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Rapid and Parallel Quantification of Small and Large RNA Species

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1158))

Abstract

Quantitative real-time PCR (qRT-PCR) is a common technique for mRNA quantification. Several methods have been developed in the past few years in order to adapt qRT-PCR also for small non-coding RNAs (sRNA). We here provide a simple and sensitive protocol that allows quantification of mRNAs, selected sRNAs, and long non-coding RNAs (lncRNA) in one cDNA sample by qRT-PCR.

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References

  1. Chen X (2010) Small RNAs – secrets and surprises of the genome. Plant J 61(6):941–958. doi:10.1111/j.1365-313X.2009.04089.x

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4):669–687, http://dx.doi.org/10.1016/j.cell.2009.01.046

    Article  CAS  PubMed  Google Scholar 

  3. Staiger D, Koster T (2011) Spotlight on post-transcriptional control in the circadian system. Cell Mol Life Sci 68(1):71–83. doi:10.1007/s00018-010-0513-5

    Article  CAS  PubMed  Google Scholar 

  4. Sire C, Moreno AB, Garcia-Chapa M, Lopez-Moya JJ, San Segundo B (2009) Diurnal oscillation in the accumulation of Arabidopsis microRNAs, miR167, miR168, miR171 and miR398. FEBS Lett 583(6):1039–1044. doi:10.1016/j.febslet.2009.02.024

    Article  CAS  PubMed  Google Scholar 

  5. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10(2):R17. doi:10.1186/gb-2009-10-2-r17

    Article  PubMed Central  PubMed  Google Scholar 

  6. Khraiwesh B (2012) Use of northern blotting for specific detection of small RNA molecules in transgenic plants. In: Dunwell JM, Wetten AC (eds) Transgenic plants, vol 847, Methods in molecular biology. Humana Press, Totowa, NJ, pp 25–32. doi:10.1007/978-1-61779-558-9_3

    Chapter  Google Scholar 

  7. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem–loop RT–PCR. Nucleic Acids Res 33(20):e179. doi:10.1093/nar/gni178

    Article  PubMed Central  PubMed  Google Scholar 

  8. Chiang RSVL (2005) Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39(4):19–525

    Google Scholar 

  9. Liu H-H, Tian X, Li Y-J, Wu C-A, Zheng C-C (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14(5):836–843. doi:10.1261/rna.895308

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Lu C, Souret F (2010) High-throughput approaches for miRNA expression analysis. Methods Mol Biol 592:107–125. doi:10.1007/978-1-60327-005-2_8

    Article  CAS  PubMed  Google Scholar 

  11. Adhikari S, Turner M, Subramanian S (2013) Hairpin priming is better-suited than in vitro polyadenylation to generate cDNA for plant miRNA qPCR. Mol Plant 6:229–231. doi:10.1093/mp/sss106

    Article  CAS  PubMed  Google Scholar 

  12. Feldmesser E, Leshkowitz D, Parmet Y, Horn-Saban S (2012) Major differences in microRNA quantification are platform and sequence dependent. BMC Proc 6(Suppl 6):P7

    Article  PubMed Central  Google Scholar 

  13. Zhang W, Gao S, Zhou X, Chellappan P, Chen Z, Zhou X, Zhang X, Fromuth N, Coutino G, Coffey M, Jin H (2011) Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol 75(1–2):93–105. doi:10.1007/s11103-010-9710-8

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Varkonyi-Gasic E, Wu R, Wood M, Walton E, Hellens R (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3(1):12

    Article  PubMed Central  PubMed  Google Scholar 

  15. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162(1):156–159. doi:10.1016/0003-2697(87)90021-2

    Article  CAS  PubMed  Google Scholar 

  16. Pfaffl MW (2006) Relative quantification. In: Dorak T (ed) Real-time PCR. International University Line, San Diego, CA, pp 63–82

    Google Scholar 

  17. Gould PD, Locke JCW, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar AJ, Hall A (2006) The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell Online 18(5):1177–1187. doi:10.1105/tpc.105.039990

    Article  CAS  Google Scholar 

  18. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139(1):5–17. doi:10.1104/pp. 105.063743

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24(11):4333–4345. doi:10.1105/tpc.112.102855

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Pant BD, Musialak-Lange M, Nuc P, May P, Buhtz A, Kehr J, Walther D, Scheible W-R (2009) Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol 150(3):1541–1555. doi:10.1104/pp. 109.139139

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the DFG (LA2633-1/2) and the Max Planck Society (MPG)—Chemical Genomics Centre (CGC) through its supporting companies AstraZeneca, Bayer CropScience, Bayer Healthcare, Boehringer-Ingelheim, and Merck-Serono.

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Correspondence to Sascha Laubinger .

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Speth, C., Laubinger, S. (2014). Rapid and Parallel Quantification of Small and Large RNA Species. In: Staiger, D. (eds) Plant Circadian Networks. Methods in Molecular Biology, vol 1158. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0700-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-0700-7_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0699-4

  • Online ISBN: 978-1-4939-0700-7

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