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Academic literature on the topic 'Small Untranslated RNA'
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Journal articles on the topic "Small Untranslated RNA"
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Silvaggi, Jessica M., John B. Perkins, and Richard Losick. "Small Untranslated RNA Antitoxin in Bacillus subtilis." Journal of Bacteriology 187, no. 19 (October 1, 2005): 6641–50. http://dx.doi.org/10.1128/jb.187.19.6641-6650.2005.
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ABSTRACT Toxin-antitoxin (TA) modules are pairs of genes in which one member encodes a toxin that is neutralized or whose synthesis is prevented by the action of the product of the second gene, an antitoxin, which is either protein or RNA. We now report the identification of a TA module in the chromosome of Bacillus subtilis in which the antitoxin is an antisense RNA. The antitoxin, which is called RatA (for RNA antitoxin A), is a small (222 nucleotides), untranslated RNA that blocks the accumulation of the mRNA for a toxic peptide TxpA (for toxic peptide A; formerly YqdB). The txpA and ratA genes are in convergent orientation and overlap by ca. 75 nucleotides, such that the 3′ region of ratA is complementary to the 3′ region of txpA. Deletion of ratA led to increased levels of txpA mRNA and lysis of the cells. Overexpression of txpA also caused cell lysis and death, a phenotype that was prevented by simultaneous overexpression of ratA. We propose that the ratA transcript is an antisense RNA that anneals to the 3′ end of the txpA mRNA, thereby triggering its degradation.
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Skryabin, Boris V., Valentina Sukonina, Ursula Jordan, Lars Lewejohann, Norbert Sachser, Ilham Muslimov, Henri Tiedge, and Jürgen Brosius. "Neuronal Untranslated BC1 RNA: Targeted Gene Elimination in Mice." Molecular and Cellular Biology 23, no. 18 (September 15, 2003): 6435–41. http://dx.doi.org/10.1128/mcb.23.18.6435-6441.2003.
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ABSTRACT Despite the potentially important roles of untranslated RNAs in cellular form or function, genes encoding such RNAs have until now received surprisingly little attention. One such gene encodes BC1 RNA, a small non-mRNA that is delivered to dendritic microdomains in neurons. We have now eliminated the BC1 RNA gene in mice. Three independent founder lines were established from separate embryonic stem cells. The mutant mice appeared to be healthy and showed no anatomical or neurological abnormalities. The gross brain morphology was unaltered in such mice, as were the subcellular distributions of two prototypical dendritic mRNAs (encoding MAP2 and CaMKIIα). Due to the relatively recent evolutionary origin of the gene, we expected molecular and behavioral consequences to be subtle. Behavioral analyses, to be reported separately, indicate that the lack of BC1 RNA appears to reduce exploratory activity.
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Macdonald, P. M., K. Kerr, J. L. Smith, and A. Leask. "RNA regulatory element BLE1 directs the early steps of bicoid mRNA localization." Development 118, no. 4 (August 1, 1993): 1233–43. http://dx.doi.org/10.1242/dev.118.4.1233.
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Deployment of the bicoid morphogen gradient in early Drosophila embryos requires the prelocalization of bicoid mRNA to the anterior pole of the egg. This anterior localization is mediated by a cis-acting localization signal contained within the 3′ untranslated region of the bicoid mRNA. Here we use a series of bicoid transgenes carrying small deletions in the 3′ untranslated region to survey for functional elements that constitute the localization signal. We identify and characterize one essential element, BLE1, which specifically directs the early steps of localization. In addition, we find that many deletions within the bicoid mRNA 3′ untranslated region impair but do not prevent localization. One such deletion specifically interferes with a later step in localization. Thus the bicoid mRNA localization signal appears to consist of multiple different elements, each responsible for different steps in the localization process.
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Hartmann, Claudia, Corinna Benz, Stefanie Brems, Louise Ellis, Van-Duc Luu, Mhairi Stewart, Iván D'Orso, et al. "Small Trypanosome RNA-Binding Proteins TbUBP1 and TbUBP2 Influence Expression of F-Box Protein mRNAs in Bloodstream Trypanosomes." Eukaryotic Cell 6, no. 11 (September 1, 2007): 1964–78. http://dx.doi.org/10.1128/ec.00279-07.
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ABSTRACT In the African trypanosome Trypanosoma brucei nearly all control of gene expression is posttranscriptional; sequences in the 3′-untranslated regions of mRNAs determine the steady-state mRNA levels by regulation of RNA turnover. Here we investigate the roles of two related proteins, TbUBP1 and TbUBP2, containing a single RNA recognition motif, in trypanosome gene expression. TbUBP1 and TbUBP2 are in the cytoplasm and nucleus, comprise ca. 0.1% of the total protein, and are not associated with polysomes or RNA degradation enzymes. Overexpression of TbUBP2 upregulated the levels of several mRNAs potentially involved in cell division, including the CFB1 mRNA, which encodes a protein with a cyclin F-box domain. CFB1 regulation was mediated by the 3′-untranslated region and involved stabilization of the mRNA. Depletion of TbUBP2 and TbUBP1 inhibited growth and downregulated expression of the cyclin F box protein gene CFB2; trans splicing was unaffected. The results of pull-down assays indicated that all tested mRNAs were bound to TbUBP2 or TbUBP1, with some preference for CFB1. We suggest that TbUBP1 and TbUBP2 may be relatively nonspecific RNA-binding proteins and that specific effects of overexpression or depletion could depend on competition between various different proteins for RNA binding.
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Davis, Brigid M., Mariam Quinones, Jason Pratt, Yanpeng Ding, and Matthew K. Waldor. "Characterization of the Small Untranslated RNA RyhB and Its Regulon in Vibrio cholerae." Journal of Bacteriology 187, no. 12 (June 15, 2005): 4005–14. http://dx.doi.org/10.1128/jb.187.12.4005-4014.2005.
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ABSTRACT Numerous small untranslated RNAs (sRNAs) have been identified in Escherichia coli in recent years, and their roles are gradually being defined. However, few of these sRNAs appear to be conserved in Vibrio cholerae, and both identification and characterization of sRNAs in V. cholerae remain at a preliminary stage. We have characterized one of the few sRNAs conserved between E. coli and V. cholerae: RyhB. Sequence conservation is limited to the central region of the gene, and RyhB in V. cholerae is significantly larger than in E. coli. As in E. coli, V. cholerae RyhB is regulated by the iron-dependent repressor Fur, and it interacts with the RNA-binding protein Hfq. The regulons controlled by RyhB in V. cholerae and E. coli appear to differ, although some overlap is evident. Analysis of gene expression in V. cholerae in the absence of RyhB suggests that the role of this sRNA is not limited to control of iron utilization. Quantitation of RyhB expression in the suckling mouse intestine suggests that iron availability is not limiting in this environment, and RyhB is not required for colonization of this mammalian host by V. cholerae.
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Higgs, David C., Risa S. Shapiro, Karen L. Kindle, and David B. Stern. "Small cis-Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 8479–91. http://dx.doi.org/10.1128/mcb.19.12.8479.
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ABSTRACT Nucleus-encoded proteins interact with cis-acting elements in chloroplast transcripts to promote RNA stability and translation. We have analyzed the structure and function of three such elements within the Chlamydomonas petD 5′ untranslated region; petD encodes subunit IV of the cytochromeb 6/f complex. These elements were delineated by linker-scanning mutagenesis, and RNA secondary structures were investigated by mapping nuclease-sensitive sites in vitro and by in vivo dimethyl sulfate RNA modification. Element I spans a maximum of 8 nucleotides (nt) at the 5′ end of the mRNA; it is essential for RNA stability and plays a role in translation. This element appears to form a small stem-loop that may interact with a previously described nucleus-encoded factor to block 5′→3′ exoribonucleolytic degradation. Elements II and III, located in the center and near the 3′ end of the 5′ untranslated region, respectively, are essential for translation, but mutations in these elements do not affect mRNA stability. Element II is a maximum of 16 nt in length, does not form an obvious secondary structure, and appears to bind proteins that protect it from dimethyl sulfate modification. Element III spans a maximum of 14 nt and appears to form a stem-loop in vivo, based on dimethyl sulfate modification and the sequences of intragenic suppressors of element III mutations. Furthermore, mutations in element II result in changes in the RNA structure near element III, consistent with a long-range interaction that may promote translation.
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Shirokikh, Nikolay E., Yulia S. Dutikova, Maria A. Staroverova, Ross D. Hannan, and Thomas Preiss. "Migration of Small Ribosomal Subunits on the 5′ Untranslated Regions of Capped Messenger RNA." International Journal of Molecular Sciences 20, no. 18 (September 10, 2019): 4464. http://dx.doi.org/10.3390/ijms20184464.
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Several control mechanisms of eukaryotic gene expression target the initiation step of mRNA translation. The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential ‘scanning’ of the 5′ untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. Thus, understanding the molecular details of the scanning mechanism remains a priority task for the field. Here, we studied the effects of inhibiting ATP-dependent translation and eIF4A in cell-free translation and reconstituted initiation reactions programmed with capped mRNAs featuring different 5′UTRs. An aptamer that blocks eIF4A in an inactive state away from mRNA inhibited translation of capped mRNA with the moderately structured β-globin sequences in the 5′UTR but not that of an mRNA with a poly(A) sequence as the 5′UTR. By contrast, the nonhydrolysable ATP analogue β,γ-imidoadenosine 5′-triphosphate (AMP-PNP) inhibited translation irrespective of the 5′UTR sequence, suggesting that complexes that contain ATP-binding proteins in their ATP-bound form can obstruct and/or actively block progression of ribosome recruitment and/or scanning on mRNA. Further, using primer extension inhibition to locate SSUs on mRNA (‘toeprinting’), we identify an SSU complex which inhibits primer extension approximately eight nucleotides upstream from the usual toeprinting stop generated by SSUs positioned over the start codon. This ‘−8 nt toeprint’ was seen with mRNA 5′UTRs of different length, sequence and structure potential. Importantly, the ‘−8 nt toeprint’ was strongly stimulated by the presence of the cap on the mRNA, as well as the presence of eIFs 4F, 4A/4B and ATP, implying active scanning. We assembled cell-free translation reactions with capped mRNA featuring an extended 5′UTR and used cycloheximide to arrest elongating ribosomes at the start codon. Impeding scanning through the 5′UTR in this system with elevated magnesium and AMP-PNP (similar to the toeprinting conditions), we visualised assemblies consisting of several SSUs together with one full ribosome by electron microscopy, suggesting direct detection of scanning intermediates. Collectively, our data provide additional biochemical, molecular and physical evidence to underpin the scanning model of translation initiation in eukaryotes.
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Waldminghaus, Torsten, Anja Fippinger, Juliane Alfsmann, and Franz Narberhaus. "RNA thermometers are common in α- and γ-proteobacteria." Biological Chemistry 386, no. 12 (December 1, 2005): 1279–86. http://dx.doi.org/10.1515/bc.2005.145.
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AbstractExpression of many rhizobial small heat-shock genes is controlled by the ROSE element, a thermoresponsive structure in the 5′-untranslated region of the corresponding mRNAs. Using a bioinformatics approach, we found more than 20 new potential ROSE-like RNA thermometers upstream of small heat-shock genes in a wide variety of α- and γ-proteobacteria. Northern blot analyses revealed heat-inducible transcripts of the representative candidateCaulobacter crescentus CC2258,Escherichia coli ibpAandSalmonella typhimurium ibpAgenes. Typical σ32-type promoters were mapped upstream of the potential RNA thermometers by primer extension. Additional translational control was demonstrated in alacZreporter system and by site-directed mutagenesis. RNA secondary structure predictions strongly suggest that the Shine-Dalgarno sequence in the RNA thermometers is masked at low temperatures. Combining two regulatory modules, a σ32promoter and a ROSE-type RNA thermometer, provides a novel stringent mechanism to control expression of small heat-shock genes.
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Kunden, Rasika D., Sarah Ghezelbash, Juveriya Q. Khan, and Joyce A. Wilson. "Location specific annealing of miR-122 and other small RNAs defines an Hepatitis C Virus 5′ UTR regulatory element with distinct impacts on virus translation and genome stability." Nucleic Acids Research 48, no. 16 (August 18, 2020): 9235–49. http://dx.doi.org/10.1093/nar/gkaa664.
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Abstract Hepatitis C virus (HCV) replication requires annealing of a liver specific small-RNA, miR-122 to 2 sites on 5′ untranslated region (UTR). Annealing has been reported to (a) stabilize the genome, (b) stimulate translation and (c) promote the formation of translationally active Internal Ribosome Entry Site (IRES) RNA structure. In this report, we map the RNA element to which small RNA annealing promotes HCV to nucleotides 1–44 and identify the relative impact of small RNA annealing on virus translation promotion and genome stabilization. We mapped the optimal region on the HCV genome to which small RNA annealing promotes virus replication to nucleotides 19–37 and found the efficiency of viral RNA accumulation decreased as annealing moved away from this region. Then, by using a panel of small RNAs that promote replication with varying efficiencies we link the efficiency of lifecycle promotion with translation stimulation. By contrast small RNA annealing stabilized the viral genome even if they did not promote virus replication. Thus, we propose that miR-122 annealing promotes HCV replication by annealing to an RNA element that activates the HCV IRES and stimulates translation, and that miR-122 induced HCV genome stabilization is insufficient alone but enhances virus replication.
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Booy, Evan P., Ryan Howard, Oksana Marushchak, Emmanuel O. Ariyo, Markus Meier, Stefanie K. Novakowski, Soumya R. Deo, Edis Dzananovic, Jörg Stetefeld, and Sean A. McKenna. "The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1." Nucleic Acids Research 42, no. 5 (December 24, 2013): 3346–61. http://dx.doi.org/10.1093/nar/gkt1340.
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Abstract RNA Helicase associated with AU-rich element (RHAU) (DHX36) is a DEAH (Aspartic acid, Glumatic Acid, Alanine, Histidine)-box RNA helicase that can bind and unwind G4-quadruplexes in DNA and RNA. To detect novel RNA targets of RHAU, we performed an RNA co-immunoprecipitation screen and identified the PITX1 messenger RNA (mRNA) as specifically and highly enriched. PITX1 is a homeobox transcription factor with roles in both development and cancer. Primary sequence analysis identified three probable quadruplexes within the 3′-untranslated region of the PITX1 mRNA. Each of these sequences, when isolated, forms stable quadruplex structures that interact with RHAU. We provide evidence that these quadruplexes exist in the endogenous mRNA; however, we discovered that RHAU is tethered to the mRNA via an alternative non–quadruplex-forming region. RHAU knockdown by small interfering RNA results in significant increases in PITX1 protein levels with only marginal changes in mRNA, suggesting a role for RHAU in translational regulation. Involvement of components of the microRNA machinery is supported by similar and non-additive increases in PITX1 protein expression on Dicer and combined RHAU/Dicer knockdown. We also demonstrate a requirement of argonaute-2, a key RNA-induced silencing complex component, to mediate RHAU-dependent changes in PITX1 protein levels. These results demonstrate a novel role for RHAU in microRNA-mediated translational regulation at a quadruplex-containing 3′-untranslated region.
Dissertations / Theses on the topic "Small Untranslated RNA"
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Simkin, Alfred T. "Evolutionary Approaches to the Study of Small Noncoding Regulatory RNA Pathways: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/721.
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Short noncoding RNAs play roles in regulating nearly every biological process, in nearly every organism, yet the exact function and importance of these molecules remains a subject of some debate. In order to gain a better understanding of the contexts in which these regulators have evolved, I have undertaken a variety of approaches to study the evolutionary history of the components that make up these pathways, in the form of two main research efforts. In the first chapter, I have used a combination of population genetics and molecular evolution techniques to show that proteins involved in the piRNA pathway are rapidly evolving, and that different components of the pathway seem to be evolving rapidly on different timescales. These rapidly evolving piRNA pathway proteins can be loosely separated into two groups. The first group appears to evolve quickly at the species level, perhaps in response to transposons that invade across species lines, while the second group appears to evolve quickly at the level of individual populations, perhaps in response to transposons that are paternally present yet novel to the maternal genome. In the second chapter of my research, I have used molecular evolution techniques and carefully devised controls to show that the binding sites of well-conserved miRNAs are among the most slowly changing short motifs in the genome, consistent with a conserved function for these short RNAs in regulatory pathways that are ancient and extremely slow to change. I have additionally discovered a major flaw in an existing approach to motif turnover calculations, which may lead to systematic biases in the published literature toward the false inference of increased regulatory complexity over time. I have implemented a revised approach to motif turnover that addresses this flaw.
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Simkin, Alfred T. "Evolutionary Approaches to the Study of Small Noncoding Regulatory RNA Pathways: A Dissertation." eScholarship@UMMS, 2007. http://escholarship.umassmed.edu/gsbs_diss/721.
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Short noncoding RNAs play roles in regulating nearly every biological process, in nearly every organism, yet the exact function and importance of these molecules remains a subject of some debate. In order to gain a better understanding of the contexts in which these regulators have evolved, I have undertaken a variety of approaches to study the evolutionary history of the components that make up these pathways, in the form of two main research efforts. In the first chapter, I have used a combination of population genetics and molecular evolution techniques to show that proteins involved in the piRNA pathway are rapidly evolving, and that different components of the pathway seem to be evolving rapidly on different timescales. These rapidly evolving piRNA pathway proteins can be loosely separated into two groups. The first group appears to evolve quickly at the species level, perhaps in response to transposons that invade across species lines, while the second group appears to evolve quickly at the level of individual populations, perhaps in response to transposons that are paternally present yet novel to the maternal genome. In the second chapter of my research, I have used molecular evolution techniques and carefully devised controls to show that the binding sites of well-conserved miRNAs are among the most slowly changing short motifs in the genome, consistent with a conserved function for these short RNAs in regulatory pathways that are ancient and extremely slow to change. I have additionally discovered a major flaw in an existing approach to motif turnover calculations, which may lead to systematic biases in the published literature toward the false inference of increased regulatory complexity over time. I have implemented a revised approach to motif turnover that addresses this flaw.
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Ghildiyal, Megha. "Endogenous Small RNAs in the Drosophila Soma: A Dissertation." eScholarship@UMMS, 2010. https://escholarship.umassmed.edu/gsbs_diss/459.
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Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNAs have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, modes of target regulation and in the biological pathways they regulate.
Historically, siRNAs were believed to arise only from exogenous double-stranded RNA triggers in organisms lacking RNA-dependent RNA polymerases. However, the discovery of endogenous siRNAs in flies expanded the biological significance of siRNAs beyond viral defense. By high throughput sequencing we identified Drosophila endosiRNAs as 21 nt small RNAs, bearing a 2´-O-methyl group at their 3´ ends, and depleted in dicer-2 mutants.
Methylation of small RNAs at the 3´ end in the soma, is a consequence of assembly into a mature Argonaute2-RNA induced silencing complex. In addition to endo-siRNAs, we observed certain miRNAs or their miRNA* partners loading into Argonaute2. We discovered, that irrespective of its biogenesis, a miRNA duplex can load into either Argonaute (Ago1 or Ago2), contingent on its structural and sequence features, followed by assignment of one of the strands in the duplex as the functional or guide strand. Usually the miRNA strand is selected as the guide in complex with Ago1 and miRNA* strand with Ago2.
In our efforts towards finding 3´ modified small RNAs in the fly soma, we also discovered 24-28nt small RNAs in certain fly genotypes, particularly ago2 and dcr-2mutants. 24-28nt small RNAs share many features with piRNAs present in the germline, and a significant fraction of the 24-28nt small RNAs originate from similar transposon clusters as somatic endo-siRNAs. Therefore the same RNA can potentially act as a precursor for both endo-siRNA and piRNA-like small RNA biogenesis. We are analyzing the genomic regions that spawn somatic small RNAs in order to understand the triggers for their production. Ultimately, we want to attain insight into the underlying complexity that interconnects these small RNA pathways.
Dysregulation of small RNAs leads to defects in germline development, organogenesis, cell growth and differentiation. This thesis research provides vital insight into the network of interactions that fine-tune the small RNA pathways. Understanding the flow of information between the small RNA pathways, a great deal of which has been revealed only in the recent years, will help us comprehend how the pathways compete and collaborate with each other, enabling each other’s optimum function.
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"Functional characterization of an exonic small non-coding RNA TIFm71." Thesis, 2011. http://library.cuhk.edu.hk/record=b6075396.
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Wang, Dakui.Thesis (Ph.D.)--Chinese University of Hong Kong, 2011.
Includes bibliographical references (leaves 208-234).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Abstract also in Chinese.
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Hsieh, Po Ting, and 謝柏廷. "Regulation of Enterovirus Viral Translation and RNA Replication: Role of Viral small RNA and 5' Untranslated Region." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/43cyca.
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chen, chun-chin, and 陳秋錦. "Functional analysis of the small RNA derived from the highly conserved 3’-untranslated region of Japanese encephalitis virus in infected mammalian cells." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/22361143479344785083.
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碩士國立東華大學
生物技術研究所
93
英文摘要 Japanese encephalitis virus (JEV) contains a single positive-strand RNA genome of 10,976 nucleotides in length and is not formally thought to generate subgenomic RNA molecules during replication. Previous studies in our lab have reported the abundant accumulation of a 3’-terminal 521- to 523-nucleotide genome fragment, representing the highly conserved region of the 3’-untranslated region, in JEV-infected cells (Journal of Virology 78:5133, 2004). To address a possible function of the small RNA during viral replication, several approaches were carried out. Systematic quantification of plus- and minus-stand viral RNA synthesis using Northern hybridization, RNase protection, and RT-Real-time PCR assays suggested that the presence of the small RNA may play a role in the limitation of minus-stand RNA synthesis. Results from Northern analysis reveals that a minus-strand complement of the small RNA is not found, but rather only a minus-strand RNA that is 2X genome size is found. To elucidate a possible function of the small RNA and its complementary sequence during viral replication, unit-length (i.e., 523-nt) plus- and minus-strand forms of the small RNA were separately transfected in virus-infected cells and the effects on plusand minus-strand accumulation were measured. By strand-specific Northern hybridization and RT-real-time PCR assays. Transfection of the plus-sense small RNA appeared not to affect plus-strand viral RNA accumulation. However, transfection of the minus-sense small RNA caused a change in the migration pattern of the normally observed 2X minus-strand RNA in that nearly equal amounts of 1X-sized minus-strand 3 RNA are now found. The effect of transfection of the small plus-strand RNA on minus-strand accumulation remains to be determined. These results suggest that features of the minus-strand RNA may play a regulatory role during RNA synthesis in vivo.
Books on the topic "Small Untranslated RNA"
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Rederstorff, Mathieu. Small non-coding RNAs: Methods and protocols. New York: Humana Press, 2015.
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Rederstorff, Mathieu. Small Non-Coding RNAs: Methods and Protocols. Springer New York, 2016.
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Rederstorff, Mathieu. Small Non-Coding RNAs: Methods and Protocols. Springer, 2022.
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Rederstorff, Mathieu. Small Non-Coding RNAs: Methods and Protocols. Springer, 2021.
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