Previous Article | Next Article 
Microbiology and Molecular Biology Reviews, December 1998, p. 1415-1434, Vol. 62, No. 4
1092-2172/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Antisense RNA: Function and Fate of Duplex RNA
in Cells of Higher Eukaryotes
Madhur
Kumar and
Gordon G.
Carmichael*
Department of Microbiology, University of
Connecticut Health Center, Farmington, Connecticut 06030-3205
There is ample evidence that cells of higher eukaryotes express double-stranded RNA molecules (dsRNAs) either naturally or as the result of viral infection or aberrant, bidirectional transcriptional readthrough. These duplex molecules can exist in either the cytoplasmic or nuclear compartments. Cells have evolved distinct ways of responding to dsRNAs, depending on the nature and location of the duplexes. Since dsRNA molecules are not thought to exist naturally within the cytoplasm, dsRNA in this compartment is most often associated with viral infections. Cells have evolved defensive strategies against such molecules, primarily involving the interferon response pathway. Nuclear dsRNA, however, does not induce interferons and may play an important posttranscriptional regulatory role. Nuclear dsRNA appears to be the substrate for enzymes which deaminate adenosine residues to inosine residues within the polynucleotide structure, resulting in partial or full unwinding. Extensively modified RNAs are either rapidly degraded or retained within the nucleus, whereas transcripts with few modifications may be transported to the cytoplasm, where they serve to produce altered proteins. This review summarizes our current knowledge about the function and fate of dsRNA in cells of higher eukaryotes and its potential manipulation as a research and therapeutic tool.
*
Corresponding author. Mailing address: Department of
Microbiology, University of Connecticut Health Center, Farmington, CT 06030-3205. Phone: (860) 679-2259. Fax: (860) 679-1239. E-mail: gcarmich{at}panda.uchc.edu.
Microbiology and Molecular Biology Reviews, December 1998, p. 1415-1434, Vol. 62, No. 4
1092-2172/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Wu, Y., Zhang, W., Yang, Y., Yu, B., Huang, A.
(2009). Identification of a novel negative regulatory element on the hepatitis B virus S-(+)-strand. Acta Biochim Biophys Sin
41: 873-882
[Abstract]
[Full Text]
-
Salem, T. Z., Garcia-Maruniak, A., Lietze, V.-U., Maruniak, J. E., Boucias, D. G.
(2009). Analysis of transcripts from predicted open reading frames of Musca domestica salivary gland hypertrophy virus. J. Gen. Virol.
90: 1270-1280
[Abstract]
[Full Text]
-
Yokota, T., Takeda, S., Lu, Q.-L., Partridge, T. A., Nakamura, A., Hoffman, E. P.
(2009). A Renaissance for Antisense Oligonucleotide Drugs in Neurology: Exon Skipping Breaks New Ground. Arch Neurol
66: 32-38
[Abstract]
[Full Text]
-
Kim, D.-S., Cho, C.-Y., Huh, J.-W., Kim, H.-S., Cho, H.-G.
(2009). EVOG: a database for evolutionary analysis of overlapping genes. Nucleic Acids Res
37: D698-D702
[Abstract]
[Full Text]
-
Faridani, O. R., McInerney, G. M., Gradin, K., Good, L.
(2008). Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions. Nucleic Acids Res
36: e99-e99
[Abstract]
[Full Text]
-
Henz, S. R., Cumbie, J. S., Kasschau, K. D., Lohmann, J. U., Carrington, J. C., Weigel, D., Schmid, M.
(2007). Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis. Plant Physiol.
144: 1247-1255
[Abstract]
[Full Text]
-
Gingeras, T. R.
(2007). Origin of phenotypes: Genes and transcripts. Genome Res
17: 682-690
[Abstract]
[Full Text]
-
Osato, N., Suzuki, Y., Ikeo, K., Gojobori, T.
(2007). Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics
176: 1299-1306
[Abstract]
[Full Text]
-
Kanda, T., Steele, R., Ray, R., Ray, R. B.
(2007). Small Interfering RNA Targeted to Hepatitis C Virus 5' Nontranslated Region Exerts Potent Antiviral Effect. J. Virol.
81: 669-676
[Abstract]
[Full Text]
-
Pandorf, C. E., Haddad, F., Roy, R. R., Qin, A. X., Edgerton, V. R., Baldwin, K. M.
(2006). Dynamics of Myosin Heavy Chain Gene Regulation in Slow Skeletal Muscle: ROLE OF NATURAL ANTISENSE RNA. J. Biol. Chem.
281: 38330-38342
[Abstract]
[Full Text]
-
Dalmay, T.
(2006). Short RNAs in environmental adaptation. Proc R Soc B
273: 1579-1585
[Abstract]
[Full Text]
-
Sun, M., Hurst, L. D., Carmichael, G. G., Chen, J.
(2006). Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity. Genome Res
16: 922-933
[Abstract]
[Full Text]
-
Weber, F., Wagner, V., Rasmussen, S. B., Hartmann, R., Paludan, S. R.
(2006). Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses.. J. Virol.
80: 5059-5064
[Abstract]
[Full Text]
-
David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C. J., Bofkin, L., Jones, T., Davis, R. W., Steinmetz, L. M.
(2006). A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA
103: 5320-5325
[Abstract]
[Full Text]
-
Tufarelli, C.
(2006). The silence RNA keeps: cis mechanisms of RNA mediated epigenetic silencing in mammals. Phil Trans R Soc B
361: 67-79
[Abstract]
[Full Text]
-
Chen, J., Sun, M., Rowley, J. D., Hurst, L. D.
(2005). The Small Introns of Antisense Genes Are Better Explained by Selection for Rapid Transcription Than by "Genomic Design". Genetics
171: 2151-2155
[Abstract]
[Full Text]
-
Barclay, C., Li, A. W., Geldenhuys, L., Baguma-Nibasheka, M., Porter, G. A., Veugelers, P. J., Murphy, P. R., Casson, A. G.
(2005). Basic Fibroblast Growth Factor (FGF-2) Overexpression Is a Risk Factor for Esophageal Cancer Recurrence and Reduced Survival, which Is Ameliorated by Coexpression of the FGF-2 Antisense Gene. Clin. Cancer Res.
11: 7683-7691
[Abstract]
[Full Text]
-
Sun, M., Hurst, L. D., Carmichael, G. G., Chen, J.
(2005). Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res
33: 5533-5543
[Abstract]
[Full Text]
-
Seitz, A., Gourevitch, D., Zhang, X.-M., Clark, L., Chen, P., Kragol, M., Levenkova, N., Rux, J., Samulewicz, S., Heber-Katz, E.
(2005). Sense and antisense transcripts of the apolipoprotein E gene in normal and ApoE knockout mice, their expression after spinal cord injury and corresponding human transcripts. Hum Mol Genet
14: 2661-2670
[Abstract]
[Full Text]
-
Coudert, A. E., Pibouin, L., Vi-Fane, B., Thomas, B. L., Macdougall, M., Choudhury, A., Robert, B., Sharpe, P. T., Berdal, A., Lezot, F.
(2005). Expression and regulation of the Msx1 natural antisense transcript during development. Nucleic Acids Res
33: 5208-5218
[Abstract]
[Full Text]
-
Espert, L., Degols, G., Lin, Y.-L., Vincent, T., Benkirane, M., Mechti, N.
(2005). Interferon-induced exonuclease ISG20 exhibits an antiviral activity against human immunodeficiency virus type 1. J. Gen. Virol.
86: 2221-2229
[Abstract]
[Full Text]
-
Yan, M.-D., Hong, C.-C., Lai, G.-M., Cheng, A.-L., Lin, Y.-W., Chuang, S.-E.
(2005). Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet
14: 1465-1474
[Abstract]
[Full Text]
-
Dahary, D., Elroy-Stein, O., Sorek, R.
(2005). Naturally occurring antisense: Transcriptional leakage or real overlap?. Genome Res
15: 364-368
[Abstract]
[Full Text]
-
Yuan, J., Cheung, P. K. M., Zhang, H. M., Chau, D., Yang, D.
(2005). Inhibition of Coxsackievirus B3 Replication by Small Interfering RNAs Requires Perfect Sequence Match in the Central Region of the Viral Positive Strand. J. Virol.
79: 2151-2159
[Abstract]
[Full Text]
-
Soldan, S. S., Plassmeyer, M. L., Matukonis, M. K., Gonzalez-Scarano, F.
(2005). La Crosse Virus Nonstructural Protein NSs Counteracts the Effects of Short Interfering RNA. J. Virol.
79: 234-244
[Abstract]
[Full Text]
-
Chen, J., Sun, M., Kent, W. J., Huang, X., Xie, H., Wang, W., Zhou, G., Shi, R. Z., Rowley, J. D.
(2004). Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res
32: 4812-4820
[Abstract]
[Full Text]
-
Robb, G. B., Carson, A. R., Tai, S. C., Fish, J. E., Singh, S., Yamada, T., Scherer, S. W., Nakabayashi, K., Marsden, P. A.
(2004). Post-transcriptional Regulation of Endothelial Nitric-oxide Synthase by an Overlapping Antisense mRNA Transcript. J. Biol. Chem.
279: 37982-37996
[Abstract]
[Full Text]
-
Wang, Q., Carmichael, G. G.
(2004). Effects of Length and Location on the Cellular Response to Double-Stranded RNA. Microbiol. Mol. Biol. Rev.
68: 432-452
[Abstract]
[Full Text]
-
Hu, X., Hipolito, S., Lynn, R., Abraham, V., Ramos, S., Wong-Staal, F.
(2004). Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus. Nucleic Acids Res
32: 4609-4617
[Abstract]
[Full Text]
-
BARTSCH, H., VOIGTSBERGER, S., BAUMANN, G., MORANO, I., LUTHER, H. P.
(2004). Detection of a novel sense-antisense RNA-hybrid structure by RACE experiments on endogenous troponin I antisense RNA. RNA
10: 1215-1224
[Abstract]
[Full Text]
-
Alifragis, P., Liapi, A., Parnavelas, J. G.
(2004). Lhx6 Regulates the Migration of Cortical Interneurons from the Ventral Telencephalon But Does Not Specify their GABA Phenotype. J. Neurosci.
24: 5643-5648
[Abstract]
[Full Text]
-
Pearson, A., Knipe, D. M., Coen, D. M.
(2004). ICP27 Selectively Regulates the Cytoplasmic Localization of a Subset of Viral Transcripts in Herpes Simplex Virus Type 1-Infected Cells. J. Virol.
78: 23-32
[Abstract]
[Full Text]
-
Chang, J., Provost, P., Taylor, J. M.
(2003). Resistance of Human Hepatitis Delta Virus RNAs to Dicer Activity. J. Virol.
77: 11910-11917
[Abstract]
[Full Text]
-
Opalinska, J. B., Gewirtz, A. M.
(2003). Therapeutic Potential of Antisense Nucleic Acid Molecules. Sci Signal
2003: pe47-pe47
[Abstract]
[Full Text]
-
Boeke, J. D.
(2003). The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis. Genome Res
13: 1975-1983
[Abstract]
[Full Text]
-
Moriyama, K., Hayashida, K., Shimada, M., Nakano, S., Nakashima, Y., Fukumaki, Y.
(2003). Antisense RNAs transcribed from the upstream region of the precore/core promoter of hepatitis B virus. J. Gen. Virol.
84: 1907-1913
[Abstract]
[Full Text]
-
Nikaido, I., Saito, C., Mizuno, Y., Meguro, M., Bono, H., Kadomura, M., Kono, T., Morris, G. A., Lyons, P. A., Oshimura, M., RIKEN GER Group, , GSL Members, , Hayashizaki, Y., Okazaki, Y.
(2003). Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling. Genome Res
13: 1402-1409
[Abstract]
[Full Text]
-
Espert, L., Degols, G., Gongora, C., Blondel, D., Williams, B. R., Silverman, R. H., Mechti, N.
(2003). ISG20, a New Interferon-induced RNase Specific for Single-stranded RNA, Defines an Alternative Antiviral Pathway against RNA Genomic Viruses. J. Biol. Chem.
278: 16151-16158
[Abstract]
[Full Text]
-
Burton, E. A., Hong, C.-S., Glorioso, J. C.
(2003). The Stable 2.0-Kilobase Intron of the Herpes Simplex Virus Type 1 Latency-Associated Transcript Does Not Function as an Antisense Repressor of ICP0 in Nonneuronal Cells. J. Virol.
77: 3516-3530
[Abstract]
[Full Text]
-
Ge, Q., McManus, M. T., Nguyen, T., Shen, C.-H., Sharp, P. A., Eisen, H. N., Chen, J.
(2003). RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc. Natl. Acad. Sci. USA
100: 2718-2723
[Abstract]
[Full Text]
-
Collins, J. E., Goward, M. E., Cole, C. G., Smink, L. J., Huckle, E. J., Knowles, S., Bye, J. M., Beare, D. M., Dunham, I.
(2003). Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22. Genome Res
13: 27-36
[Abstract]
[Full Text]
-
Ahlquist, P.
(2002). RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing. Science
296: 1270-1273
[Abstract]
[Full Text]
-
Chen, S.-H., Lee, L. Y., Garber, D. A., Schaffer, P. A., Knipe, D. M., Coen, D. M.
(2002). Neither LAT nor Open Reading Frame P Mutations Increase Expression of Spliced or Intron-Containing ICP0 Transcripts in Mouse Ganglia Latently Infected with Herpes Simplex Virus. J. Virol.
76: 4764-4772
[Abstract]
[Full Text]
-
Gorlach, J. M., McDade, H. C., Perfect, J. R., Cox, G. M.
(2002). Antisense repression in Cryptococcus neoformans as a laboratory tool and potential antifungal strategy. Microbiology
148: 213-219
[Abstract]
[Full Text]
-
Elmendorf, H. G., Singer, S. M., Nash, T. E.
(2001). The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids Res
29: 4674-4683
[Abstract]
[Full Text]
-
Diaz, M., Verkoczy, L. K., Flajnik, M. F., R. Klinman, N.
(2001). Decreased Frequency of Somatic Hypermutation and Impaired Affinity Maturation but Intact Germinal Center Formation in Mice Expressing Antisense RNA to DNA Polymerase {{zeta}}. J. Immunol.
167: 327-335
[Abstract]
[Full Text]
-
Blin-Wakkach, C., Lezot, F., Ghoul-Mazgar, S., Hotton, D., Monteiro, S., Teillaud, C., Pibouin, L., Orestes-Cardoso, S., Papagerakis, P., Macdougall, M., Robert, B., Berdal, A.
(2001). Endogenous Msx1 antisense transcript: In vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc. Natl. Acad. Sci. USA
10.1073/pnas.131497098v1
[Abstract]
[Full Text]
-
Calin-Jageman, I., Amarasinghe, A. K., Nicholson, A. W.
(2001). Ethidium-dependent uncoupling of substrate binding and cleavage by Escherichia coli ribonuclease III. Nucleic Acids Res
29: 1915-1925
[Abstract]
[Full Text]
-
Beckley, S. A., Liu, P., Stover, M. L., Gunderson, S. I., Lichtler, A. C., Rowe, D. W.
(2001). Reduction of Target Gene Expression by a Modified U1 snRNA. Mol. Cell. Biol.
21: 2815-2825
[Abstract]
[Full Text]
-
Sohn, H. W., Shin, Y. K., Lee, I.-S., Bae, Y. M., Suh, Y. H., Kim, M. K., Kim, T. J., Jung, K. C., Park, W. S., Park, C.-S., Chung, D. H., Ahn, K., Kim, I. S., Ko, Y. H., Bang, Y. J., Kim, C. W., Park, S. H.
(2001). CD99 Regulates the Transport of MHC Class I Molecules from the Golgi Complex to the Cell Surface. J. Immunol.
166: 787-794
[Abstract]
[Full Text]
-
Blair, C. D., Adelman, Z. N., Olson, K. E.
(2000). Molecular Strategies for Interrupting Arthropod-Borne Virus Transmission by Mosquitoes. Clin. Microbiol. Rev.
13: 651-661
[Abstract]
[Full Text]
-
Hastings, M. L., Ingle, H. A., Lazar, M. A., Munroe, S. H.
(2000). Post-transcriptional Regulation of Thyroid Hormone Receptor Expression by cis-Acting Sequences and a Naturally Occurring Antisense RNA. J. Biol. Chem.
275: 11507-11513
[Abstract]
[Full Text]
-
Johnson, B. W., Olson, K. E., Allen-Miura, T., Rayms-Keller, A., Carlson, J. O., Coates, C. J., Jasinskiene, N., James, A. A., Beaty, B. J., Higgs, S.
(1999). Inhibition of luciferase expression in transgenic Aedes aegypti mosquitoes by Sindbis virus expression of antisense luciferase RNA. Proc. Natl. Acad. Sci. USA
96: 13399-13403
[Abstract]
[Full Text]
-
Smith, H. B.
(1999). Interfering with Viral Infection: Plants Do It Too. Plant Cell
11: 1191-1194
[Full Text]
-
Blin-Wakkach, C., Lezot, F., Ghoul-Mazgar, S., Hotton, D., Monteiro, S., Teillaud, C., Pibouin, L., Orestes-Cardoso, S., Papagerakis, P., Macdougall, M., Robert, B., Berdal, A.
(2001). Endogenous Msx1 antisense transcript: In vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc. Natl. Acad. Sci. USA
98: 7336-7341
[Abstract]
[Full Text]