Abstract
Most annotated genomes show a large number of sense–antisense transcripts that can generate double-stranded RNAs. We describe a method to clone these dsRNAs from total RNA preparations.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Chen J, Sun M, Kent WJ, Huang X, Xie H, Wang W, Zhou G, Shi RZ, Rowley JD (2004) Over 20 % of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32(16):4812–4820. doi:10.1093/nar/gkh818
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740):1564–1566. doi:10.1126/science.1112009
He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The antisense transcriptomes of human cells. Science 322(5909):1855–1857. doi:10.1126/science.1163853
Steigele S, Nieselt K (2005) Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res 33(16):5034–5044. doi:10.1093/nar/gki804
Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302(5646):842–846. doi:10.1126/science.1088305
Lasa I, Toledo-Arana A, Gingeras TR (2012) An effort to make sense of antisense transcription in bacteria. RNA Biol 9(8):1039–1044. doi:10.4161/rna.21167
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464(7286):250–255. doi:10.1038/nature08756
Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Hartig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rugheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stulke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Volker U, Bessieres P, Noirot P (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335(6072):1103–1106. doi:10.1126/science.1206848
Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE 4(10):e7526. doi:10.1371/journal.pone.0007526
Dornenburg JE, Devita AM, Palumbo MJ, Wade JT (2010) Widespread antisense transcription in Escherichia coli. MBio 1 (1). doi:10.1128/mBio.00024-10
O’Carroll D, Schaefer A (2013) General principals of miRNA biogenesis and regulation in the brain. Neuropsychopharmacology 38(1):39–54. doi:10.1038/npp.2012.87
Gantier MP, Williams BR (2007) The response of mammalian cells to double-stranded RNA. Cytokine Growth Factor Rev 18(5–6):363–371. doi:10.1016/j.cytogfr.2007.06.016
Li JB, Church GM (2013) Deciphering the functions and regulation of brain-enriched A-to-I RNA editing. Nat Neurosci 16(11):1518–1522. doi:10.1038/nn.3539
Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G (2004) In search of antisense. Trends Biochem Sci 29(2):88–94. doi:10.1016/j.tibs.2003.12.002
Lapidot M, Pilpel Y (2006) Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep 7(12):1216–1222. doi:10.1038/sj.embor.7400857
Morris KV, Santoso S, Turner AM, Pastori C, Hawkins PG (2008) Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 4(11):e1000258. doi:10.1371/journal.pgen.1000258
Froberg JE, Yang L, Lee JT (2013) Guided by RNAs: X-inactivation as a model for lncRNA function. J Mol Biol 425(19):3698–3706. doi:10.1016/j.jmb.2013.06.031
Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175):202–206. doi:10.1038/nature06468
Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, van der Brug MP, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30(5):453–459. doi:10.1038/nbt.2158
Batra R, Charizanis K, Swanson MS (2010) Partners in crime: bidirectional transcription in unstable microsatellite disease. Hum Mol Genet 19(R1):R77–R82. doi:10.1093/hmg/ddq132
Faghihi MA, Wahlestedt C (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10(9):637–643. doi:10.1038/nrm2738
Magistri M, Faghihi MA, St Laurent G 3rd, Wahlestedt C (2012) Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet 28(8):389–396. doi:10.1016/j.tig.2012.03.013
Kung JT, Colognori D, Lee JT (2013) Long noncoding RNAs: past, present, and future. Genetics 193(3):651–669. doi:10.1534/genetics.112.146704
Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P (2013) The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat Rev Microbiol 11(2):75–82. doi:10.1038/nrmicro2934
Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S (2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Res 39(22):9720–9730. doi:10.1093/nar/gkr684
Acknowledgment
This work was supported by GM083187 and P20GM1034865-10 from the NIH and an endowment of the University of Kentucky.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Shen, M., Falaleeva, M., Korotkova, N., Stamm, S. (2015). Direct Cloning of Double-Stranded RNAs. In: Rederstorff, M. (eds) Small Non-Coding RNAs. Methods in Molecular Biology, vol 1296. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2547-6_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2547-6_6
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2546-9
Online ISBN: 978-1-4939-2547-6
eBook Packages: Springer Protocols