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.
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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
Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159
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
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297
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
Bologna NG, Voinnet O (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65:473–503
Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16(12):727–741
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
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
Couzigou JM, Combier JP (2016) Plant microRNAs: key regulators of root architecture and biotic interactions. New Phytol 212(1):22–35
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Web Server issue):W155–W159
Dai X, Zhuang Z, Zhao PX (2011) Computational analysis of miRNA targets in plants: current status and challenges. Brief Bioinform 12(2):115–121
Datta R, Paul S (2015) Plant microRNAs: master regulator of gene expression mechanism. Cell Biol Int 39(11):1185–1190
Die JV, Roman B (2012) RNA quality assessment: a view from plant qPCR studies. J Exp Bot 63(17):6069–6077
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
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
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
Hausser J, Zavolan M (2014) Identification and consequences of miRNA-target interactions – beyond repression of gene expression. Nat Rev Genet 15(9):599–612
He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522–531
Henderson IR, Jacobsen SE (2008) Sequencing sliced ends reveals microRNA targets. Nat Biotechnol 26(8):881–882
Ito H (2013) Small RNAs and regulation of transposons in plants. Genes Genet Syst 88(1):3–7
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(Database issue):D68–D73
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
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
Li C, Zhang B (2016) MicroRNAs in control of plant development. J Cell Physiol 231(2):303–313
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
Li J, Reichel M, Li Y, Millar AA (2014) The functional scope of plant microRNA-mediated silencing. Trends Plant Sci 19(12):750–756
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
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
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
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
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
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
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
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
Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4):513–520
Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510
Salone V, Rederstorff M (2015) Stem-loop RT-PCR based quantification of small non-coding RNAs. Methods Mol Biol 1296:103–108
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
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
Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z (2015) Amplification-based method for microRNA detection. Biosens Bioelectron 71:322–331
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
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
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
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
Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16(8):2001–2019
Tang G (2010) Plant microRNAs: an insight into their gene structures and evolution. Semin Cell Dev Biol 21(8):782–789
Thomson DW, Bracken CP, Goodall GJ (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res 39(16):6845–6853
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
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
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
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
Xie M, Zhang S, Yu B (2015) microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 72(1):87–99
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
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
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
Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 66(7):1749–1761
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
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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
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DOI: https://doi.org/10.1007/978-3-030-23964-0_9
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