Journal articles: 'Antisense RNA'

1

Eguchi, Yutaka, Tateo Itoh, and Jun-ichi Tomizawa. "Antisense RNA." Annual Review of Biochemistry 60, no. 1 (June 1991): 631–52. http://dx.doi.org/10.1146/annurev.bi.60.070191.003215.

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Weitzman, Jonathan B. "Antisense RNA." Genome Biology 3 (2002): spotlight—20020125–01. http://dx.doi.org/10.1186/gb-spotlight-20020125-01.

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3

PESTKA, SIDNEY. "Antisense RNA." Annals of the New York Academy of Sciences 660, no. 1 (October 1992): 251–62. http://dx.doi.org/10.1111/j.1749-6632.1992.tb21077.x.

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4

Nordström, Kurt. "Antisense RNA." Trends in Biochemical Sciences 10, no. 6 (June 1985): 232. http://dx.doi.org/10.1016/0968-0004(85)90138-0.

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Lacombe, Julie, Ekaterina Viazovkina, Pascal N. Bernatchez, Annie Galarneau, Masad J. Damha, and Martin G. Sirois. "Antisense inhibition of Flk-1 by oligonucleotides composed of 2'-deoxy-2'-fluoro-β-D-arabino- and 2'-deoxy-nucleosides." Canadian Journal of Physiology and Pharmacology 80, no. 10 (October 1, 2002): 951–61. http://dx.doi.org/10.1139/y02-123.

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The design of new antisense oligomers with improved binding affinity for targeted RNA, while still activating RNase H, is a major research area in medicinal chemistry. RNase H recognizes the RNADNA duplex and cleaves the complementary mRNA strand, providing the main mechanism by which antisense oligomers elicit their activities. It has been shown that configuration inversion at the C2' position of the DNA sugar moiety (arabinonucleic acid, ANA), combined with the substitution of the 2'OH group by a fluorine atom (2' F-ANA) increases the oligomer's binding affinity for targeted RNA. In the present study, we evaluated the antisense activity of mixed-backbone phosphorothioate oligomers composed of 2'-deoxy-2'-fluoro-β-D-arabinose and 2'-deoxyribose sugars (S-2' F-ANADNA chimeras). We determined their abilities to inhibit the protein expression and phosphorylation of Flk-1, a vascular endothelial growth factor receptor (VEGF), and VEGF biological effects on endothelial cell proliferation, migration, and platelet-activating factor synthesis. Treatment of endothelial cells with chimeric oligonucleotides reduced Flk-1 protein expression and phosphorylation more efficiently than with phosphorothioate antisenses (S-DNA). Nonetheless, these two classes of antisenses inhibited VEGF activities equally. Herein, we also demonstrated the capacity of the chimeric oligomers to elicit RNase H activity and their improved binding affinity for complementary RNA as compared with S-DNA.Key words: antisense DNA, 2' F-ANA nucleosides, mixed-backbone antisense, Flk-1, VEGF.

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6

TURGUT, Kenan. "Antisense RNA Technology." Turkish Journal of Agriculture and Forestry 20, no. 5 (January 1, 1996): 455–58. http://dx.doi.org/10.55730/1300-011x.2897.

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7

Liu, Zhong, and Gordon G. Carmichael. "Nuclear antisense RNA." Molecular Biotechnology 2, no. 2 (October 1994): 107–18. http://dx.doi.org/10.1007/bf02824803.

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8

Brantl, Sabine. "Antisense-RNA regulation and RNA interference." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1575, no. 1-3 (May 2002): 15–25. http://dx.doi.org/10.1016/s0167-4781(02)00280-4.

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9

Werner, Andreas. "Natural Antisense Transcripts." RNA Biology 2, no. 2 (April 2005): 53–62. http://dx.doi.org/10.4161/rna.2.2.1852.

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Funato, Tadao, Mayu Takeda, and Mami Yoshida. "World of antisense RNA." SEIBUTSU BUTSURI KAGAKU 51, no. 3 (2007): 207–9. http://dx.doi.org/10.2198/sbk.51.207.

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11

Corey, David R. "RNA learns from antisense." Nature Chemical Biology 3, no. 1 (January 2007): 8–11. http://dx.doi.org/10.1038/nchembio0107-8.

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12

Skeiky, Yasir A. W., and Kostas Iatrou. "Silkmoth chorion antisense RNA." Journal of Molecular Biology 213, no. 1 (May 1990): 53–66. http://dx.doi.org/10.1016/s0022-2836(05)80121-4.

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13

Dolnick, Bruce J. "Naturally occurring antisense RNA." Pharmacology & Therapeutics 75, no. 3 (September 1997): 179–84. http://dx.doi.org/10.1016/s0163-7258(97)00050-8.

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14

Weintraub, Harold M. "Antisense RNA and DNA." Scientific American 262, no. 1 (January 1990): 40–46. http://dx.doi.org/10.1038/scientificamerican0190-40.

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15

Chai, Haina, Chao Sun, Jun Liu, Haihui Sheng, Renyan Zhao, and Zhiqiang Feng. "The Relationship Between ZEB1-AS1 Expression and the Prognosis of Patients With Advanced Gastric Cancer Receiving Chemotherapy." Technology in Cancer Research & Treatment 18 (January 1, 2019): 153303381984906. http://dx.doi.org/10.1177/1533033819849069.

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Long noncoding RNA ZEB1 antisense RNA 1 plays a vital role in tumorigenesis and metastasis. However, the role of ZEB1 antisense RNA 1 in gastric cancer remains unclear. This study aimed to investigate the expression level of ZEB1 antisense RNA 1 in gastric cancer tissues and evaluate its association with clinicopathological features and prognosis of patients with advanced gastric cancer receiving chemotherapy. The expression levels of ZEB1 antisense RNA 1 were examined in 224 pairs of gastric cancer and adjacent noncancerous tissues by quantitative real-time polymerase chain reaction. The associations between ZEB1 antisense RNA 1 expression and clinicopathological features or survival of patients with advanced gastric cancer were assessed. The results showed that the expression levels of ZEB1 antisense RNA 1 in gastric cancer tissues were significantly higher than those in the paracancerous tissues ( P < .001). Moreover, the high ZEB1 antisense RNA 1 expression was associated with tumor, nodes, and metastases stage IV ( P = .018) and loss of E-cadherin expression ( P = .033). Multivariate Cox hazards regression analysis revealed that high ZEB1 antisense RNA 1 expression was an independent risk factor for predicting poor prognosis in patients with advanced gastric cancer (hazard ratio = 1.530, 95% confidence interval, 1.052-2.224, P = .026). In conclusion, the present findings suggest that ZEB1 antisense RNA 1 is an independent prognostic factor for patients with advanced gastric cancer receiving chemotherapy.

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16

Si, Huaijun, Jun Liu, Jian Huang, and Conghua Xie. "Functional analysis of a class I patatin gene SK24-1 in microtuber formation of transgenic potatoes." Canadian Journal of Plant Science 88, no. 4 (July 1, 2008): 593–98. http://dx.doi.org/10.4141/cjps07031.

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Expression of a class I patatin cDNA clone, SK24-1, in Escherichia coli revealed that the cDNA clone possessed lipid acyl hydrolase (LAH) activity. Transformed potato plants were obtained via Agrobacterium-mediated transformation using the chimeric constructs containing the sense and antisense cDNA under the control cauliflower mosaic virus 35S (CaMV 35S) promoter. In some sense transformed plants, both sense patatin RNA and LAH activity were increased and further resulted in a significant increase of percentage of plantlets that formed microtubers and numbers of microtubers per plantlet in vitro. All antisense plants displayed a reduction in LAH activity. Both sense and antisense RNA could be detected in antisense plants, but transcripts of antisense RNA resulted in a reduction of endogenous sense RNA. Moreover, expression of antisense cDNA in some antisense transformed plants led to a significant decrease in the number of microtubers formed. These results suggest that SK24-1 was involved in regulating microtuber formation. Key words: Patatin, potato, Escherichia coli, sense RNA, antisense RNA

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17

Harland, R., and H. Weintraub. "Translation of mRNA injected into Xenopus oocytes is specifically inhibited by antisense RNA." Journal of Cell Biology 101, no. 3 (September 1, 1985): 1094–99. http://dx.doi.org/10.1083/jcb.101.3.1094.

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The bacteriophage SP6 promoter and RNA polymerase were used to synthesize sense and antisense RNAs coding for the enzymes thymidine kinase (TK) and chloramphenicol acetyl transferase (CAT). Injection of antisense CAT RNA into frog oocytes inhibited expression of sense CAT mRNA. Similarly, antisense TK RNA inhibited expression of sense TK mRNA. Antisense RNAs were stable in oocytes and had no detectable effect on either the expression of endogenous proteins or on the expression of nonhomologous RNA transcripts. CAT activity expressed from a plasmid transcribed in the oocyte nucleus was also inhibited by antisense RNA injected into the oocyte cytoplasm. The data suggest that antisense RNA will be useful in identifying the function of specific mRNA sequences during early development of the frog.

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18

Krystal, G. W., B. C. Armstrong, and J. F. Battey. "N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts." Molecular and Cellular Biology 10, no. 8 (August 1990): 4180–91. http://dx.doi.org/10.1128/mcb.10.8.4180-4191.1990.

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Nuclear runoff transcription studies revealed nearly equivalent sense and antisense transcription across exon 1 of the N-myc locus. Antisense primary transcription initiates at multiple sites in intron 1 and gives rise to stable polyadenylated and nonpolyadenylated transcripts. This pattern of antisense transcription, which is directed by RNA polymerase II, is independent of gene amplification and cell type. The nonpolyadenylated antisense transcripts have 5' ends which are complementary to the 5' ends of the N-myc sense mRNA. We determined, by using an RNase protection technique designed to detect in vivo duplexes, that most of the cytoplasmic nonpolyadenylated antisense RNA exists in an RNA-RNA duplex with approximately 5% of the sense N-myc mRNA. Duplex formation appeared to occur with only a subset of the multiple forms of the N-myc mRNA, with the precise transcriptional initiation site of the RNA playing a role in determining this selectivity. Cloning of each strand of the RNA-RNA duplex revealed that most duplexes included both exon 1 and intron 1 sequences, suggesting that duplex formation could modulate RNA processing by preserving a population of N-myc mRNA which retains intron 1.

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Krystal, G. W., B. C. Armstrong, and J. F. Battey. "N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts." Molecular and Cellular Biology 10, no. 8 (August 1990): 4180–91. http://dx.doi.org/10.1128/mcb.10.8.4180.

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Nuclear runoff transcription studies revealed nearly equivalent sense and antisense transcription across exon 1 of the N-myc locus. Antisense primary transcription initiates at multiple sites in intron 1 and gives rise to stable polyadenylated and nonpolyadenylated transcripts. This pattern of antisense transcription, which is directed by RNA polymerase II, is independent of gene amplification and cell type. The nonpolyadenylated antisense transcripts have 5' ends which are complementary to the 5' ends of the N-myc sense mRNA. We determined, by using an RNase protection technique designed to detect in vivo duplexes, that most of the cytoplasmic nonpolyadenylated antisense RNA exists in an RNA-RNA duplex with approximately 5% of the sense N-myc mRNA. Duplex formation appeared to occur with only a subset of the multiple forms of the N-myc mRNA, with the precise transcriptional initiation site of the RNA playing a role in determining this selectivity. Cloning of each strand of the RNA-RNA duplex revealed that most duplexes included both exon 1 and intron 1 sequences, suggesting that duplex formation could modulate RNA processing by preserving a population of N-myc mRNA which retains intron 1.

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20

Ma, Qiang, Rungui Niu, Wei Huang, Liangshan Da, Yanlei Tang, Daowen Jiang, Yanfeng Xi, and Congjun Zhang. "Long Noncoding RNA PTPRG Antisense RNA 1 Reduces Radiosensitivity of Nonsmall Cell Lung Cancer Cells Via Regulating MiR-200c-3p/TCF4." Technology in Cancer Research & Treatment 19 (January 1, 2020): 153303382094261. http://dx.doi.org/10.1177/1533033820942615.

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Background: PTPRG antisense RNA 1 has been well-documented to exert an oncogenic role in diverse neoplasms. However, the precise role of PTPRG antisense RNA 1 in regulating radiosensitivity of nonsmall cell lung cancer cells remains largely elusive. Methods: Expression levels of PTPRG antisense RNA 1 and miR-200c-3p in nonsmall cell lung cancer tissues and cells were detected by quantitative real-time polymerase chain reaction, while transcription factor 4 expression was examined by immunohistochemistry and Western blot. After nonsmall cell lung cancer cells were exposed to X-ray with different doses in vitro, Cell Counting Kit -8 assay and colony formation assay were conducted to determine the influence of PTPRG antisense RNA 1 on cell viability. Interaction between miR-200c-3p and PTPRG antisense RNA 1 as well as transcription factor 4 was investigated by dual luciferase reporter assay. Result: In nonsmall cell lung cancer tissues, the expressions of PTPRG antisense RNA 1 and transcription factor 4 were significantly upregulated, whereas the expression of miR-200c-3p was downregulated. It was also proved that PTPRG antisense RNA 1 and 3′-untranslated region of transcription factor 4 can bind to miR-200c-3p. Under X-ray irradiation, overexpressed PTPRG antisense RNA 1 could promote the viability and enhance the radioresistance of nonsmall cell lung cancer cells, and this effect was partially weakened by miR-200c-3p mimics. Transcription factor 4 was identified as a target gene of miR-200c-3p, which could be positively regulated by PTPRG antisense RNA 1. Conclusion: PTPRG antisense RNA 1 reduces the radiosensitivity of nonsmall cell lung cancer cells via modulating miR-200c-3p/TCF4 axis.

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21

Delihas, Nicholas, Steven E. Rokita, and Ping Zheng. "Natural antisense RNA/target RNA interactions: Possible models for antisense oligonucleotide drug design." Nature Biotechnology 15, no. 8 (August 1997): 751–53. http://dx.doi.org/10.1038/nbt0897-751.

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22

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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23

Chen, Guozhu, Cheryl L. Patten, and Herb E. Schellhorn. "Controlled Expression of an rpoS Antisense RNA Can Inhibit RpoS Function in Escherichia coli." Antimicrobial Agents and Chemotherapy 47, no. 11 (November 2003): 3485–93. http://dx.doi.org/10.1128/aac.47.11.3485-3493.2003.

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ABSTRACT We show that an inducible rpoS antisense RNA complementary to the rpoS message can inhibit expression of RpoS in both exponential and stationary phases and can attenuate expression of the rpoS regulon in Escherichia coli. Plasmids containing rpoS antisense DNA expressed under the control of the T7lac promoter and T7 RNA polymerase were constructed, and expression of the rpoS antisense RNA was optimized in the pET expression system. rpoS antisense RNA levels could be manipulated to effectively control the expression of RpoS and RpoS-dependent genes. RpoS expression was inhibited by the expression of rpoS antisense RNA in both exponential and stationary phases in E. coli. RpoS-dependent catalase HPII was also downregulated, as determined by catalase activity assays and with native polyacrylamide gels stained for catalase. Induced RpoS antisense expression also reduced the level of RpoS-dependent glycogen synthesis. These results demonstrate that controlled expression of antisense RNA can be used to attenuate expression of a regulator required for the expression of host adaptation functions and may offer a basis for designing effective antimicrobial agents.

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Mourão, Kira, Nicholas J. Schurch, Radek Lucoszek, Kimon Froussios, Katarzyna MacKinnon, Céline Duc, Gordon Simpson, and Geoffrey J. Barton. "Detection and mitigation of spurious antisense expression with RoSA." F1000Research 8 (June 7, 2019): 819. http://dx.doi.org/10.12688/f1000research.18952.1.

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Antisense transcription is known to have a range of impacts on sense gene expression, including (but not limited to) impeding transcription initiation, disrupting post-transcriptional processes, and enhancing, slowing, or even preventing transcription of the sense gene. Strand-specific RNA-Seq protocols preserve the strand information of the original RNA in the data, and so can be used to identify where antisense transcription may be implicated in regulating gene expression. However, our analysis of 199 strand-specific RNA-Seq experiments reveals that spurious antisense reads are often present in these datasets at levels greater than 1% of sense gene expression levels. Furthermore, these levels can vary substantially even between replicates in the same experiment, potentially disrupting any downstream analysis, if the incorrectly assigned antisense counts dominate the set of genes with high antisense transcription levels. Currently, no tools exist to detect or correct for this spurious antisense signal. Our tool, RoSA (Removal of Spurious Antisense), detects the presence of high levels of spurious antisense read alignments in strand-specific RNA-Seq datasets. It uses incorrectly spliced reads on the antisense strand and/or ERCC spikeins (if present in the data) to calculate both global and gene-specific antisense correction factors. We demonstrate the utility of our tool to filter out spurious antisense transcript counts in an Arabidopsis thaliana RNA-Seq experiment. Availability: RoSA is open source software available under the GPL licence via the Barton Group GitHub page https://github.com/bartongroup.

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Božič, Tim, Matja Zalar, Boris Rogelj, Janez Plavec, and Primož Šket. "Structural Diversity of Sense and Antisense RNA Hexanucleotide Repeats Associated with ALS and FTLD." Molecules 25, no. 3 (January 25, 2020): 525. http://dx.doi.org/10.3390/molecules25030525.

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The hexanucleotide expansion GGGGCC located in C9orf72 gene represents the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). Since the discovery one of the non-exclusive mechanisms of expanded hexanucleotide G4C2 repeats involved in ALS and FTLD is RNA toxicity, which involves accumulation of pathological sense and antisense RNA transcripts. Formed RNA foci sequester RNA-binding proteins, causing their mislocalization and, thus, diminishing their biological function. Therefore, structures adopted by pathological RNA transcripts could have a key role in pathogenesis of ALS and FTLD. Utilizing NMR spectroscopy and complementary methods, we examined structures adopted by both guanine-rich sense and cytosine-rich antisense RNA oligonucleotides with four hexanucleotide repeats. While both oligonucleotides tend to form dimers and hairpins, the equilibrium of these structures differs with antisense oligonucleotide being more sensitive to changes in pH and sense oligonucleotide to temperature. In the presence of K+ ions, guanine-rich sense RNA oligonucleotide also adopts secondary structures called G-quadruplexes. Here, we also observed, for the first time, that antisense RNA oligonucleotide forms i-motifs under specific conditions. Moreover, simultaneous presence of sense and antisense RNA oligonucleotides promotes formation of heterodimer. Studied structural diversity of sense and antisense RNA transcripts not only further depicts the complex nature of neurodegenerative diseases but also reveals potential targets for drug design in treatment of ALS and FTLD.

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Ward, Alex M., David Rekosh, and Marie-Louise Hammarskjold. "Trafficking through the Rev/RRE Pathway Is Essential for Efficient Inhibition of Human Immunodeficiency Virus Type 1 by an Antisense RNA Derived from the Envelope Gene." Journal of Virology 83, no. 2 (October 29, 2008): 940–52. http://dx.doi.org/10.1128/jvi.01520-08.

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ABSTRACT A human immunodeficiency virus type 1 (HIV-1)-based vector expressing an antisense RNA directed against HIV-1 is currently in clinical trials. This vector has shown a remarkable ability to inhibit HIV-1 replication, in spite of the fact that therapeutic use of unmodified antisense RNAs has generally been disappointing. To further analyze the basis for this, we examined the effects of different plasmid-based HIV-1 long-terminal-repeat-driven constructs expressing antisense RNA to the same target region in HIV-1 but containing different export elements. Two of these vectors were designed to express antisense RNA containing either a Rev response element (RRE) or a Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE). In the third vector, no specific transport element was provided. Efficient inhibition of HIV-1 virus production was obtained with the RRE-driven antisense RNA. This construct also efficiently inhibited p24 production from a pNL4-3 provirus that used the MPMV CTE for RNA export. In contrast, little inhibition was observed with the constructs lacking an RRE. Furthermore, when the RRE-driven antisense RNA was redirected to the Tap/Nxf1 pathway, utilized by the MPMV CTE, through the expression of a RevM10-Tap fusion protein, the efficiency of antisense inhibition was greatly reduced. These results indicate that efficient inhibition requires trafficking of the antisense RNA through the Rev/RRE pathway. Mechanistic studies indicated that the Rev/RRE-mediated inhibition did not involve either nuclear retention or degradation of target mRNA, since target RNA was found to export and associate normally with polyribosomes. However, protein levels were significantly reduced. Taken together, our results suggest a new mechanism for antisense inhibition of HIV mediated by Rev/RRE.

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Adachi, Hironori, Martin Hengesbach, Yi-Tao Yu, and Pedro Morais. "From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies." Biomedicines 9, no. 5 (May 14, 2021): 550. http://dx.doi.org/10.3390/biomedicines9050550.

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Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.

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Hofhaus, Götz, Norbert Gattermann, and José Antonio Enrı́quez. "Antisense RNA Crossing Mitochondrial Membrane?" Blood 92, no. 8 (October 15, 1998): 2994–95. http://dx.doi.org/10.1182/blood.v92.8.2994.

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SCZAKIEL, GEORG. "The Design of Antisense RNA." Antisense and Nucleic Acid Drug Development 7, no. 4 (August 1997): 439–44. http://dx.doi.org/10.1089/oli.1.1997.7.439.

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Reis, Eduardo M., Rodrigo Louro, Helder I. Nakaya, and Sergio Verjovski-Almeida. "As Antisense RNA Gets Intronic." OMICS: A Journal of Integrative Biology 9, no. 1 (March 2005): 2–12. http://dx.doi.org/10.1089/omi.2005.9.2.

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Pines, Ophry, and Masayori Inouye. "Antisense RNA regulation in prokaryotes." Trends in Genetics 2 (January 1986): 284–87. http://dx.doi.org/10.1016/0168-9525(86)90270-2.

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Bryant, John A. "Antisense RNA makes good sense." Trends in Biotechnology 7, no. 2 (February 1989): 20–21. http://dx.doi.org/10.1016/0167-7799(89)90052-8.

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Bull, J. J., A. Jacobson, M. R. Badgett, and I. J. Molineux. "Viral escape from antisense RNA." Molecular Microbiology 28, no. 4 (March 1, 2002): 835–46. http://dx.doi.org/10.1046/j.1365-2958.1998.00847.x.

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Liu, Z., D. B. Batt, and G. G. Carmichael. "Targeted nuclear antisense RNA mimics natural antisense-induced degradation of polyoma virus early RNA." Proceedings of the National Academy of Sciences 91, no. 10 (May 10, 1994): 4258–62. http://dx.doi.org/10.1073/pnas.91.10.4258.

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Weaver, Keith E., Erik A. Ehli, Jessica S. Nelson, and Smita Patel. "Antisense RNA Regulation by Stable Complex Formation in the Enterococcus faecalis Plasmid pAD1 par Addiction System." Journal of Bacteriology 186, no. 19 (October 1, 2004): 6400–6408. http://dx.doi.org/10.1128/jb.186.19.6400-6408.2004.

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ABSTRACT The par stability determinant, encoded by the Enterococcus faecalis plasmid pAD1, is the only antisense RNA regulated postsegregational killing system identified in gram-positive bacteria. Because of the unique organization of the par locus, the par antisense RNA, RNA II, binds to its target, RNA I, at relatively small, interspersed regions of complementarity. The results of this study suggest that, rather than targeting the antisense bound message for rapid degradation, as occurs in most other antisense RNA regulated systems, RNA I and RNA II form a relatively stable, presumably translationally inactive complex. The stability of the RNA I-RNA II complex would allow RNA I to persist in an untranslated state unless or until the encoding plasmid was lost. After plasmid loss, RNA II would be removed from the complex, allowing translational activation of RNA I. The mechanism of RNA I activation in vivo is unknown, but in vitro dissociation experiments suggest that active removal of RNA II, for example by a cellular RNase, may be required.

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Player, RK Maitra, RH Silverman, and PF Torrence. "Targeting RNase L to Human Immunodeficiency Virus RNA with 2-5A-Antisense." Antiviral Chemistry and Chemotherapy 9, no. 3 (June 1998): 225–31. http://dx.doi.org/10.1177/095632029800900303.

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In an attempt to develop a lead for the application of 2–5A-antisense to the targeted destruction of human immunodeficiency virus (HIV) RNA, specific target sequences within the HIV mRNAs were identified by analysis of the theoretical secondary structure. 2-5A-antisense chimeras were chosen against a total of 11 different sequences: three in the gag mRNA, three in the rev mRNA and five in the tat mRNA. 2-5A-antisense chimera synthesis was accomplished using solid-phase phosphoramidite chemistry. These chimeras were evaluated for their activity in a cell-free assay system using purified recombinant human RNase L to effect cleavage of 32P-labelled RNA transcripts of plasmids derived from HIV NL4-3. This screening revealed that of the three 2-5A-antisense chimeras targeted against gag mRNA, only one had significant HIV RNA cleavage activity, approximately10-fold-reduced compared to the parent 2-5A tetramer and comparable to that reported for the prototypical 2-5A-anti-PKR chimera, targeted against PKR mRNA. The cleavage activity of this chimera was specific, since a scrambled antisense domain chimera and a chimera without the key 5′-monophosphate moiety were both inactive. The 10 other 2-5A-antisense chimeras against tat and rev had significantly less activity. These results imply that HIV gag RNA, like PKR RNA and a model HIV tat-oligoA- vif RNA, can be cleaved using the 2-5A-antisense approach. The results further imply that not all regions of a potential RNA target are accessible to the 2-5A-antisense approach.

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Kole, Ryszard, Adrian R. Krainer, and Sidney Altman. "RNA therapeutics: beyond RNA interference and antisense oligonucleotides." Nature Reviews Drug Discovery 11, no. 2 (January 20, 2012): 125–40. http://dx.doi.org/10.1038/nrd3625.

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Veres, Gabor, Uwe Junker, Jenny Baker, Carmen Barske, Creton Kalfoglou, Heini Ilves, Sonia Escaich, Hideto Kaneshima, and Ernst Böhnlein. "Comparative Analyses of Intracellularly Expressed Antisense RNAs as Inhibitors of Human Immunodeficiency Virus Type 1 Replication." Journal of Virology 72, no. 3 (March 1, 1998): 1894–901. http://dx.doi.org/10.1128/jvi.72.3.1894-1901.1998.

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ABSTRACT The antiviral activities of intracellularly expressed antisense RNAs complementary to the human immunodeficiency virus type 1 (HIV-1) pol, vif, and env genes and the 3′ long terminal repeat (LTR) sequence were evaluated in this comparative study. Retroviral vectors expressing the antisense RNAs as part of the Moloney murine leukemia virus LTR promoter-directed retroviral transcript were constructed. The CD4+ T-cell line CEM-SS was transduced with retroviral constructs, and Northern blot analyses showed high steady-state antisense RNA expression levels. The most efficient inhibition of HIV-1 replication was observed with theenv antisense RNA, followed by the polcomplementary sequence, leading to 2- to 3-log10 reductions in p24 antigen production even at high inoculation doses (4 × 104 50% tissue culture infective doses) of the HIV-1 strain HXB3. The strong antiviral effect correlated with a reduction of HIV-1 steady-state RNA levels, and with intracellular Tat protein production, suggesting that antisense transcripts act at an early step of HIV-1 replication. A lower steady-state antisense RNA level was detected in transduced primary CD4+ lymphocytes than in CEM-SS cells. Nevertheless, replication of the HIV-1 JR-CSF isolate was reduced with both the pol and envantisense RNA. Intracellularly expressed antisense sequences demonstrated more pronounced antiviral efficacy than thetrans-dominant RevM10 protein, making these antisense RNAs a promising gene therapy strategy for HIV-1.

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Sullenger, B. A., T. C. Lee, C. A. Smith, G. E. Ungers, and E. Gilboa. "Expression of chimeric tRNA-driven antisense transcripts renders NIH 3T3 cells highly resistant to Moloney murine leukemia virus replication." Molecular and Cellular Biology 10, no. 12 (December 1990): 6512–23. http://dx.doi.org/10.1128/mcb.10.12.6512-6523.1990.

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NIH 3T3 cells infected with Moloney murine leukemia virus (MoMLV) express high levels of virus-specific RNA. To inhibit replication of the virus, we stably introduced chimeric tRNA genes encoding antisense templates into NIH 3T3 cells via a retroviral vector. Efficient expression of hybrid tRNA-MoMLV antisense transcripts and inhibition of MoMLV replication were dependent on the use of a particular type of retroviral vector, the double-copy vector, in which the chimeric tRNA gene was inserted in the 3' long terminal repeat. MoMLV replication was inhibited up to 97% in cells expressing antisense RNA corresponding to the gag gene and less than twofold in cells expressing antisense RNA corresponding to the pol gene. RNA and protein analyses suggest that inhibition was exerted at the level of translation. These results suggest that RNA polymerase III-based antisense inhibition systems can be used to inhibit highly expressed viral genes and render cells resistant to viral replication via intracellular immunization strategies.

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40

Sullenger, B. A., T. C. Lee, C. A. Smith, G. E. Ungers, and E. Gilboa. "Expression of chimeric tRNA-driven antisense transcripts renders NIH 3T3 cells highly resistant to Moloney murine leukemia virus replication." Molecular and Cellular Biology 10, no. 12 (December 1990): 6512–23. http://dx.doi.org/10.1128/mcb.10.12.6512.

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NIH 3T3 cells infected with Moloney murine leukemia virus (MoMLV) express high levels of virus-specific RNA. To inhibit replication of the virus, we stably introduced chimeric tRNA genes encoding antisense templates into NIH 3T3 cells via a retroviral vector. Efficient expression of hybrid tRNA-MoMLV antisense transcripts and inhibition of MoMLV replication were dependent on the use of a particular type of retroviral vector, the double-copy vector, in which the chimeric tRNA gene was inserted in the 3' long terminal repeat. MoMLV replication was inhibited up to 97% in cells expressing antisense RNA corresponding to the gag gene and less than twofold in cells expressing antisense RNA corresponding to the pol gene. RNA and protein analyses suggest that inhibition was exerted at the level of translation. These results suggest that RNA polymerase III-based antisense inhibition systems can be used to inhibit highly expressed viral genes and render cells resistant to viral replication via intracellular immunization strategies.

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41

Schuh, Reinhard, and Herbert Jäckle. "Probing Drosophila gene function by antisense RNA." Genome 31, no. 1 (January 1, 1989): 422–25. http://dx.doi.org/10.1139/g89-063.

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The conventional technique for assigning a particular genetic function to a cloned transcription unit has relied on the rescue of the mutant phenotype by germ line transformation. An alternative approach is to mimic a mutant phenotype by the use of antisense RNA injections to produce phenocopies. This approach has been successfully used to identify genes involved in early pattern forming processes in the Drosophila embryo. At the time when antisense RNA is injected, the embryo develops as a syncytium composed of about 5000 nuclei which share a common cytoplasm. The gene interactions required to establish the body plan occur before cellularization at the blastoderm stage. Thus the nuclei and their exported transcripts are accessible to the injected antisense RNA. The antisense RNA interferes with the endogenous RNA by an as yet unidentified mechanism. The extent of interference is only partial and produces phenocopies with characteristics of weak mutant alleles. In our lab and others, this approach has been successfully used to identify several genes required for normal Drosophila pattern formation.Key words: Drosophila segmentation, phenocopy, antisense RNA, Krüppel gene.

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42

Fang, H., Y. Shen, and J. S. Taylor. "Native mRNA antisense-accessible sites library for the selection of antisense oligonucleotides, PNAs, and siRNAs." RNA 16, no. 7 (May 24, 2010): 1429–35. http://dx.doi.org/10.1261/rna.1940610.

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Fire, A., D. Albertson, S. W. Harrison, and D. G. Moerman. "Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle." Development 113, no. 2 (October 1, 1991): 503–14. http://dx.doi.org/10.1242/dev.113.2.503.

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We have used an antisense strategy to effectively disrupt the expression of two genes encoding myofilament proteins present in C. elegans body wall muscles. DNA segments from the unc-22 and unc-54 genes have been placed in reverse orientation in vectors designed to produce RNA in body wall muscles. When the resulting plasmids are injected into oocytes, progeny with defects in muscle function are produced. These animals have phenotypes consistent with reduction and/or elimination of function of the gene to which antisense RNA has been produced: twitching and disorganization of muscle filaments for the unc-22 antisense constructs and lack of muscle tone, slow movement, and egg laying defects for the unc-54 antisense constructs. A fraction of the affected animals transmit the defective-muscle trait to subsequent generations. In these cases the transforming DNA is present at high copy number and cosegregates with the observed muscle defects. We have examined several of the unc-22 antisense plasmid transformed lines to determine the mechanistic basis for the observed phenotypes. The RNA product of the endogenous unc-22 locus is present at normal levels and this RNA is properly spliced in the region homologous to the antisense RNA. No evidence for modification of this RNA by deamination of adenosine to inosine was found. In affected animals the level of protein product from the endogenous unc-22 locus is greatly reduced. Antisense RNA produced from the transforming DNA was detected and was much more abundant than ‘sense’ RNA from the endogenous locus. These data suggest that the observed phenotypes result from interference with a late step in gene expression, such as transport into the cytoplasm or translation.

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Moreno, Renata, Aurelio Hidalgo, Felipe Cava, Roberto Fernández-Lafuente, José Manuel Guisán, and José Berenguer. "Use of an Antisense RNA Strategy To Investigate the Functional Significance of Mn-Catalase in the Extreme Thermophile Thermus thermophilus." Journal of Bacteriology 186, no. 22 (November 15, 2004): 7804–6. http://dx.doi.org/10.1128/jb.186.22.7804-7806.2004.

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ABSTRACT The expression of an antisense RNA revealed that an Mn-catalase was required in Thermus thermophilus for aerobic but not for anaerobic growth. The antisense system is based on the constitutive expression of a “bicistronic” transcript consisting of the kanamycin resistance gene mRNA followed by the antisense RNA against the selected target.

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Sturino, Joseph M., and Todd R. Klaenhammer. "Expression of Antisense RNA Targeted against Streptococcus thermophilus Bacteriophages." Applied and Environmental Microbiology 68, no. 2 (February 2002): 588–96. http://dx.doi.org/10.1128/aem.68.2.588-596.2002.

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ABSTRACT Antisense RNA complementary to a putative helicase gene (hel3.1) of a cos-type Streptococcus thermophilus bacteriophage was used to impede the proliferation of a number of cos-type S. thermophilus bacteriophages and one pac-type bacteriophage. The putative helicase gene is a component of the Sfi21-type DNA replication module, which is found in a majority of the S. thermophilus bacteriophages of industrial importance. All bacteriophages that strongly hybridized a 689-bp internal hel3.1 probe were sensitive to the expression of antisense hel3.1 RNA. A 40 to 70% reduction in efficiency of plaquing (EOP) was consistently observed, with a concomitant decrease in plaque size relative to that of the S. thermophilus parental strain. When progeny were released, the burst size was reduced. Growth curves of S. thermophilus NCK1125, in the presence of variable levels of bacteriophage κ3, showed that antisense hel3.1 conferred protection, even at a multiplicity of infection of approximately 1.0. When the hel3.1 antisense RNA cassette was expressed in cis from the κ3-derived phage-encoded resistance (PER) plasmid pTRK690::ori3.1, the EOP for bacteriophages sensitive to PER and antisense targeting was reduced to between 10−7 and 10−8, beyond the resistance conferred by the PER element alone (less than 10−6). These results illustrate the first successful applications of antisense RNA and explosive delivery of antisense RNA to inhibit the proliferation of S. thermophilus bacteriophages.

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Woo, Ho-Hyung, and Setsuko K. Chambers. "Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3′ end polymorphism in breast cancer cells." RNA 27, no. 9 (June 21, 2021): 1068–81. http://dx.doi.org/10.1261/rna.078749.121.

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Sense-antisense mRNA pairs generated by convergent transcription is a way of gene regulation. c-fms gene is closely juxtaposed to the HMGXB3 gene in the opposite orientation, in chromosome 5. The intergenic region (IR) between c-fms and HMGXB3 genes is 162 bp. We found that a small portion (∼4.18%) of HMGXB3 mRNA is transcribed further downstream, including the end of the c-fms gene generating antisense mRNA against c-fms mRNA. Similarly, a small portion (∼1.1%) of c-fms mRNA is transcribed further downstream, including the end of the HMGXB3 gene generating antisense mRNA against the HMGXB3 mRNA. Insertion of the strong poly(A) signal sequence in the IR results in decreased c-fms and HMGXB3 antisense mRNAs, resulting in up-regulation of both c-fms and HMGXB3 mRNA expression. miR-324-5p targets HMGXB3 mRNA 3′ UTR, and as a result, regulates c-fms mRNA expression. HuR stabilizes c-fms mRNA, and as a result, down-regulates HMGXB3 mRNA expression. UALCAN analysis indicates that the expression pattern between c-fms and HMGXB3 proteins are opposite in vivo in breast cancer tissues. Together, our results indicate that the mRNA encoded by the HMGXB3 gene can influence the expression of adjacent c-fms mRNA, or vice versa.

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Soulez, M., C. G. Rouviere, P. Chafey, D. Hentzen, M. Vandromme, N. Lautredou, N. Lamb, A. Kahn, and D. Tuil. "Growth and differentiation of C2 myogenic cells are dependent on serum response factor." Molecular and Cellular Biology 16, no. 11 (November 1996): 6065–74. http://dx.doi.org/10.1128/mcb.16.11.6065.

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In order to study to what extent and at which stage serum response factor (SRF) is indispensable for myogenesis, we stably transfected C2 myogenic cells with, successively, a glucocorticoid receptor expression vector and a construct allowing for the expression of an SRF antisense RNA under the direction of the mouse mammary tumor virus long terminal repeat. In the clones obtained, SRF synthesis is reversibly down-regulated by induction of SRF antisense RNA expression by dexamethasone, whose effect is antagonized by the anti-hormone RU486. Two kinds of proliferation and differentiation patterns have been obtained in the resulting clones. Some clones with a high level of constitutive SRF antisense RNA expression are unable to differentiate into myotubes; their growth can be blocked by further induction of SRF antisense RNA expression by dexamethasone. Other clones are able to differentiate and are able to synthesize SRF, MyoD, myogenin, and myosin heavy chain at confluency. When SRF antisense RNA expression is induced in proliferating myoblasts by dexamethasone treatment, cell growth is blocked and cyclin A concentration drops. When SRF antisense RNA synthesis is induced in arrested confluent myoblasts cultured in a differentiation medium, cell fusion is blocked and synthesis of not only SRF but also MyoD, myogenin, and myosin heavy chain is inhibited. Our results show, therefore, that SRF synthesis is indispensable for both myoblast proliferation and myogenic differentiation.

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MILITELLO, K. T. "RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum." RNA 11, no. 4 (April 1, 2005): 365–70. http://dx.doi.org/10.1261/rna.7940705.

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Magán, Andrés, Fabian Amman, Fatinah El-Isa, Natascha Hartl, Ilya Shamovsky, Evgeny Nudler, Renée Schroeder, and Nadezda Sedlyarova. "iRAPs curb antisense transcription in E. coli." Nucleic Acids Research 47, no. 20 (September 19, 2019): 10894–905. http://dx.doi.org/10.1093/nar/gkz791.

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Abstract RNA polymerase-binding RNA aptamers (RAPs) are natural RNA elements that control transcription in cis by directly contacting RNA polymerase. Many RAPs inhibit transcription by inducing Rho-dependent termination in Escherichia coli. Here, we studied the role of inhibitory RAPs (iRAPs) in modulation of antisense transcription (AT) using in silico and in vivo approaches. We revisited the antisense transcriptome in cells with impaired AT regulators (Rho, H-NS and RNaseIII) and searched for the presence of RAPs within antisense RNAs. Many of these RAPs were found at key genomic positions where they terminate AT. By exploring the activity of several RAPs both in a reporter system and in their natural genomic context, we confirmed their significant role in AT regulation. RAPs coordinate Rho activity at the antisense strand and terminate antisense transcripts. In some cases, they stimulated sense expression by alleviating ongoing transcriptional interference. Essentially, our data postulate RAPs as key determinants of Rho-mediated AT regulation in E. coli.

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Werner, Andreas, Mark Carlile, and Daniel Swan. "What do natural antisense transcripts regulate?" RNA Biology 6, no. 1 (January 2009): 43–48. http://dx.doi.org/10.4161/rna.6.1.7568.

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Journal articles on the topic 'Antisense RNA'

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