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Journal articles on the topic 'Cellular RNA'

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Author: Grafiati
Published: 4 June 2021
Last updated: 20 February 2023

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1

Tanabe, Shihori. "Cellular Internalization And RNA Regulation Of RNA Virus." Advances In Clinical And Medical Research 1, no. 1 (May 11, 2020): 1. http://dx.doi.org/10.52793/acmr.2020.1(1)-02.

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2

Elfaituri, Safa, and Fatma Emaetig. "Cellular Internalization And RNA Regulation Of RNA Virus." Advances In Clinical And Medical Research 1, no. 1 (May 11, 2020): 1–11. http://dx.doi.org/10.52793/acmr.2022.3(2)-29.

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3

Wurtmann, Elisabeth J., and Sandra L. Wolin. "RNA under attack: Cellular handling of RNA damage." Critical Reviews in Biochemistry and Molecular Biology 44, no. 1 (February 2009): 34–49. http://dx.doi.org/10.1080/10409230802594043.

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4

Kretz, Markus. "TINCR, staufen1, and cellular differentiation." RNA Biology 10, no. 10 (October 2013): 1597–601. http://dx.doi.org/10.4161/rna.26249.

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5

Wang, Miao, Zeqian Gao, Li Pan, and Yongguang Zhang. "Cellular microRNAs and Picornaviral Infections." RNA Biology 11, no. 7 (June 12, 2014): 808–16. http://dx.doi.org/10.4161/rna.29357.

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6

DeRose, Victoria J. "Sensing cellular magnesium with RNA." Nature Chemical Biology 3, no. 11 (November 2007): 693–94. http://dx.doi.org/10.1038/nchembio1107-693.

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7

Casci, Tanita. "RNA device rewires cellular networks." Nature Reviews Molecular Cell Biology 12, no. 1 (December 8, 2010): 5. http://dx.doi.org/10.1038/nrm3034.

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8

Biamonti, Giuseppe, and Javier F. Caceres. "Cellular stress and RNA splicing." Trends in Biochemical Sciences 34, no. 3 (March 2009): 146–53. http://dx.doi.org/10.1016/j.tibs.2008.11.004.

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9

Yi, Chengqi, and Tao Pan. "Cellular Dynamics of RNA Modification." Accounts of Chemical Research 44, no. 12 (December 20, 2011): 1380–88. http://dx.doi.org/10.1021/ar200057m.

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10

Parlea, Lorena, Anu Puri, Wojciech Kasprzak, Eckart Bindewald, Paul Zakrevsky, Emily Satterwhite, Kenya Joseph, Kirill A. Afonin, and Bruce A. Shapiro. "Cellular Delivery of RNA Nanoparticles." ACS Combinatorial Science 18, no. 9 (August 26, 2016): 527–47. http://dx.doi.org/10.1021/acscombsci.6b00073.

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11

Casci, Tanita. "RNA device rewires cellular networks." Nature Reviews Cancer 11, no. 1 (December 9, 2010): 8. http://dx.doi.org/10.1038/nrc2988.

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12

Casci, Tanita. "RNA device rewires cellular networks." Nature Reviews Genetics 12, no. 1 (December 7, 2010): 4–5. http://dx.doi.org/10.1038/nrg2926.

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13

Faridani, O. R., G. M. McInerney, K. Gradin, and L. Good. "Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions." Nucleic Acids Research 36, no. 16 (August 1, 2008): e99-e99. http://dx.doi.org/10.1093/nar/gkn445.

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14

Chen, Y. Grace, Walter E. Kowtoniuk, Isha Agarwal, Yinghua Shen, and David R. Liu. "LC/MS analysis of cellular RNA reveals NAD-linked RNA." Nature Chemical Biology 5, no. 12 (October 11, 2009): 879–81. http://dx.doi.org/10.1038/nchembio.235.

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15

Wojciechowska, Marzena, and Wlodzimierz J. Krzyzosiak. "Cellular toxicity of expanded RNA repeats: focus on RNA foci." Human Molecular Genetics 20, no. 19 (July 4, 2011): 3811–21. http://dx.doi.org/10.1093/hmg/ddr299.

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16

Reniewicz, Patryk, Joanna Zyzak, and Jakub Siednienko. "The cellular receptors of exogenous RNA." Postępy Higieny i Medycyny Doświadczalnej 70 (April 21, 2016): 337–48. http://dx.doi.org/10.5604/17322693.1199987.

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17

Townshend, Brent, Andrew B. Kennedy, Joy S. Xiang, and Christina D. Smolke. "High-throughput cellular RNA device engineering." Nature Methods 12, no. 10 (August 10, 2015): 989–94. http://dx.doi.org/10.1038/nmeth.3486.

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18

Dowdy, Steven F. "Overcoming cellular barriers for RNA therapeutics." Nature Biotechnology 35, no. 3 (February 27, 2017): 222–29. http://dx.doi.org/10.1038/nbt.3802.

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19

Riddihough, Guy. "RNA editing helps identify cellular RNAs." Science Signaling 8, no. 393 (September 8, 2015): ec260-ec260. http://dx.doi.org/10.1126/scisignal.aad3741.

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20

Graveley, Brenton R. "RNA Matchmaking: Finding Cellular Pairing Partners." Molecular Cell 63, no. 2 (July 2016): 186–89. http://dx.doi.org/10.1016/j.molcel.2016.07.001.

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21

Majumder, Subhabrata, Christopher M. DeMott, Sergey Reverdatto, David S. Burz, and Alexander Shekhtman. "Total Cellular RNA Modulates Protein Activity." Biochemistry 55, no. 32 (August 3, 2016): 4568–73. http://dx.doi.org/10.1021/acs.biochem.6b00330.

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22

Riddihough, G. "RNA editing helps identify cellular RNAs." Science 349, no. 6252 (September 3, 2015): 1066–68. http://dx.doi.org/10.1126/science.349.6252.1066-q.

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23

Abdelmohsen, Kotb, and Myriam Gorospe. "Noncoding RNA control of cellular senescence." Wiley Interdisciplinary Reviews: RNA 6, no. 6 (September 1, 2015): 615–29. http://dx.doi.org/10.1002/wrna.1297.

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24

Haines, Dale S., Kenneth I. Strauss, and David H. Gillespie. "Cellular response to double-stranded RNA." Journal of Cellular Biochemistry 46, no. 1 (May 1991): 9–20. http://dx.doi.org/10.1002/jcb.240460104.

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25

Nielsen, Finn Cilius, Heidi Theil Hansen, and Jan Christiansen. "RNA assemblages orchestrate complex cellular processes." BioEssays 38, no. 7 (May 12, 2016): 674–81. http://dx.doi.org/10.1002/bies.201500175.

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26

Thoner, Timothy W., Xiang Ye, John Karijolich, and Kristen M. Ogden. "Reovirus Low-Density Particles Package Cellular RNA." Viruses 13, no. 6 (June 8, 2021): 1096. http://dx.doi.org/10.3390/v13061096.

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Packaging of segmented, double-stranded RNA viral genomes requires coordination of viral proteins and RNA segments. For mammalian orthoreovirus (reovirus), evidence suggests either all ten or zero viral RNA segments are simultaneously packaged in a highly coordinated process hypothesized to exclude host RNA. Accordingly, reovirus generates genome-containing virions and “genomeless” top component particles. Whether reovirus virions or top component particles package host RNA is unknown. To gain insight into reovirus packaging potential and mechanisms, we employed next-generation RNA-sequencing to define the RNA content of enriched reovirus particles. Reovirus virions exclusively packaged viral double-stranded RNA. In contrast, reovirus top component particles contained similar proportions but reduced amounts of viral double-stranded RNA and were selectively enriched for numerous host RNA species, especially short, non-polyadenylated transcripts. Host RNA selection was not dependent on RNA abundance in the cell, and specifically enriched host RNAs varied for two reovirus strains and were not selected solely by the viral RNA polymerase. Collectively, these findings indicate that genome packaging into reovirus virions is exquisitely selective, while incorporation of host RNAs into top component particles is differentially selective and may contribute to or result from inefficient viral RNA packaging.
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27

Nilsson, D., and P. Sunnerhagen. "Cellular stress induces cytoplasmic RNA granules in fission yeast." RNA 17, no. 1 (November 22, 2010): 120–33. http://dx.doi.org/10.1261/rna.2268111.

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28

Galicia-Vazquez, G., R. Cencic, F. Robert, A. Q. Agenor, and J. Pelletier. "A cellular response linking eIF4AI activity to eIF4AII transcription." RNA 18, no. 7 (May 15, 2012): 1373–84. http://dx.doi.org/10.1261/rna.033209.112.

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29

Modahl, Lucy E., Thomas B. Macnaughton, Nongliao Zhu, Deborah L. Johnson, and Michael M. C. Lai. "RNA-Dependent Replication and Transcription of Hepatitis Delta Virus RNA Involve Distinct Cellular RNA Polymerases." Molecular and Cellular Biology 20, no. 16 (August 15, 2000): 6030–39. http://dx.doi.org/10.1128/mcb.20.16.6030-6039.2000.

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ABSTRACT Cellular DNA-dependent RNA polymerase II (pol II) has been postulated to carry out RNA-dependent RNA replication and transcription of hepatitis delta virus (HDV) RNA, generating a full-length (1.7-kb) RNA genome and a subgenomic-length (0.8-kb) mRNA. However, the supporting evidence for this hypothesis was ambiguous because the previous experiments relied on DNA-templated transcription to initiate HDV RNA synthesis. Furthermore, there is no evidence that the same cellular enzyme is involved in the synthesis of both RNA species. In this study, we used a novel HDV RNA-based transfection approach, devoid of any artificial HDV cDNA intermediates, to determine the enzymatic and metabolic requirements for the synthesis of these two RNA species. We showed that HDV subgenomic mRNA transcription was inhibited by a low concentration of α-amanitin (<3 μg/ml) and could be partially restored by an α-amanitin-resistant mutant pol II; however, surprisingly, the synthesis of the full-length (1.7-kb) antigenomic RNA was not affected by α-amanitin to a concentration higher than 25 μg/ml. By several other criteria, such as the differing requirement for the de novo-synthesized hepatitis delta antigen and temperature dependence, we further showed that the metabolic requirements of subgenomic HDV mRNA synthesis are different from those for the synthesis of genomic-length HDV RNA and cellular pol II transcripts. The synthesis of the two HDV RNA species could also be uncoupled under several different conditions. These findings provide strong evidence that pol II, or proteins derived from pol II transcripts, is involved in mRNA transcription from the HDV RNA template. In contrast, the synthesis of the 1.7-kb HDV antigenomic RNA appears not to be dependent on pol II. These results reveal that there are distinct molecular mechanisms for the synthesis of these two RNA species.
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30

Michelini, Flavia, Ameya P. Jalihal, Sofia Francia, Chance Meers, Zachary T. Neeb, Francesca Rossiello, Ubaldo Gioia, et al. "From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond." Chemical Reviews 118, no. 8 (March 30, 2018): 4365–403. http://dx.doi.org/10.1021/acs.chemrev.7b00487.

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31

Engelhardt, Othmar G., Matt Smith, and Ervin Fodor. "Association of the Influenza A Virus RNA-Dependent RNA Polymerase with Cellular RNA Polymerase II." Journal of Virology 79, no. 9 (May 1, 2005): 5812–18. http://dx.doi.org/10.1128/jvi.79.9.5812-5818.2005.

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ABSTRACT Transcription by the influenza virus RNA-dependent RNA polymerase is dependent on cellular RNA processing activities that are known to be associated with cellular RNA polymerase II (Pol II) transcription, namely, capping and splicing. Therefore, it had been hypothesized that transcription by the viral RNA polymerase and Pol II might be functionally linked. Here, we demonstrate for the first time that the influenza virus RNA polymerase complex interacts with the large subunit of Pol II via its C-terminal domain. The viral polymerase binds hyperphosphorylated forms of Pol II, indicating that it targets actively transcribing Pol II. In addition, immunofluorescence analysis is consistent with a new model showing that influenza virus polymerase accumulates at Pol II transcription sites. The present findings provide a framework for further studies to elucidate the mechanistic principles of transcription by a viral RNA polymerase and have implications for the regulation of Pol II activities in infected cells.
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32

Wolin, Sandra L., and Lynne E. Maquat. "Cellular RNA surveillance in health and disease." Science 366, no. 6467 (November 14, 2019): 822–27. http://dx.doi.org/10.1126/science.aax2957.

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The numerous quality control pathways that target defective ribonucleic acids (RNAs) for degradation play key roles in shaping mammalian transcriptomes and preventing disease. These pathways monitor most steps in the biogenesis of both noncoding RNAs (ncRNAs) and protein-coding messenger RNAs (mRNAs), degrading ncRNAs that fail to form functional complexes with one or more proteins and eliminating mRNAs that encode abnormal, potentially toxic proteins. Mutations in components of diverse RNA surveillance pathways manifest as disease. Some mutations are characterized by increased interferon production, suggesting that a major role of these pathways is to prevent aberrant cellular RNAs from being recognized as “non-self.” Other mutations are common in cancer, or result in developmental defects, revealing the importance of RNA surveillance to cell and organismal function.
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33

Magalhães, Maria LB, Michelle Byrom, Amy Yan, Linsley Kelly, Na Li, Raquel Furtado, Deborah Palliser, Andrew D. Ellington, and Matthew Levy. "A General RNA Motif for Cellular Transfection." Molecular Therapy 20, no. 3 (March 2012): 616–24. http://dx.doi.org/10.1038/mt.2011.277.

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34

Sun, Lei, Furqan M. Fazal, Pan Li, James P. Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T. Kool, Howard Y. Chang, and Qiangfeng Cliff Zhang. "RNA structure maps across mammalian cellular compartments." Nature Structural & Molecular Biology 26, no. 4 (March 18, 2019): 322–30. http://dx.doi.org/10.1038/s41594-019-0200-7.

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35

Paige, Jeremy S., Thinh Nguyen-Duc, Wenjiao Song, and Samie R. Jaffrey. "Fluorescence Imaging of Cellular Metabolites with RNA." Science 335, no. 6073 (March 8, 2012): 1194. http://dx.doi.org/10.1126/science.1218298.

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36

Roche, B., B. Arcangioli, and R. A. Martienssen. "RNA interference is essential for cellular quiescence." Science 354, no. 6313 (October 13, 2016): aah5651. http://dx.doi.org/10.1126/science.aah5651.

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37

Kim, Jongmin, Peng Yin, and Alexander A. Green. "Ribocomputing: Cellular Logic Computation Using RNA Devices." Biochemistry 57, no. 6 (December 19, 2017): 883–85. http://dx.doi.org/10.1021/acs.biochem.7b01072.

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38

Belsham, Graham J., and Nahum Sonenberg. "Picornavirus RNA translation: roles for cellular proteins." Trends in Microbiology 8, no. 7 (July 2000): 330–35. http://dx.doi.org/10.1016/s0966-842x(00)01788-1.

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39

Na, Zhenkun, Yang Luo, Jeremy A. Schofield, Stephanie Smelyansky, Alexandra Khitun, Sowndarya Muthukumar, Eugene Valkov, Matthew D. Simon, and Sarah A. Slavoff. "The NBDY Microprotein Regulates Cellular RNA Decapping." Biochemistry 59, no. 42 (October 15, 2020): 4131–42. http://dx.doi.org/10.1021/acs.biochem.0c00672.

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40

Langdon, Erin, and Amy S. Gladfelter. "RNA-Based Control of Cellular Phase Transitions." Biophysical Journal 112, no. 3 (February 2017): 4a—5a. http://dx.doi.org/10.1016/j.bpj.2016.11.045.

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41

Wakarchuk, David A., and Richard I. Hamilton. "Cellular double-stranded RNA in Phaseolus vulgaris." Plant Molecular Biology 5, no. 1 (1985): 55–63. http://dx.doi.org/10.1007/bf00017873.

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42

Gaglia, Marta Maria, and Britt A. Glaunsinger. "Viruses and the cellular RNA decay machinery." Wiley Interdisciplinary Reviews: RNA 1, no. 1 (May 6, 2010): 47–59. http://dx.doi.org/10.1002/wrna.3.

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43

Zaher, Hani. "Cellular Consequences and Repair of Oxidised RNA." Free Radical Biology and Medicine 128 (November 2018): S12. http://dx.doi.org/10.1016/j.freeradbiomed.2018.10.388.

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44

Rhine, Kevin, Velinda Vidaurre, and Sua Myong. "RNA Droplets." Annual Review of Biophysics 49, no. 1 (May 6, 2020): 247–65. http://dx.doi.org/10.1146/annurev-biophys-052118-115508.

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Liquid–liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent platform for achieving multivalency and can accommodate many RNA binding proteins. Recent findings have highlighted the diverse function of RNA in tuning phase-separation propensity up or down, altering viscoelastic properties and thereby driving immiscibility between different condensates. In addition to contributing to the biophysical properties of droplets, RNA is a functionally critical constituent that defines the identity of cellular condensates and controls the temporal and spatial distribution of specific RNP granules. In this review, we summarize what we have learned so far about such roles of RNA in the context of in vitro and in vivo studies.
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45

Greijer, Astrid E., Chantal A. J. Dekkers, and Jaap M. Middeldorp. "Human Cytomegalovirus Virions Differentially Incorporate Viral and Host Cell RNA during the Assembly Process." Journal of Virology 74, no. 19 (October 1, 2000): 9078–82. http://dx.doi.org/10.1128/jvi.74.19.9078-9082.2000.

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ABSTRACT While analyzing human cytomegalovirus (HCMV) gene expression in infected cells by RNA-specific nucleic acid sequence-based amplification (NASBA), positive results were observed for HCMV RNA encoded by several viral genes immediately after the addition of the virus. UV-inactivated virus also gave a positive NASBA result without establishing active infection, suggesting that RNA was associated with the inoculum. Highly purified virions devoid of cellular contamination proved to be positive for viral RNA encoding both immediate-early (UL123) and late (UL65) gene products. Virion-associated RNA might be incorporated specifically or without selection during the virion assembly. In the latter case, cellular RNA would also be present in the virion. A high-abundant cellular RNA encoded by GAPDH and even U1A RNA, which is expressed at low levels, were detected in the virion fraction, whereas cellular DNA was absent. Virion fractionation revealed that cellular RNA was absent in purified de-enveloped capsids. In conclusion, cellular and viral RNA was present between the capsid and envelope of the virion, whereas in the capsid only viral RNA could be detected. The results suggest that virion-associated viral and cellular RNA is incorporated nonspecifically during virion assembly.
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46

Spellberg, Michael J., and Michael T. Marr. "FOXO regulates RNA interference in Drosophila and protects from RNA virus infection." Proceedings of the National Academy of Sciences 112, no. 47 (November 9, 2015): 14587–92. http://dx.doi.org/10.1073/pnas.1517124112.

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Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.
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47

Ernst, R. K., M. Bray, D. Rekosh, and M. L. Hammarskjöld. "A structured retroviral RNA element that mediates nucleocytoplasmic export of intron-containing RNA." Molecular and Cellular Biology 17, no. 1 (January 1997): 135–44. http://dx.doi.org/10.1128/mcb.17.1.135.

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A common feature of gene expression in all retroviruses is that unspliced, intron-containing RNA is exported to the cytoplasm despite the fact that cellular RNAs which contain introns are usually restricted to the nucleus. In complex retroviruses, the export of intron-containing RNA is mediated by specific viral regulatory proteins (e.g., human immunodeficiency virus type 1 [HIV-1] Rev) that bind to elements in the viral RNA. However, simpler retroviruses do not encode such regulatory proteins. Here we show that the genome of the simpler retrovirus Mason-Pfizer monkey virus (MPMV) contains an element that serves as an autonomous nuclear export signal for intron-containing RNA. This element is essential for MPMV replication; however, its function can be complemented by HIV-1 Rev and the Rev-responsive element. The element can also facilitate the export of cellular intron-containing RNA. These results suggest that the MPMV element mimics cellular RNA transport signals and mediates RNA export through interaction with endogenous cellular factors.
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48

Hannan, Katherine M., Lawrence I. Rothblum, and Leonard S. Jefferson. "Regulation of ribosomal DNA transcription by insulin." American Journal of Physiology-Cell Physiology 275, no. 1 (July 1, 1998): C130—C138. http://dx.doi.org/10.1152/ajpcell.1998.275.1.c130.

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The experiments reported here used 3T6-Swiss albino mouse fibroblasts and H4-II-E-C3 rat hepatoma cells as model systems to examine the mechanism(s) through which insulin regulates rDNA transcription. Serum starvation of 3T6 cells for 72 h resulted in a marked reduction in rDNA transcription. Treatment of serum-deprived cells with insulin was sufficient to restore rDNA transcription to control values. In addition, treatment of exponentially growing H4-II-E-C3 with insulin stimulated rDNA transcription. However, for both cell types, the stimulation of rDNA transcription in response to insulin was not associated with a change in the cellular content of RNA polymerase I. Thus we conclude that insulin must cause alterations in formation of the active RNA polymerase I initiation complex and/or the activities of auxiliary rDNA transcription factors. In support of this conclusion, insulin treatment of both cell types was found to increase the nuclear content of upstream binding factor (UBF) and RNA polymerase I-associated factor 53. Both of these factors are thought to be involved in recruitment of RNA polymerase I to the rDNA promoter. Nuclear run-on experiments demonstrated that the increase in cellular content of UBF was due to elevated transcription of the UBF gene. In addition, overexpression of UBF was sufficient to directly stimulate rDNA transcription from a reporter construct. The results demonstrate that insulin is capable of stimulating rDNA transcription in both 3T6 and H4-II-E-C3 cells, at least in part by increasing the cellular content of components required for assembly of RNA polymerase I into an active complex.
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49

Choi, Seungdo, Geonhu Lee, and Jongmin Kim. "Cellular Computational Logic Using Toehold Switches." International Journal of Molecular Sciences 23, no. 8 (April 12, 2022): 4265. http://dx.doi.org/10.3390/ijms23084265.

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The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in Escherichia coli. Specifically, de-novo-designed riboregulators, known as toehold switches, were concatenated to enhance the functionality of an OR gate, and a previously utilized antisense RNA strategy was further optimized to construct orthogonal NIMPLY gates. These optimized synthetic logic gates were able to be seamlessly integrated to achieve final arithmetic operations on small molecule inputs in cells. Toehold-switch-based ribocomputing devices may provide a fundamental basis for synthetic RNA-based arithmetic logic units or higher-order systems in cells.
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50

Koonin, Eugene V. "Carl Woese's vision of cellular evolution and the domains of life." RNA Biology 11, no. 3 (January 16, 2014): 197–204. http://dx.doi.org/10.4161/rna.27673.

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