra/1226.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

29

Klepsch, Maximilian Andreas [Verfasser], Thomas [Gutachter] Rudel, and Thomas [Gutachter] Dandekar. "Small RNA-binding complexes in Chlamydia trachomatis identified by Next-Generation Sequencing techniques / Maximilian Andreas Klepsch ; Gutachter: Thomas Rudel, Thomas Dandekar." Würzburg : Universität Würzburg, 2020. http://d-nb.info/1204831866/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

30

Lehmann, Melanie [Verfasser], and Katrin [Akademischer Betreuer] Hartmann. "Untersuchungen zur möglichen Wirksamkeit von small interfering RNA auf die Vermehrung des felinen Leukämievirus in vitro / Melanie Lehmann. Betreuer: Katrin Hartmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1077986882/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

31

Soulé, Stéphanie. "Caractérisation fonctionnelle de jouvence, un petit ARN nucléolaire requis dans l’épithélium de l’intestin chez la drosophile ninaD Regulates Cholesterol Homeostasis From the Midgut and Protects Against Neurodegeneration Jouvence a Small Nucleolar RNA Required in the Gut Extends Lifespan in Drosophila." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL054.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Le vieillissement massif de la population et le bond incroyable ces dernières décennies de l’espérance de vie ont entraîné une prise de conscience de l’importance de ce problème. La nécessité de mieux appréhender les mécanismes du vieillissement est devenue une urgence de santé publique. De nombreux groupes de recherche se consacrent depuis quelques années à l'identification de gènes et de voies de signalisation impliqués dans le processus du vieillissement. Ce processus biologique, qui touche chaque espèce et chaque individu de manière spécifique, se caractérise par un déclin graduel de la fonction de nombreux processus physiologiques en fonction de l’âge. Toutefois même s’il est inéluctable, le vieillissement est influençable. En effet, de nombreux facteurs, autant intrinsèques (facteurs génétiques, télomérases, stress oxydatif), qu’extrinsèques (hygiène de vie, pollution, alimentation) vont influencer le vieillissement. C’est d’ailleurs un facteur de risque important dans le développement de nombreuses pathologies associées à l’âge (le diabète de type II, le cancer, les maladies neurodégénératives, les maladies cardiovasculaires). De plus, il a déjà été démontré dans la littérature que la modulation d’un seul gène peut influencer, autant positivement que négativement, le vieillissement d’un individu. Plus que l’allongement de la durée de vie, c’est une durée de vie sans déficience (concept du « bien vieillir ») qui fait l’objet des principales recherches. Les gènes ayant des effets sur ce processus sont habituellement des gènes jouant un rôle important dans une voie de signalisation et donc, sont souvent conservés à travers l’évolution. Les travaux décrits dans cette thèse concernent l’implication d’un nouveau snoARN (jouvence), requis dans l’épithélium de l’intestin, dans les mécanismes du vieillissement de la drosophile. Ils ont en particulier révélé la capacité de ce snoARN à augmenter de manière spectaculaire la durée de vie des mouches en enrayant les mécanismes du vieillissement et en luttant contre les effets délétères associés. jouvence permettrait ainsi de lutter contre les maladies associées à la vieillesse telles que la neurodégénérescence, l’hyperplasie intestinale, mais également contre les troubles métaboliques, tout en prolongeant la durée de vie de l’organisme. Il serait impliqué dans différentes voies métaboliques pouvant avoir un impact sur la santé à long terme des drosophiles. jouvence semble réguler le métabolisme lipidique, l’homéostasie intestinale, ainsi que la résistance au stress. Par contre, son inactivation de provoque des effets néfastes qui mènent à la dégradation rapide de plusieurs fonctions métaboliques et à la mort prématurée des mouches. Les résultats obtenus dans cette étude dévoilent un lien entre jouvence et le contrôle du vieillissement en santé chez la drosophile
The massive ageing of the population and the incredible leap in life expectancy in recent decades have led to an awareness of the importance of this problem. The need to better understand the mechanisms of ageing has become a public health emergency. Many research groups have been working for several years to identify genes and signalling pathways involved in the aging process.This biological process, which affects each species and each individual independently, is characterized by a gradual decline of function of many physiological processes as a function of age. However, even though it is inevitable, aging is still subject to influence. Indeed, many factors, both intrinsic (genetic factors, telomerases, oxidative stress) and environmental (lifestyle, diet, pollution) will influence aging. Aging is also an important risk factor for the development of many diseases such as type 2 diabetes, cancer, neurodegenerative and cardiovascular diseases. Moreover, it has already been reported in the literature that modulation of a single gene can influence, both positively and negatively, the aging process of an individual. More than the extension of life expectancy, it is a life expectancy without deficiency (concept of "aging well") that is the subject of major research. Genes with effects on this process are usually genes that play an important role in a signalling pathway, and therefore are often conserved across evolution. The work described in this thesis shows the involvement of a new snoRNA (jouvence), required in the intestinal epithelium, in the aging mechanisms of the fly D. melanogaster. In particular, they revealed the ability of this snoRNA to dramatically increase the lifespan of flies by halting the mechanisms of aging and fighting against the associated deleterious effects. jouvence would thus make it possible to fight against diseases associated with old age such as neurodegeneration, intestinal hyperplasia, but also against metabolic disorders, while prolonging the lifespan of the organism. This snoRNA appears to be involved in various metabolic pathways that may impact on long-term health of fruit flies. jouvence appears to regulate lipid metabolism, intestinal homeostasis, and stress resistance. On the other hand, its inactivation causes adverse effects that lead to the rapid degradation of several metabolic functions and premature death of flies. The results obtained in this study reveal a link between youthfulness and the control of healthy aging in D. melanogaster

32

Riccardi, Laura Verfasser], and Gerhard [Akademischer Betreuer] [Stock. "Modeling the free energy landscape of biomolecules: small RNAs and peptide aggregation = Biomolekulare Energielandschaften von kleinen RNA-Molekuelen und der Peptid-Aggregation." Freiburg : Universität, 2013. http://d-nb.info/1114144983/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

33

Seekircher, Stephanie [Verfasser], and Petra [Akademischer Betreuer] Dersch. "Identification of regulatory factors that control the synthesis of the small regulatory RNA CsrC in Yersinia pseudotuberculosis / Stephanie Seekircher ; Betreuer: Petra Dersch." Braunschweig : Technische Universität Braunschweig, 2014. http://d-nb.info/1175821209/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

34

Röpke, Luise [Verfasser], Reinhard Akademischer Betreuer] Wetzker, Matthias [Akademischer Betreuer] Dürst, and Frank [Akademischer Betreuer] [Große. "Small hairpin RNA-vermittelte Inhibierung der Genexpression von Phosphoinositid 3-Kinasen in humanen Neuroblastomzellen / Luise Röpke. Gutachter: Reinhard Wetzker ; Matthias Dürst ; Frank Große." Jena : Thüringer Universitäts- und Landesbibliothek Jena, 2011. http://d-nb.info/1016619901/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

35

Pernitzsch, Sandy Ramona [Verfasser], Cynthia Mira [Gutachter] Sharma, and Dagmar [Gutachter] Beier. "Functional Characterization of the abundant and conserved small regulatory RNA RepG in Helicobacter pylori / Sandy Ramona Pernitzsch ; Gutachter: Cynthia Mira Sharma, Dagmar Beier." Würzburg : Universität Würzburg, 2016. http://d-nb.info/1241045542/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

36

Xu, Qinghao. "Small interfering RNAs that target NR1 and ERK2 : in the spinal cord block inflammatory pain signaling /." Access full-text from WCMC, 2008. http://proquest.umi.com/pqdweb?did=1528353711&sid=8&Fmt=2&clientId=8424&RQT=309&VName=PQD.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

37

Iu, Yan Yu. "Enhancement of gene silencing effects of small interfering RNAs to N-methyld-D-asparate receptors by gold nonoparticiples." HKBU Institutional Repository, 2013. http://repository.hkbu.edu.hk/etd_ra/1552.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

38

Schulz, Elena [Verfasser], Alexander [Gutachter] Baraniskin, and Claus [Gutachter] Doberauer. "Zirkulierende Fragmente der small nuclear RNA U2 als neuer diagnostischer Biomarker für das primäre ZNS-Lymphom / Elena Schulz ; Gutachter: Alexander Baraniskin, Claus Doberauer ; Medizinische Fakultät." Bochum : Ruhr-Universität Bochum, 2018. http://d-nb.info/1163451320/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

39

Knüppel, Robert Michael [Verfasser], Ferreira-Cerca [Akademischer Betreuer] Sébastien, Meister [Akademischer Betreuer] Gunter, and Randau [Akademischer Betreuer] Lennart. "Small changes, unexpected consequences: Molecular insights into substrate-dependent adaptation of KsgA/Dim1-dependent ribosomal RNA modifications in archaea / Robert Michael Knüppel ; Ferreira-Cerca Sébastien, Meister Gunter, Randau Lennart." Regensburg : Universitätsbibliothek Regensburg, 2021. http://d-nb.info/1232073997/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

40

Davila, Gallesio Jimena [Verfasser], Markus [Akademischer Betreuer] Bohnsack, Jörg [Gutachter] Enderlein, Gerhard [Gutachter] Braus, Blanche [Gutachter] Schwappach, Michael [Gutachter] Meinecke, Michael [Gutachter] Thumm, and Ralf [Gutachter] Ficner. "The roles of RNA helicases and other ribosome biogenesis factors during small subunit maturation / Jimena Davila Gallesio ; Gutachter: Jörg Enderlein, Gerhard Braus, Blanche Schwappach, Michael Meinecke, Michael Thumm, Ralf Ficner ; Betreuer: Markus Bohnsack." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1211556816/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

41

Kim, NaJung. "Rationale design of polymeric siRNA delivery systems." Diss., University of Iowa, 2011. https://ir.uiowa.edu/etd/1237.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Regulation of gene expression using small interfering RNA (siRNA) is a promising strategy for research and treatment of numerous diseases. However, siRNA cannot easily cross the cell membrane due to its inherent instability, large molecular weight and anionic nature. For this reason, a carrier that protects, delivers and unloads siRNA is required for successful gene silencing. The goal of this research was to develop a potential siRNA delivery system for in vitro and in vivo applications using cationic polymers, chitosan and polyethylenimine (PEI), poly(ethylene glycol) (PEG), mannose, and poly(D,L-lactic-co-glycolic acid) (PLGA). Furthermore, the delivery system was constructed in two different ways to explore the effect of mannose location in the structure. In the first approach, mannose and PEG were directly conjugated to the chitosan/PEI backbone, while mannose was connected to the chitosan/PEI backbone through PEG spacer in the second approach. First, the ability of modified chitosan polymers to complex and deliver siRNA for gene silencing was investigated. Despite the modified chitosan polymers successfully formed nanoplexes with siRNA, entered target cells and reduced cytotoxicity of unmodified chitosan, they showed limited gene silencing efficiency. For this reason, modified PEIs were examined to improve in vitro gene knockdown. The modified PEI polymers also complexed with siRNA and facilitated endocytosis of the nanoplexes. In addition, the modifications reduced inherent cytotoxicity of unmodified PEI without compromising the gene silencing efficiency on both mRNA and protein levels. Interestingly, we found that complexation of siRNA with PEI-PEG-mannose resulted in higher cell uptake and gene silencing than complexes made with mannose-PEI-PEG. Finally, the effect of sustained release of the mannosylated pegylated PEI/siRNA nanoplexes on gene silencing was tested by encapsulating the nanoplexes within PLGA microparticles. The modified PEIs enhanced the entrapment efficiency of siRNA into the particles and resulted in reduced initial burst followed by sustained release. Incorporating the modified PEIs increased cellular uptake of siRNA, whereas it did not enhance in vitro gene knockdown efficiency due to the sustained release properties. The modified PEIs reduced the in vitro cytotoxicity and in vivo hepatotoxicity of the PLGA microparticles. In addition, encapsulating the nanoplexes into PLGA microparticles further reduced the cytotoxicity of PEI. Throughout the study, the second structure was proven more efficacious than the first structure in cellular uptake, gene silencing, siRNA encapsulation, and sustained release. We have developed novel polymeric siRNA delivery systems that enhance delivery efficiency and cellular uptake of siRNA. They have great potential for utility as a long-acting siRNA delivery system in biomedical research.

42

Kunze, Doreen [Verfasser], Pée Karl-Heinz [Akademischer Betreuer] van, and Manfred P. [Akademischer Betreuer] Wirth. "Small interfering RNA-vermittelte Hemmung der Apoptoseinhibitoren BCL2, BCL-XL, XIAP und Survivin in Zellkultur- und Mausmodellen des humanen Harnblasenkarzinoms / Doreen Kunze. Gutachter: Karl-Heinz van Pée ; Manfred P. Wirth. Betreuer: Karl-Heinz van Pée." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2012. http://d-nb.info/1067729836/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

43

Deichelbohrer, Stephan [Verfasser], and Hans Peter [Akademischer Betreuer] Wendel. "Gene-Silencing der Adhäsionsmoleküle P-Selectin (CD 62P) und PECAM-1 (CD 31) mittels small interfering RNA (siRNA) an humanen Endothelzellen der Vena saphena magna (HSVEC) unter dem Aspekt der Protektion aorto-koronarer Bypässe / Stephan Deichelbohrer ; Betreuer: Hans Peter Wendel." Tübingen : Universitätsbibliothek Tübingen, 2016. http://d-nb.info/1198122293/34.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

44

Samarsky, Dmitry A. "Box C/D small nucleolar RNAs: Biogenesis, structure and utilization for in vivo ribozyme studies." 1998. https://scholarworks.umass.edu/dissertations/AAI9841920.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Eukaryotic cells contain scores of small nucleolar RNAs (snoRNAs), which are required for maturation of pre-rRNA. Two large snoRNA families exist defined by vital box C/D and box H/ACA motifs. The goal of the present study was to gain new insights into the structure and biogenesis of the box C/D snoRNAs; the knowledge developed from this effort was then recruited for practical applications. The investigation was conducted with the phylogenetically conserved U14 and U3 box C/D snoRNAs, from the yeast Saccharomyces cerevisiae. The specific aims included: (1) identification of cis-elements sufficient for biogenesis of the U14 snoRNA; (2) development of a functional map for the U3 snoRNA, and; (3) development of a U3-based model ribozyme system for in vivo studies. Conclusions derived from the U14 biogenesis studies are: (1) production of U14 involves ordered folding of the precursor RNA, and this step is required for formation of the vital box C/D structure motif, and; (2) the active box C/D motif, which is now predicted to consist solely of the box C and D elements, is necessary and sufficient for both accumulation and targeting RNA to the nucleolus. A general model for box C/D snoRNA biogenesis is proposed. Functional mapping of U3 revealed that: (1) boxes C$\sp\prime$ and D and flanking helices are critical for U3 accumulation; (2) boxes B and C are not essential for U3 production, but are important for function, due most likely to binding of a trans-acting factor(s); (3) the 5$\sp\prime$ portion of U3 is required for function, but not stability, and; (4) the non-conserved hairpins, which account for 50% of the molecule, are not required for accumulation or function. Based on the knowledge obtained with U14 and U3, a model ribozyme system featuring chimeric U3:ribozyme RNAs, or "snorbozymes", was developed and tested in vivo. Remarkably, the cleavage efficiency by a hammerhead ribozyme, both in cis- and in trans-configurations, appears quantitative! Other advantages of the system are: (1) a final product is stable, and; (2) authentic in vivo cleavage can be easily distinguished from artifactual cleavages. Snorbozymes are predicted to be useful for targeting natural transcripts in any eukaryotes, for fundamental research or practical applications.

45

Ellis, Joseph. "The RNA world: a look at Ribonuclease P RNA, small nucleolar RNA, 6S RNA, and the small ribosomal subunit /." 2006. http://www.lib.ncsu.edu/theses/available/etd-10202006-081103/unrestricted/etd.pdf.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

46

Canzler, Sebastian. "Insights into the Evolution of small nucleolar RNAs: Prediction, Comparison, Annotation." Doctoral thesis, 2016. https://ul.qucosa.de/id/qucosa%3A15255.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

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.

47

Ni, Jingwei. "The major function of eukaryotic small nucleolar RNAs is nucleotide modification in ribosomal RNA." 1998. https://scholarworks.umass.edu/dissertations/AAI9909197.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Small nucleolar RNAs (snoRNAs) can be divided into two large families based on conserved sequence elements. These two classes are the box C/D snoRNAs and the box H/ACA snoRNAs. At the onset of this thesis study, a small number of snoRNAs were known to be required for processing (cleavage) of pre-ribosomal RNA; the function of majority of snoRNAs remained an enigma. The thesis research revealed two important and exciting discoveries: (1) the box C/D snoRNAs are mainly involved in guiding the formation of 2$\sp\prime$-O-methylation in rRNA, and; (2) most box HACA snoRNAs direct $\Psi$ modification of rRNA. Taken together, I demonstrated that the main function of the snoRNAs is nucleotide modification of ribosomal RNA.

48

Lempicki, Richard A. "A search for cellular components that interact with the U14 small nucleolar RNA of yeast." 1994. https://scholarworks.umass.edu/dissertations/AAI9434503.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

U14 is an evolutionary conserved small nucleolar RNA required for 18S ribosomal RNA production in the yeast Saccharomyces cerevisiae. This study attempts to identify cellular components that interact with U14 RNA with the aim of gaining insight into U14 function and identifying strategies for characterizing this activity. The objectives include: (1) development of a hypothetical secondary folding model for U14 RNA; (2) biochemical characterization of the U14 small nuclear ribonucleoprotein particle (snRNP); (3) identification of U14 binding proteins through biochemical and genetic approaches, and; (4) a genetic test to determine if U14 interacts with 18S RNA through an essential, complementary segment in U14 RNA, i.e. domain 18S-A. Two U14 consensus secondary structures were established by phylogenetic folding analysis. These structures are supported by a variety of genetic observations, but are only partially consistent with biochemical probing data developed by others. Additional research is required to determine the actual folding properties of U14 in vivo. Biochemical characterization showed that natural U14 RNA does not contain a trimethylguanosine (TMG) cap, while U14 synthesized from the GAL1 promoter does. Natural U14 occurs in two classes of RNP complexes: (i) a 10S RNP presumed to be a free snRNP and, (ii) a polydisperse, larger complex containing fibrillarin. The direct association of fibrillarin with in vitro synthesized U14 was not detected using a variety of assays. Analysis of the higher order structures sedimenting at approximately 90S revealed the presence of over one dozen snRNAs, two-thirds of which appear to be associated with fibrillarin. Several extragenic suppressor mutations were collected that relieve a lethal mutation in the box C sequence. One of these was identified as a putative sugar transport protein. It seems unlikely that this protein is directly related to U14 function per se, but may play a role in the regulation of U14 activity, possibly by influencing proteins that interact with U14 RNA or DNA. Mutations in a domain A-related sequence of 18S rDNA resulted in under-accumulation of 18S RNA, demonstrating the importance of this region for 18S RNA stability. This effect was not influenced by complementary changes in domain A of U14 RNA. The significance of these results are discussed in the context of U14 function and ribosome biogenesis.

49

Liu, Ben. "A new strategy for RNA structure probing in vivo: Targeting methylation small nucleolar RNPs to new sites in ribosomal RNA." 2003. https://scholarworks.umass.edu/dissertations/AAI3110523.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

Eukaryotic ribosomal RNAs (rRNAs) contain scores of 2′-O-methylated nucleotides that are formed by a large family of small RNA:protein machines called snoRNPs. The snoRNPs contain a small nucleolar RNA (snoRNA) and several proteins. Nucleotides to be modified are selected by the snoRNA component through base pairing with a long (10–21 nucleotides) guide sequence, and methylation is catalyzed by one of the snoRNP proteins. Modifications can be targeted to new sites by outfitting a snoRNA with a new guide sequence. In this thesis, targeting ribosome methylation to new sites in vivo was used to interfere with yeast rRNA function for the purpose of functional mapping. New snoRNAs were: (1) targeted to individual nucleotides known or predicted to have important roles, or (2) used in a gene library format to target all nucleotides in the reaction center of the ribosome. For several sites examined in detail, interference was shown not to be due to a simple anti-sense phenomenon. The results indicate that this new strategy is, indeed, effective for identifying important rRNA regions. The deleterious effects of novel methylations on rRNA function were analyzed at different levels for sensitive nucleotides located in the peptidyl transferase center (PTC). Detailed analyses were conducted on: cell growth, global translation, rDNA transcription, pre-rRNA processing, and ribosome production. The results show that the interfering snoRNPs can cause severe growth defects by two general means: (1) disrupting ribosome production, causing a low yield or; (2) creating ribosomes that are functionally defective. This novel approach should also be useful for functional mapping of other RNAs in Saccharomyces cerevisiae, and for use in other organisms as well including humans.

50

Tsao, Yu-Lun, and 曹毓倫. "Human nucleolar phosphoprotein 140 and small delta antigen coordinately regulate the ribosomal RNA synthesis and viral replication." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/73347018103638825246.

Повний текст джерела

Стилі APA, Harvard, Vancouver, ISO та ін.

Анотація:

碩士
國立臺灣大學
生物化學暨分子生物學研究所
96
Hepatitis delta virus (HDV) is a spherical virus particle with envelope. It contains a 1.7 kb single-stranded circular RNA genome of negative polarity. HDV is considered to be a satellite virus of hepatitis B virus (HBV). It requires HBV surface envelope protein to form infectious virus particles. HDV encodes two forms of delta antigen (HDAg). The small form of HDAg (HDAg-S, 195 amino acids, 24 kDa) is required for the HDV RNA replication, while the large form of delta antigen (HDAg-L, 214 amino acids, 27 kDa) is required for the viral assembly. Earlier studies from our laboratory have identified an interaction between HDAg-S and nucleolin that is critical for the nucleolar targeting of HDAg-S and HDV replication. In addition, HDAg-S interacts with the largest subunit of RNA polymerase I, RPA194. Furthermore, HDAg-S inhibits the de novo synthesis of rRNA. These results indicate that HDAg-S may regulate the synthesis of HDV antigenomic RNA and rRNA through interacting with RNA polymerase I. Previous studies have demonstrated an interaction of RPA194 with the middle domain of human nucleolar phosphoprotein 140 (hNopp140) from amino acid residues 204 to 382 of hNopp140. hNopp140 is thought to be the basic unit of nucleolus structure and involves in the synthesis of ribosomal RNA. Interestingly, HDAg-S shares conserved sequences with the middle domain of hNopp140. In this study, an association among the conserved region a of RPA194, HDAg-S, and hNopp140 was demonstrated by GST pull-down assay. HADg-S interacts with RPA194 through its amino acid residues 88 to 164. In addition, RPA194 co-sedimented with both HDAg-S and hNopp140 in sucrose gradient centrifugation. The presence of HDAg-S may therefore influence the interaction between hNopp140 and RNA polymerase I, resulting in an inhibition of the de novo synthesis of rRNA. At low dose actinomycin D which selectively inhibits RNA polymerase I activity, HDAg-S translocated from the nucleolus to the nucleoplasm of transfected cells. The phenomenon was also observed when hNopp140 known to inhibit synthesis of rRNA was overexpressed. Unexpectedly, HDV total RNA as well as antigenomic RNA increased in RPA194 knockdown cells. In summary, hNopp140 and HDAg-S coordinately regulate the synthesis of rRNA and HDV RNA.