111
Views
1
CrossRef citations to date
0
Altmetric
Original Article

Identification of novel microRNAs in rice (Oryza sativa) based on the cleavage signals in precursors

, , , , &
Pages 506-513 | Received 01 Jul 2017, Accepted 12 Jul 2018, Published online: 13 Nov 2018

References

  • Alptekin B, Akpinar BA, Budak H. 2017. A comprehensive prescription for plant miRNA identification. Front Plant Sci. 7:2058
  • Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. 2009. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37:D885–D890.
  • Baumann K. 2013. Plant cell biology: mobile miRNAs for stem cell maintenance. Nat Rev Mol Cell Biol. 14:128–129.
  • Budak H, Bulut R, Kantar M, Alptekin B. 2015. miRNA nomenclature and the need for a revised naming prescription. Brief Funct Genomics. 15:65–71.
  • Carthew RW, Sontheimer EJ. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell. 136:642–655.
  • Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, Wu SH. 2010. 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci USA. 107:15269–15274.
  • Chen ZH, Gao XQ, Zhang J. 2015. Alteration of osa-miR156e expression affects rice plant architecture and strigolactones (SLs) pathway. Plant Cell Rep. 34(5):767–781.
  • 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.
  • Coutinho PM, Deleury E, Davies GJ, Henrissat B. 2003. An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 328:307–317.
  • Cuperus JT, Fahlgren N, Carrington JC. 2011. Evolution and functional diversification of MIRNA genes. Plant Cell. 23:431–442.
  • Denman RB. 1993. Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques. 15:1090–1095.
  • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, et al. 2007. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2:e219.
  • Gao S, Yang L, Zeng H, Zhou Z, Yang Z, Li H, Sun D, Xie F, Zhang B. 2016. A cotton miRNA is involved in regulation of plant response to salt stress. Sci Rep. 6:19736.
  • Garcia D. 2008. A miRacle in plant development: role of microRNAs in cell differentiation and patterning. Semin Cell Dev Biol. 19:586–595.
  • 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. 26:941–946.
  • Gong S, Ding Y, Zhu C. 2015. Role of miRNA in plant seed development. Hereditas. 37:554–560.
  • He C, Li YX, Zhang G, Gu Z, Yang R, Li J, Lu ZJ, Zhou ZH, Zhang C, Wang J. 2012. MiRmat: mature microRNA sequence prediction. PLoS One. 7:e51673.
  • Henderson IR, Jacobsen SE. 2008. Sequencing sliced ends reveals microRNA targets. Nat Biotechnol. 26:881–882.
  • Ito Y, Nakanomyo I, Motose H, Iwamoto K, Sawa S, Dohmae N, Fukuda H. 2006. Dodeca-CLE peptides as suppressors of plant stem cell differentiation. Science. 313:842–845.
  • Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell. 14:787–799.
  • Li S, Le B, Ma X, Li S, You C, Yu Y, Zhang B, Liu L, Gao L, Shi T, et al. 2016. Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife. 5:e22750.
  • Ma X, Shao C, Wang H, Jin Y, Meng Y. 2013. Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa). BMC Genomics. 14:510.
  • Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, et al. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 133:116–127.
  • Moseler A, Aller I, Wagner S, Nietzel T, Przybyla-Toscano J, Mühlenhoff U, Lill R, Berndt C, Rouhier N, Schwarzländer M, et al. 2015. The mitochondrial monothiol glutaredoxin S15 is essential for iron-sulfur protein maturation in Arabidopsis thaliana. Proc Natl Acad Sci USA. 112:13735–13740.
  • Park W, Li J, Song R, Messing J, Chen X. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol. 12:1484–1495.
  • Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, et al. 2013. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54:e6.
  • Shao C, Chen M, Meng Y. 2013. A reversed framework for the identification of microRNA-target pairs in plants. Brief Bioinform. 14:293–301.
  • Ströher E, Grassl J, Carrie C, Fenske R, Whelan J, Millar AH. 2016. Glutaredoxin S15 is involved in Fe-S cluster transfer in mitochondria influencing lipoic acid-dependent enzymes, plant growth, and arsenic tolerance in Arabidopsis. Plant Physiol. 170:1284–1299.
  • Voinnet O. 2009. Origin, biogenesis and activity of plant microRNAs. Cell. 136:669–687.
  • Wang Y, Tong X, Qiu J, Li Z, Zhao J, Hou Y, Tang L, Zhang J. 2017. A phosphoproteomic landscape of rice (Oryza sativa) tissues. Physiol Plant. 160(4):458–475.
  • Wang Z, Xing S, Birkenbihl RP, Zachgo S. 2009. Conserved functions of Arabidopsis and rice CC-type glutaredoxins in flower development and pathogen response. Mol Plant. 2:323–335.
  • Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. 2009. Rice microRNA effector complexes and targets. Plant Cell. 21:3421–3435.
  • Xu W, Di C, Zhou S, Liu J, Li L, Liu F, Yang X, Ling Y, Su Z. 2015. Rice transcriptome analysis to identify possible herbicide quinclorac detoxification genes. Front Genet. 6:306.
  • Xuan W, Murphy E, Beeckman T, Audenaert D, Smet ID. 2013. Synthetic molecules: helping to unravel plant signal transduction. J Chem Biol. 6:43–50.
  • Yu L, Meng Y, Shao C, Kahrizi D. 2015. Are ta-siRNAs only originated from the cleavage site of miRNA on its target RNAs and phased in 21-nt increments? Gene. 569:127–135.
  • Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M. 2016. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep. 6:18901.
  • Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR. 2003. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. 31:229–233.
  • Zhang Y. 2005. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res. 33:W701–W704.
  • Zhang Z, Jiang L, Wang J, Chen M. 2014. MTide: an integrated tool for the identification of miRNA-target interaction in plants. Bioinformatics. 31:290–291.
  • Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. 2006. Conservation and divergence of plant microRNA genes. Plant J. 46:243–259.
  • Ziemann M, Bhave M, Zachgo S. 2009. Origin and diversification of land plant CC-type glutaredoxins. Genome Biol Evol. 1:265–277.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.