Journal articles: 'RNA'

1

OHNO, Hirohisa, and Hirohide SAITO. "RNA/RNP Nanotechnology for Biological Applications." Seibutsu Butsuri 56, no. 1 (2016): 023–26. http://dx.doi.org/10.2142/biophys.56.023.

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2

SHIROGUCHI, Katsuyuki. "RNA Sequencing." Seibutsu Butsuri 53, no. 6 (2013): 290–94. http://dx.doi.org/10.2142/biophys.53.290.

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3

Shi, Rui-Zhu, Yuan-Qing Pan, and Li Xing. "RNA Helicase A Regulates the Replication of RNA Viruses." Viruses 13, no. 3 (February 25, 2021): 361. http://dx.doi.org/10.3390/v13030361.

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The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

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4

Afonin, Kirill A., Mathias Viard, Ioannis Kagiampakis, Christopher L. Case, Marina A. Dobrovolskaia, Jen Hofmann, Ashlee Vrzak, et al. "Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles." ACS Nano 9, no. 1 (December 18, 2014): 251–59. http://dx.doi.org/10.1021/nn504508s.

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5

Kim, Hyunjong, and Juhee Ryu. "Mechanism of Circular RNAs and Their Potential as Novel Therapeutic Agents in Retinal Vascular Diseases." Yakhak Hoeji 67, no. 6 (December 31, 2023): 325–34. http://dx.doi.org/10.17480/psk.2023.67.6.325.

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Maintaining and preserving visual function became critical in this aging society. The number of patients with retinal vascular disease such as retinopathy of prematurity, age-related macular degeneration, and diabetic retinopathy is gradually increasing due to increased life expectancy, advancements in the technology of delivering premature babies, and complications due to eating habits. To treat these retinal vascular diseases, surgical intervention such as laser photocoagulation and anti-vascular endothelial growth factor (VEGF) drugs can be considered. However, these treatment options are accompanied by various complications and adverse effects. Thus, new treatments focusing on the pathogenesis of retinal vascular disease need to be developed. Various evidences suggest that circular RNA is involved in the pathogenesis of retinal disease. In this article, we discuss about currently used treatments of retinal vascular diseases and the emerging role of circular RNAs in the pathogenesis of retinal vascular diseases. Therefore, understanding the mechanism of circular RNA regulating retinal disease and developing therapeutics using these circular RNAs may offer novel treatment options to cure retinal vascular disease.

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6

Rajkowitsch, Lukas, Doris Chen, Sabine Stampfl, Katharina Semrad, Christina Waldsich, Oliver Mayer, Michael F. Jantsch, Robert Konrat, Udo Bläsi, and Renée Schroeder. "RNA Chaperones, RNA Annealers and RNA Helicases." RNA Biology 4, no. 3 (July 2007): 118–30. http://dx.doi.org/10.4161/rna.4.3.5445.

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7

Sengoku, T., O. Nureki, and S. Yokoyama. "Structural basis for RNA translocation by RNA helicase." Seibutsu Butsuri 43, supplement (2003): S98. http://dx.doi.org/10.2142/biophys.43.s98_2.

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8

Tang, Lin. "Mapping RNA–RNA interactions." Nature Methods 17, no. 8 (July 31, 2020): 760. http://dx.doi.org/10.1038/s41592-020-0922-9.

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9

Ligoxygakis, P. "RNA that synthesizes RNA." Trends in Genetics 17, no. 7 (July 1, 2001): 380. http://dx.doi.org/10.1016/s0168-9525(01)02391-5.

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10

Ogasawara, Shinzi, and Ai Yamada. "RNA Editing with Viral RNA-Dependent RNA Polymerase." ACS Synthetic Biology 11, no. 1 (January 3, 2022): 46–52. http://dx.doi.org/10.1021/acssynbio.1c00332.

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11

Ahlquist, P. "RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing." Science 296, no. 5571 (May 17, 2002): 1270–73. http://dx.doi.org/10.1126/science.1069132.

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12

Arnott, Struther, R. Chandrasekaran, R. P. Millane, and H. S. Park. "RNA-RNA, DNA-DNA, and DNA-RNA Polymorphism." Biophysical Journal 49, no. 1 (January 1986): 3–5. http://dx.doi.org/10.1016/s0006-3495(86)83568-8.

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13

Yano, A., and K. Harada. "2P142 Inhibition of RNA-protein interaction by RNA-RNA interaction." Seibutsu Butsuri 45, supplement (2005): S155. http://dx.doi.org/10.2142/biophys.45.s155_2.

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14

Taylor, J. P. "RNA That Gets RAN in Neurodegeneration." Science 339, no. 6125 (March 14, 2013): 1282–83. http://dx.doi.org/10.1126/science.1236450.

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15

Stackebrandt, Erko, Werner Liesack, and Dagmar Witt. "Ribosomal RNA and rDNA sequence analyses." Gene 115, no. 1-2 (June 1992): 255–60. http://dx.doi.org/10.1016/0378-1119(92)90567-9.

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16

Zhang, X., D. Wu, L. Chen, X. Li, J. Yang, D. Fan, T. Dong, et al. "RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction." RNA 20, no. 7 (May 6, 2014): 989–93. http://dx.doi.org/10.1261/rna.044776.114.

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17

Alkan, Can, Emre Karakoç, Joseph H. Nadeau, S. Cenk Sahinalp, and Kaizhong Zhang. "RNA–RNA Interaction Prediction and Antisense RNA Target Search." Journal of Computational Biology 13, no. 2 (March 2006): 267–82. http://dx.doi.org/10.1089/cmb.2006.13.267.

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18

Newburn, Laura R., and K. Andrew White. "Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses." Viruses 11, no. 8 (August 14, 2019): 751. http://dx.doi.org/10.3390/v11080751.

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RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.

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19

Cazenave, C., and O. C. Uhlenbeck. "RNA template-directed RNA synthesis by T7 RNA polymerase." Proceedings of the National Academy of Sciences 91, no. 15 (July 19, 1994): 6972–76. http://dx.doi.org/10.1073/pnas.91.15.6972.

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20

McGinness, Kathleen E., and Gerald F. Joyce. "RNA-Catalyzed RNA Ligation on an External RNA Template." Chemistry & Biology 9, no. 3 (March 2002): 297–307. http://dx.doi.org/10.1016/s1074-5521(02)00110-2.

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21

Predki, Paul F., L. Mike Nayak, Morris B. C. Gottlieb, and Lynne Regan. "Dissecting RNA-protein interactions: RNA-RNA recognition by Rop." Cell 80, no. 1 (January 1995): 41–50. http://dx.doi.org/10.1016/0092-8674(95)90449-2.

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22

Günzl, Arthur, Thomas Bruderer, Gabriele Laufer, Bernd Schimanski, Lan-Chun Tu, Hui-Min Chung, Pei-Tseng Lee, and Mary Gwo-Shu Lee. "RNA Polymerase I Transcribes Procyclin Genes and Variant Surface Glycoprotein Gene Expression Sites in Trypanosoma brucei." Eukaryotic Cell 2, no. 3 (June 2003): 542–51. http://dx.doi.org/10.1128/ec.2.3.542-551.2003.

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ABSTRACT In eukaryotes, RNA polymerase (pol) I exclusively transcribes the large rRNA gene unit (rDNA) and mRNA is synthesized by RNA pol II. The African trypanosome, Trypanosoma brucei, represents an exception to this rule. In this organism, transcription of genes encoding the variant surface glycoprotein (VSG) and the procyclins is resistant to α-amanitin, indicating that it is mediated by RNA pol I, while other protein-coding genes are transcribed by RNA pol II. To obtain firm proof for this concept, we generated a T. brucei cell line which exclusively expresses protein C epitope-tagged RNA pol I. Using an anti-protein C immunoaffinity matrix, we specifically depleted RNA pol I from transcriptionally active cell extracts. The depletion of RNA pol I impaired in vitro transcription initiated at the rDNA promoter, the GPEET procyclin gene promoter, and a VSG gene expression site promoter but did not affect transcription from the spliced leader (SL) RNA gene promoter. Fittingly, induction of RNA interference against the RNA pol I largest subunit in insect-form trypanosomes significantly reduced the relative transcriptional efficiency of rDNA, procyclin genes, and VSG expression sites in vivo whereas that of SL RNA, αβ-tubulin, and heat shock protein 70 genes was not affected. Our studies unequivocally show that T. brucei harbors a multifunctional RNA pol I which, in addition to transcribing rDNA, transcribes procyclin genes and VSG gene expression sites.

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23

HONDA, Tomoyuki, and Keizo TOMONAGA. "Possible roles of endogenous RNA virus elements in RNA virus infection." Uirusu 66, no. 1 (2016): 39–46. http://dx.doi.org/10.2222/jsv.66.39.

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24

Xue, Yuanchao. "Architecture of RNA–RNA interactions." Current Opinion in Genetics & Development 72 (February 2022): 138–44. http://dx.doi.org/10.1016/j.gde.2021.11.007.

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25

Röthlisberger, Pascal, Christian Berk, and Jonathan Hall. "RNA Chemistry for RNA Biology." CHIMIA International Journal for Chemistry 73, no. 5 (May 29, 2019): 368–73. http://dx.doi.org/10.2533/chimia.2019.368.

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Advances in the chemical synthesis of RNA have opened new possibilities to address current questions in RNA biology. Access to site-specifically modified oligoribonucleotides is often a pre-requisite for RNA chemical-biology projects. Driven by the enormous research efforts for development of oligonucleotide therapeutics, a wide range of chemical modifications have been developed to modulate the intrinsic properties of nucleic acids in order to fit their use as therapeutics or research tools. The RNA synthesis platform, supported by the NCCR RNA & Disease, aims to provide access to a large variety of chemically modified nucleic acids. In this review, we describe some of the recent projects that involved work of the platform and highlight how RNA chemistry supports new discoveries in RNA biology.

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26

GUTHRIE, CHRISTINE. "Catalytic RNA and RNA Splicing." American Zoologist 29, no. 2 (May 1989): 557–67. http://dx.doi.org/10.1093/icb/29.2.557.

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27

Fu, Xiang-Dong. "RNA helicases regulate RNA condensates." Cell Research 30, no. 4 (March 9, 2020): 281–82. http://dx.doi.org/10.1038/s41422-020-0296-7.

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28

Newman, Andy. "RNA enzymes for RNA splicing." Nature 413, no. 6857 (October 2001): 695–96. http://dx.doi.org/10.1038/35099665.

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29

Abe, Hiroshi. "Nanostructured RNA for RNA Intereference." YAKUGAKU ZASSHI 133, no. 3 (March 1, 2013): 373–78. http://dx.doi.org/10.1248/yakushi.12-00239-4.

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30

Khemici, Vanessa, and Patrick Linder. "RNA helicases in RNA decay." Biochemical Society Transactions 46, no. 1 (January 19, 2018): 163–72. http://dx.doi.org/10.1042/bst20170052.

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RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.

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31

Meyer, Irmtraud M. "Predicting novel RNA–RNA interactions." Current Opinion in Structural Biology 18, no. 3 (June 2008): 387–93. http://dx.doi.org/10.1016/j.sbi.2008.03.006.

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32

Westhof, Eric, Benoît Masquida, and Luc Jaeger. "RNA tectonics: towards RNA design." Folding and Design 1, no. 4 (August 1996): R78—R88. http://dx.doi.org/10.1016/s1359-0278(96)00037-5.

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33

Peng, LiNa, YuJiao Li, Lan Zhang, and WenQiang Yu. "Moving RNA moves RNA forward." Science China Life Sciences 56, no. 10 (September 5, 2013): 914–20. http://dx.doi.org/10.1007/s11427-013-4545-6.

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34

Li, Thomas J. X., and Christian M. Reidys. "Combinatorics of RNA–RNA interaction." Journal of Mathematical Biology 64, no. 3 (May 4, 2011): 529–56. http://dx.doi.org/10.1007/s00285-011-0423-7.

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35

Muckstein, U., H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker. "Thermodynamics of RNA-RNA binding." Bioinformatics 22, no. 10 (January 29, 2006): 1177–82. http://dx.doi.org/10.1093/bioinformatics/btl024.

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36

SCHMIDT, FRANCIS J., BONGRAE CHO, and HUGH B. NICHOLAS. "RNA Libraries and RNA Recognitiona." Annals of the New York Academy of Sciences 782, no. 1 (May 1996): 526–33. http://dx.doi.org/10.1111/j.1749-6632.1996.tb40590.x.

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37

Menzel, Peter, Stefan E. Seemann, and Jan Gorodkin. "RILogo: visualizing RNA–RNA interactions." Bioinformatics 28, no. 19 (July 23, 2012): 2523–26. http://dx.doi.org/10.1093/bioinformatics/bts461.

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38

Kok, Chee Choy, and Peter C. McMinn. "Picornavirus RNA-dependent RNA polymerase." International Journal of Biochemistry & Cell Biology 41, no. 3 (March 2009): 498–502. http://dx.doi.org/10.1016/j.biocel.2008.03.019.

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39

Hammond, T. M., and N. P. Keller. "RNA Silencing inAspergillus nidulansIs Independent of RNA-Dependent RNA Polymerases." Genetics 169, no. 2 (November 15, 2004): 607–17. http://dx.doi.org/10.1534/genetics.104.035964.

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40

Skeparnias, Ilias, and Jinwei Zhang. "Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions." Non-Coding RNA 7, no. 4 (December 15, 2021): 81. http://dx.doi.org/10.3390/ncrna7040081.

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Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.

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41

Snider, Daltry L., and Stacy M. Horner. "RNA modification of an RNA modifier prevents self-RNA sensing." PLOS Biology 19, no. 7 (July 30, 2021): e3001342. http://dx.doi.org/10.1371/journal.pbio.3001342.

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42

Koh, Hye Ran, Li Xing, Lawrence Kleiman, and Sua Myong. "Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing." Nucleic Acids Research 42, no. 13 (June 9, 2014): 8556–64. http://dx.doi.org/10.1093/nar/gku523.

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43

Shioda, Norifumi. "RNA toxicity and RAN translation in repeat expansion disorders." Folia Pharmacologica Japonica 150, no. 3 (2017): 165. http://dx.doi.org/10.1254/fpj.150.165.

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44

KIKUCHI, Yo. "Current RNA World." Journal of the Japan Veterinary Medical Association 52, no. 1 (1999): 1–5. http://dx.doi.org/10.12935/jvma1951.52.1.

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45

付, 洪. "Multifunction of LncRNA RMRP RNA." Biophysics 08, no. 02 (2020): 19–27. http://dx.doi.org/10.12677/biphy.2020.82002.

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46

Turner, Richard. "RNA." Nature 418, no. 6894 (July 2002): 213. http://dx.doi.org/10.1038/418213a.

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47

Darnell, James E. "RNA." Scientific American 253, no. 4 (October 1985): 68–78. http://dx.doi.org/10.1038/scientificamerican1085-68.

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48

Karbstein, Katrin, and Jennifer A. Doudna. "RNA." Chemistry & Biology 11, no. 2 (February 2004): 149–51. http://dx.doi.org/10.1016/j.chembiol.2004.02.007.

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49

Nybo, Kristie. "RNA Methods: RNA Extraction from Plasma." BioTechniques 47, no. 4 (October 2009): 821–23. http://dx.doi.org/10.2144/000113235.

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50

Rabhi, Makhlouf, Roman Tuma, and Marc Boudvillain. "RNA remodeling by hexameric RNA helicases." RNA Biology 7, no. 6 (November 2010): 655–66. http://dx.doi.org/10.4161/rna.7.6.13570.

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Journal articles on the topic 'RNA'

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