Genomes and Genes
Summary: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
- Schwartz J, Younger S, Nguyen N, Hardy D, Monia B, Corey D, et al. Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol. 2008;15:842-8 pubmed publisher..Our data demonstrate that antisense transcripts have a central role in recognition of the PR promoter by both activating and inhibitory agRNAs. ..
- Zamanian Daryoush M, Marques J, Gantier M, Behlke M, John M, Rayman P, et al. Determinants of cytokine induction by small interfering RNA in human peripheral blood mononuclear cells. J Interferon Cytokine Res. 2008;28:221-33 pubmed publisher..In accordance with this, specific chemical modifications differentially altered cytokine production, suggesting recruitment of different TLRs in a sequence-dependent manner. ..
- Beltran M, Puig I, Peña C, Garcia J, Alvarez A, Peña R, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 2008;22:756-69 pubmed publisher..Therefore, the results presented in this article reveal the existence of a NAT capable of activating Zeb2 expression, explain the mechanism involved in this activation, and demonstrate that this NAT regulates E-cadherin expression. ..
- Stark A, Bushati N, Jan C, Kheradpour P, Hodges E, Brennecke J, et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 2008;22:8-13 pubmed publisher..We also report sense/antisense miRNAs in mouse and find antisense transcripts close to many miRNAs in both flies and mammals, suggesting that additional sense/antisense pairs exist. ..
- Zofall M, Fischer T, Zhang K, Zhou M, Cui B, Veenstra T, et al. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature. 2009;461:419-22 pubmed publisher..These analyses suggest that as well as performing other functions, H2A.Z is a component of a genome indexing mechanism that cooperates with heterochromatin and RNAi factors to suppress read-through antisense transcripts. ..
- Parenti R, Paratore S, Torrisi A, Cavallaro S. A natural antisense transcript against Rad18, specifically expressed in neurons and upregulated during beta-amyloid-induced apoptosis. Eur J Neurosci. 2007;26:2444-57 pubmed..These experiments suggest the existence of a NAT that exerts a post-transcriptional control over Rad18. ..
- Zubko E, Meyer P. A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation. Plant J. 2007;52:1131-9 pubmed..In all tissue types tested, we detect a pool of antisense RNA of approximately 35 nt, which derives from the region where Sho sense and antisense transcripts overlap...
- Xie S, Ren Z, Zhang J, Guo X, Wang Q, Wang S, et al. Restoration of the balanced alpha/beta-globin gene expression in beta654-thalassemia mice using combined RNAi and antisense RNA approach. Hum Mol Genet. 2007;16:2616-25 pubmed..Lentiviral vectors of short hairpin RNA (shRNA) targeting alpha-globin and/or antisense RNA facilitating beta-globin correct splicing were microinjected into beta(654) single-cell embryos...
- Wei C, Qin F, Zhu L, Zhou W, Chen Y, Wang Y, et al. Microstructure and ultrastructure of high-amylose rice resistant starch granules modified by antisense RNA inhibition of starch branching enzyme. J Agric Food Chem. 2010;58:1224-32 pubmed publisherA high-amylose transgenic rice line (TRS) modified by antisense RNA inhibition of starch branching enzymes revealed a resistant starch-rich quality...
- Pasmant E, Laurendeau I, Heron D, Vidaud M, Vidaud D, Bieche I. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 2007;67:3963-9 pubmed
- Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol. 2007;10:102-9 pubmed..Although the final product of antisense RNA/target RNA binding is a full duplex that is degraded by RNase III, inhibition does not require complete duplex ..
- Core L, Waterfall J, Lis J. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322:1845-8 pubmed publisher..These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription. ..
- Li K, Blum Y, Verma A, Liu Z, Pramanik K, Leigh N, et al. A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. Blood. 2010;115:133-9 pubmed publisher..These results directly implicate noncoding RNA-mediated transcriptional regulation of gene expression as a fundamental control mechanism for physiologic processes, such as vascular development. ..
- Luttges J, Hahn S, Heidenblut A. Manual microdissection combined with antisense RNA-longSAGE for the analysis of limited cell numbers. Methods Mol Biol. 2010;576:135-54 pubmed publisher..a strategy for combining linear amplification of RNA with longSAGE is described that allows the use of antisense RNA (aRNA) generated via the well-established linear amplification of RNA procedure together with the conventional ..
- Hernandez J, Alonso I, Pellicer S, Luisa Peleato M, Cases R, Strasser R, et al. Mutants of Anabaena sp. PCC 7120 lacking alr1690 and alpha-furA antisense RNA show a pleiotropic phenotype and altered photosynthetic machinery. J Plant Physiol. 2010;167:430-7 pubmed publisher..These results reveal that expression of the alpha-furA-alr1690 message is required for maintenance of a proper thylakoid arrangement, efficient regulation of iron uptake and optimal yield of the photosynthetic machinery. ..
- Preker P, Nielsen J, Kammler S, Lykke Andersen S, Christensen M, Mapendano C, et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science. 2008;322:1851-4 pubmed publisher..We propose that PROMPT transcription is a common characteristic of RNA polymerase II (RNAPII) transcribed genes with a possible regulatory potential. ..
- André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, et al. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res. 2008;36:5955-69 pubmed publisher..We proposed a regulatory model in which the antisense RNA controlled the expression of the ubiG operon in cis via transcriptional interference at the ubiG locus.
- Liu Y, Wu N, Dong J, Gao Y, Zhang X, Shao N, et al. SsrA (tmRNA) acts as an antisense RNA to regulate Staphylococcus aureus pigment synthesis by base pairing with crtMN mRNA. FEBS Lett. 2010;584:4325-9 pubmed publisher..Furthermore, it was demonstrated that ssrA could act as an antisense RNA aside from its well-known biological function, and crtMN, encoding two essential enzymes for the pigment ..
- Li J, Zhang Y, Kong L, Liu Q, Wei L. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res. 2008;36:4833-44 pubmed publisher..In 30 cases, trans-SAs were related to cis-SAs through paralogues, suggesting a possible mechanism for the origin of trans-SAs. All trans-SAs are available at http://trans.cbi.pku.edu.cn/. ..
- Ebralidze A, Guibal F, Steidl U, Zhang P, Lee S, Bartholdy B, et al. PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Dev. 2008;22:2085-92 pubmed publisher..We propose that such antisense RNAs will likely be important in the regulation of many genes and may be the reason for the large number of overlapping complementary transcripts with so far unknown function. ..
- Lu C, Jeong D, Kulkarni K, Pillay M, Nobuta K, German R, et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A. 2008;105:4951-6 pubmed publisher..These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes. ..
- Silby M, Levy S. Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1. PLoS Genet. 2008;4:e1000094 pubmed publisher..We therefore designate iiv14 "cosA". These data suggest that, as is the case with eukaryotes, some bacterial genomes are more densely coded than currently recognized. ..
- Militello K, Refour P, Comeaux C, Duraisingh M. Antisense RNA and RNAi in protozoan parasites: working hard or hardly working?. Mol Biochem Parasitol. 2008;157:117-26 pubmed
- Perocchi F, Xu Z, Clauder Münster S, Steinmetz L. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. 2007;35:e128 pubmed..Our findings thus facilitate a more accurate assessment of the extent and position of antisense transcription, towards a better understanding of its role in cells. ..
- Mundodi V, Kucknoor A, Alderete J. Antisense RNA decreases AP33 gene expression and cytoadherence by T. vaginalis. BMC Microbiol. 2007;7:64 pubmed..These results using both antisense inhibition of gene expression and AP33 synthesis and the heterologous expression of AP33 in T. foetus confirms a role for this protein as an adhesin in T. vaginalis. ..
- Zemanova M, Kaderábková P, Pátek M, Knoppová M, Silar R, Nesvera J. Chromosomally encoded small antisense RNA in Corynebacterium glutamicum. FEMS Microbiol Lett. 2008;279:195-201 pubmedThe first observation of chromosomally encoded small antisense RNA in Corynebacterium glutamicum is reported...
- Tochitani S, Hayashizaki Y. Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation. Biochem Biophys Res Commun. 2008;372:691-6 pubmed publisher..2AS overexpression. These results together imply that Nkx2.2AS has a certain biological function which is likely to be not only based on the affect on transcription level of Nkx2.2 coding gene in cis, but also on the other mechanisms. ..
- Georg J, Honsel A, Voss B, Rennenberg H, Hess W. A long antisense RNA in plant chloroplasts. New Phytol. 2010;186:615-22 pubmed publisherBased on computational prediction of RNA secondary structures, a long antisense RNA (asRNA) was found in chloroplasts of Arabidopsis, Nicotiana tabacum and poplar, which occurs in two to three major transcripts...
- MacFarlane L, Gu Y, Casson A, Murphy P. Regulation of fibroblast growth factor-2 by an endogenous antisense RNA and by argonaute-2. Mol Endocrinol. 2010;24:800-12 pubmed publisher..Using a luciferase reporter system, we show that these effects are mediated by interaction of the endogenous antisense RNA with the 3'-untranslated region of the FGF-2 mRNA...
- Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess W. Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol. 2009;5:305 pubmed publisher..Extrapolated to the whole genome, approximately 10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks. ..
- Mukherjee R, Plesa G, Sherrill Mix S, Richardson M, Riley J, Bushman F. HIV sequence variation associated with env antisense adoptive T-cell therapy in the hNSG mouse model. Mol Ther. 2010;18:803-11 pubmed publisher..Unexpectedly, this enrichment was only detected after the challenge with HIV-1(BaL), where the viral genome would form an imperfect duplex with envAS, and not HIV-1(NL4-3), where a perfectly matched duplex would form. ..
- Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, et al. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev. 2007;21:1353-66 pubmed..We demonstrate that the 3' domain acts primarily as an antisense RNA and rapidly anneals to these mRNAs, forming long RNA duplexes...
- Ho E, Donaldson M, Saville B. Detection of antisense RNA transcripts by strand-specific RT-PCR. Methods Mol Biol. 2010;630:125-38 pubmed publisher..Results indicate that optimization of the screens requires proper controls to confirm removal of gDNA contamination and to rule out self-priming as a source of first strand products. ..
- Aravin A, Sachidanandam R, Girard A, Fejes Toth K, Hannon G. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science. 2007;316:744-7 pubmed..Mili mutants derepress LINE-1 (L1) and intracisternal A particle and lose DNA methylation of L1 elements, demonstrating an evolutionarily conserved role for PIWI proteins in transposon suppression. ..
- Liu C, Yang Z, Liu C, Wang R, Tien P, Dale R, et al. Myostatin antisense RNA-mediated muscle growth in normal and cancer cachexia mice. Gene Ther. 2008;15:155-60 pubmed..Taken together, these results demonstrate the feasibility using antisense strategy for the treatment of muscle wasting conditions. ..
- Wei C, Xu B, Qin F, Yu H, Chen C, Meng X, et al. C-type starch from high-amylose rice resistant starch granules modified by antisense RNA inhibition of starch branching enzyme. J Agric Food Chem. 2010;58:7383-8 pubmed publisher..A transgenic rice line (TRS) enriched amylose and RS had been developed by antisense RNA inhibition of starch branching enzymes...
- Scheele C, Petrovic N, Faghihi M, Lassmann T, Fredriksson K, Rooyackers O, et al. The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genomics. 2007;8:74 pubmed
- Faghihi M, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol. 2009;10:637-43 pubmed publisher..Recent evidence indicates that antisense transcripts are frequently functional and use diverse transcriptional and post-transcriptional gene regulatory mechanisms to carry out a wide variety of biological roles. ..
- Jiang S, Christoffels A, Ramamoorthy R, Ramachandran S. Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. Plant Physiol. 2009;150:1997-2008 pubmed publisher..Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms. ..
- Seila A, Calabrese J, Levine S, Yeo G, Rahl P, Flynn R, et al. Divergent transcription from active promoters. Science. 2008;322:1849-51 pubmed publisher..These results suggest that divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation. ..
- Yu W, Gius D, Onyango P, Muldoon Jacobs K, Karp J, Feinberg A, et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature. 2008;451:202-6 pubmed publisher..transcriptome analysis shows that up to 70% of transcripts have antisense partners and that perturbation of antisense RNA can alter the expression of the sense gene...
- Yang B, Lan X, Li X, Yin X, Li B, Han X, et al. A novel bi-functional DNA vaccine expressing VP1 protein and producing antisense RNA targeted to 5'UTR of foot-and-mouth disease virus can induce both rapid inhibitory effect and specific immune response in mice. Vaccine. 2008;26:5477-83 pubmed publisher..against viral challenge, a novel strategy was performed to generate a novel bi-functional vector expressing antisense RNA targeted to 5' untranslated regions (UTR) and VP1 protein of foot-and-mouth disease virus (FMDV)...
- Dallosso A, Hancock A, Malik S, Salpekar A, King Underwood L, Pritchard Jones K, et al. Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer. RNA. 2007;13:2287-99 pubmed..These results show that WT1 encodes conserved antisense RNAs that may have an important regulatory role in WT1 expression via RNA:RNA interactions, and which can become deregulated by a variety of mechanisms in cancer. ..
- Zhang Q, Zhang J, Moe O, Hsia C. Synergistic upregulation of erythropoietin receptor (EPO-R) expression by sense and antisense EPO-R transcripts in the canine lung. Proc Natl Acad Sci U S A. 2008;105:7612-7 pubmed publisher..This demonstrates synergism between sense-antisense EPO-R transcripts in response to physiological stimulation in a robust model of induced lung growth. ..
- Korneev S, Korneeva E, Lagarkova M, Kiselev S, Critchley G, O SHEA M. Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells. RNA. 2008;14:2030-7 pubmed publisher..As NOS2A has a role in neurogenesis, our results suggest that the anti-NOS2A RNA is involved in the regulation of neuronal differentiation of hESCs through the modulation of NOS2A gene expression. ..
- Smalheiser N, Lugli G, Torvik V, Mise N, Ikeda R, Abe K. Natural antisense transcripts are co-expressed with sense mRNAs in synaptoneurosomes of adult mouse forebrain. Neurosci Res. 2008;62:236-9 pubmed publisher..This study provides evidence that a new class of noncoding RNAs (natural antisense transcripts) are expressed near synapses, and encourages further studies of their roles in neuronal function. ..
- Cervantes Rivera R, Romero López C, Berzal Herranz A, Cevallos M. Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d. J Bacteriol. 2010;192:3268-78 pubmed publisher..All repABC operons share three protein-encoding genes (repA, repB, and repC), an antisense RNA (ctRNA) coding gene, and at least one centromere-like region (parS)...
- Galante P, Vidal D, de Souza J, Camargo A, de Souza S. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol. 2007;8:R40 pubmed..We propose an evolutionary and functional model in which alternative polyadenylation and retroposition account for the origin of a significant number of functional S-AS pairs in mammalian genomes. ..
- Gowda M, Venu R, Li H, Jantasuriyarat C, Chen S, Bellizzi M, et al. Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. Plant Physiol. 2007;144:524-33 pubmed..These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages. ..