Skip to main content

Flax Small RNAs

  • 348 Accesses

Part of the Plant Genetics and Genomics: Crops and Models book series (PGG,volume 23)

Abstract

Small RNAs (short RNA molecules, generally, 20-24 nucleotides in length) are the key regulators of numerous biological processes in plants. The most extensively studied small RNAs in plant species are microRNAs (miRNAs), which regulate gene expression at the post-transcriptional level. In flax, miRNAs were predicted on the basis of genome and transcriptome sequencing data. Moreover, high-throughput sequencing of small RNAs and evaluation of miRNA levels using quantitative PCR allowed determination of miRNAs in various tissues and under stress conditions and identification of differentially expressed miRNAs. Furthermore, the target genes of miRNAs were predicted. Obtained results brought important knowledge about the regulation of cell processes in flax plants via miRNA. However, further analysis covering more classes of small RNAs is needed.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-030-23964-0_9
  • Chapter length: 16 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-3-030-23964-0
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   139.99
Price excludes VAT (USA)
Hardcover Book
USD   199.99
Price excludes VAT (USA)
Fig. 9.1
Fig. 9.2
Fig. 9.3

References

  • Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 15(1):78–91

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159

    CAS  PubMed  CrossRef  Google Scholar 

  • Barozai MYK (2012) In silico identification of micrornas and their targets in fiber and oil producing plant flax (Linum usitatissimum L.). Pak J Bot 44:1357–1362

    CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297

    CAS  PubMed  CrossRef  Google Scholar 

  • Barvkar VT, Pardeshi VC, Kale SM, Qiu S, Rollins M, Datla R, Gupta VS, Kadoo NY (2013) Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): characterization of flax miRNA genes. Planta 237(4):1149–1161

    CAS  PubMed  CrossRef  Google Scholar 

  • Bologna NG, Voinnet O (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65:473–503

    CAS  PubMed  CrossRef  Google Scholar 

  • Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16(12):727–741

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR et al (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20):e179

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ et al (2016) miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 44(D1):D239–D247

    CAS  PubMed  CrossRef  Google Scholar 

  • Couzigou JM, Combier JP (2016) Plant microRNAs: key regulators of root architecture and biotic interactions. New Phytol 212(1):22–35

    CAS  PubMed  CrossRef  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Web Server issue):W155–W159

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Dai X, Zhuang Z, Zhao PX (2011) Computational analysis of miRNA targets in plants: current status and challenges. Brief Bioinform 12(2):115–121

    CAS  PubMed  CrossRef  Google Scholar 

  • Datta R, Paul S (2015) Plant microRNAs: master regulator of gene expression mechanism. Cell Biol Int 39(11):1185–1190

    CAS  PubMed  CrossRef  Google Scholar 

  • Die JV, Roman B (2012) RNA quality assessment: a view from plant qPCR studies. J Exp Bot 63(17):6069–6077

    CAS  PubMed  CrossRef  Google Scholar 

  • Fenart S, Ndong YP, Duarte J, Riviere N, Wilmer J, van Wuytswinkel O, Lucau A, Cariou E, Neutelings G, Gutierrez L et al (2010) Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. BMC Genomics 11:592

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R et al (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26(8):941–946

    CAS  PubMed  CrossRef  Google Scholar 

  • Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–D144

    CAS  PubMed  CrossRef  Google Scholar 

  • Hausser J, Zavolan M (2014) Identification and consequences of miRNA-target interactions – beyond repression of gene expression. Nat Rev Genet 15(9):599–612

    CAS  PubMed  CrossRef  Google Scholar 

  • He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522–531

    CAS  PubMed  CrossRef  Google Scholar 

  • Henderson IR, Jacobsen SE (2008) Sequencing sliced ends reveals microRNA targets. Nat Biotechnol 26(8):881–882

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Ito H (2013) Small RNAs and regulation of transposons in plants. Genes Genet Syst 88(1):3–7

    CAS  PubMed  CrossRef  Google Scholar 

  • Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(Database issue):D68–D73

    CAS  PubMed  CrossRef  Google Scholar 

  • Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12(2):206–212

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Li C, Zhang B (2016) MicroRNAs in control of plant development. J Cell Physiol 231(2):303–313

    CAS  PubMed  CrossRef  Google Scholar 

  • Li J, Yang Z, Yu B, Liu J, Chen X (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15(16):1501–1507

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Li J, Reichel M, Li Y, Millar AA (2014) The functional scope of plant microRNA-mediated silencing. Trends Plant Sci 19(12):750–756

    CAS  PubMed  CrossRef  Google Scholar 

  • Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297(5589):2053–2056

    CAS  PubMed  CrossRef  Google Scholar 

  • Ma X, Tang Z, Qin J, Meng Y (2015) The use of high-throughput sequencing methods for plant microRNA research. RNA Biol 12(7):709–719

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Melnikova NV, Belenikin MS, Bolsheva NL, Dmitriev AA, Speranskaya AS, Krinitsina AA, Samatadze TE, Amosova AV, Muravenko OV, Zelenin AV et al (2014) Flax inorganic phosphate deficiency responsive miRNAs. J Agric Sci 6(6):156–160

    Google Scholar 

  • Melnikova NV, Dmitriev AA, Belenikin MS, Speranskaya AS, Krinitsina AA, Rachinskaia OA, Lakunina VA, Krasnov GS, Snezhkina AV, Sadritdinova AF et al (2015) Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L. Biochimie 109:36–41

    CAS  PubMed  CrossRef  Google Scholar 

  • Melnikova NV, Dmitriev AA, Belenikin MS, Koroban NV, Speranskaya AS, Krinitsina AA, Krasnov GS, Lakunina VA, Snezhkina AV, Sadritdinova AF et al (2016) Identification, expression analysis, and target prediction of flax genotroph microRNAs under normal and nutrient stress conditions. Front Plant Sci 7:399

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Moss TY, Cullis CA (2012) Computational prediction of candidate microRNAs and their targets from the completed Linum usitatissimum genome and EST database. J Nucleic Acids Investig 3:e2, 9–17

    CrossRef  Google Scholar 

  • Neutelings G, Fenart S, Lucau-Danila A, Hawkins S (2012) Identification and characterization of miRNAs and their potential targets in flax. J Plant Physiol 169(17):1754–1766

    CAS  PubMed  CrossRef  Google Scholar 

  • Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I (2015) Prediction of miRNA targets. Methods Mol Biol 1269:207–229

    CAS  PubMed  CrossRef  Google Scholar 

  • Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4):513–520

    CAS  PubMed  CrossRef  Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    CAS  PubMed  CrossRef  Google Scholar 

  • Salone V, Rederstorff M (2015) Stem-loop RT-PCR based quantification of small non-coding RNAs. Methods Mol Biol 1296:103–108

    CAS  PubMed  CrossRef  Google Scholar 

  • Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8(4):517–527

    CAS  PubMed  CrossRef  Google Scholar 

  • Shao C, Chen M, Meng Y (2013) A reversed framework for the identification of microRNA-target pairs in plants. Brief Bioinform 14(3):293–301

    CAS  PubMed  CrossRef  Google Scholar 

  • Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z (2015) Amplification-based method for microRNA detection. Biosens Bioelectron 71:322–331

    CAS  PubMed  CrossRef  Google Scholar 

  • Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH (2016) MicroRNAs as potential targets for abiotic stress tolerance in plants. Front Plant Sci 7:817

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Song C, Fang J, Wang C, Guo L, Nicholas KK, Ma Z (2010) MiR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs. PLoS One 5(6):e10861

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Steele AD (1991) Shift in genomic RNA patterns of human rotaviruses isolated from white children in South Africa. S Afr Med J 79(3):143–145

    CAS  PubMed  Google Scholar 

  • Sun X, Zhang Y, Zhu X, Korir NK, Tao R, Wang C, Fang J (2014) Advances in identification and validation of plant microRNAs and their target genes. Physiol Plant 152(2):203–218

    CAS  PubMed  CrossRef  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16(8):2001–2019

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Tang G (2010) Plant microRNAs: an insight into their gene structures and evolution. Semin Cell Dev Biol 21(8):782–789

    CAS  PubMed  CrossRef  Google Scholar 

  • Thomson DW, Bracken CP, Goodall GJ (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res 39(16):6845–6853

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Tong L, Xue H, Xiong L, Xiao J, Zhou Y (2015) Improved RT-PCR assay to quantitate the pri-, pre-, and mature microRNAs with higher efficiency and accuracy. Mol Biotechnol 57(10):939–946

    CAS  PubMed  CrossRef  Google Scholar 

  • Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M et al (2011) Gene expression analysis of flax seed development. BMC Plant Biol 11:74

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R et al (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72(3):461–473

    PubMed  CrossRef  CAS  Google Scholar 

  • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38(3):465–475

    CAS  PubMed  CrossRef  Google Scholar 

  • Xie M, Zhang S, Yu B (2015) microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 72(1):87–99

    CAS  PubMed  CrossRef  Google Scholar 

  • Yang LH, Wang SL, Tang LL, Liu B, Ye WL, Wang LL, Wang ZY, Zhou MT, Chen BC (2014) Universal stem-loop primer method for screening and quantification of microRNA. PLoS One 9(12):e115293

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307(5711):932–935

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Yu Y, Wu G, Yuan H, Cheng L, Zhao D, Huang W, Zhang S, Zhang L, Chen H, Zhang J et al (2016) Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses. BMC Plant Biol 16(1):124

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 66(7):1749–1761

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Res 38(Database issue):D806–D813

    CAS  PubMed  CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Verify currency and authenticity via CrossMark

Cite this chapter

Dmitriev, A.A., Kudryavtseva, A.V., Melnikova, N.V. (2019). Flax Small RNAs. In: Cullis, C. (eds) Genetics and Genomics of Linum. Plant Genetics and Genomics: Crops and Models, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-23964-0_9

Download citation