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Direct Cloning of Double-Stranded RNAs

  • Protocol
Small Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1296))

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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.

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References

  1. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. 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

    Article  PubMed  Google Scholar 

  3. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. 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

    Article  CAS  PubMed  Google Scholar 

  6. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. 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

    Article  CAS  PubMed  Google Scholar 

  8. 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

    Article  CAS  PubMed  Google Scholar 

  9. 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

    Article  PubMed Central  PubMed  Google Scholar 

  10. Dornenburg JE, Devita AM, Palumbo MJ, Wade JT (2010) Widespread antisense transcription in Escherichia coli. MBio 1 (1). doi:10.1128/mBio.00024-10

  11. 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

    Article  PubMed Central  PubMed  Google Scholar 

  12. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. 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

    Article  CAS  PubMed  Google Scholar 

  15. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. 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

    Article  PubMed Central  PubMed  Google Scholar 

  17. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Faghihi MA, Wahlestedt C (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10(9):637–643. doi:10.1038/nrm2738

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. 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

    Article  CAS  PubMed  Google Scholar 

  25. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgment

This work was supported by GM083187 and P20GM1034865-10 from the NIH and an endowment of the University of Kentucky.

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Correspondence to Stefan Stamm .

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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

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  • 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

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