Bologna NG, Voinnet O. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol. 2014;65:473–503.
Article
CAS
PubMed
Google Scholar
Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W. Transcriptional control of gene expression by microRNAs. Cell. 2010;140(1):111–22.
Article
CAS
PubMed
Google Scholar
Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell. 2009;136(4):669–87.
Article
CAS
PubMed
Google Scholar
Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. Plant J. 2010;62(5):742–59.
Article
CAS
PubMed
Google Scholar
Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843–54.
Article
CAS
PubMed
Google Scholar
Zhang BH, Pan XP, Cobb GP, Anderson TA. Plant microRNA: A small regulatory molecule with big impact. Dev Biol. 2006;289(1):3–16.
Article
CAS
PubMed
Google Scholar
Ambros V. The functions of animal microRNAs. Nature. 2004;431(7006):350–5.
Article
CAS
PubMed
Google Scholar
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, et al. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell. 2010;38(6):803–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cullen BR. Viruses and microRNAs: RISCy interactions with serious consequences. Genes Dev. 2011;25(18):1881–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol. 2006;57:19–53.
Article
CAS
PubMed
Google Scholar
Zhang B, Wang Q, Pan X. MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol. 2007;210(2):279–89.
Article
CAS
PubMed
Google Scholar
Sun G. MicroRNAs and their diverse functions in plants. Plant Mol Biol. 2012;80(1):17–36.
Article
CAS
PubMed
Google Scholar
Briggs WR, Christie JM. Phototropins 1 and 2: versatile plant blue-light receptors. Trends Plant Sci. 2002;7(5):204–10.
Article
CAS
PubMed
Google Scholar
Jenkins GI, Christie JM, Fuglevand G, Long JC, Jackson JA. Plant responses to UV and blue light: biochemical and genetic approaches. Plant Sci. 1995;112(2):117–38.
Article
CAS
Google Scholar
Hayes S, Velanis CN, Jenkins GI, Franklin KA. UV-B detected by the UVR8 photoreceptor antagonizes auxin signaling and plant shade avoidance. Proc Natl Acad Sci U S A. 2014;111(32):11894–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jenkins GI. The UV-B photoreceptor UVR8: from structure to physiology. Plant Cell. 2014;26(1):21–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cashmore AR, Jarillo JA, Wu YJ, Liu D. Cryptochromes: blue light receptors for plants and animals. Science. 1999;284(5415):760–5.
Article
CAS
PubMed
Google Scholar
Lin C, Shalitin D. Cryptochrome structure and signal transduction. Annu Rev Plant Biol. 2003;54:469–96.
Article
CAS
PubMed
Google Scholar
Lin C. Blue light receptors and signal transduction. Plant Cell. 2002;14(Suppl):S207–225.
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Zhou B, Sun M, Li Y, Kawabata S. UV-A light induces anthocyanin biosynthesis in a manner distinct from synergistic blue + UV-B light and UV-A/blue light responses in different parts of the hypocotyls in turnip seedlings. Plant Cell Physiol. 2012;53(8):1470–80.
Article
CAS
PubMed
Google Scholar
Casati P: Analysis of UV-B regulated miRNAs and their targets in maize leaves. Plant Signal Behav 2013, 8(10):doi: 10 4161/psb 26758
Jung JH, Seo YH, Seo PJ, Reyes JL, Yun J, Chua NH, Park CM. The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell. 2007;19(9):2736–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou B, Li Y, Xu Z, Yan H, Homma S, Kawabata S. Ultraviolet A-specific induction of anthocyanin biosynthesis in the swollen hypocotyls of turnip (Brassica rapa). J Exp Bot. 2007;58(7):1771–81.
Article
CAS
PubMed
Google Scholar
Baucher M, Moussawi J, Vandeputte OM, Monteyne D, Mol A, Perez-Morga D, El Jaziri M. A role for the miR396/GRF network in specification of organ type during flower development, as supported by ectopic expression of Populus trichocarpa miR396c in transgenic tobacco. Plant Biol (Stuttg). 2013;15(5):892–8.
Article
CAS
Google Scholar
Casadevall R, Rodriguez RE, Debernardi JM, Palatnik JF, Casati P. Repression of growth regulating factors by the microRNA396 inhibits cell proliferation by UV-B radiation in Arabidopsis leaves. Plant Cell. 2013;25(9):3570–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang H, Zhao X, Li J, Cai H, Deng XW, Li L. MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell. 2014;26(12):4933–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH. Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol. 2012;12:218.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, Prins M, van Tunen A, He Y. Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot. 2012;63(2):1025–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou B, Fan P, Li Y. High-throughput sequence analysis of small RNAs in skotomorphogenic seedlings of Brassica rapa ssp. rapa. Gene. 2014;548(1):68–74.
Article
CAS
PubMed
Google Scholar
Zhou B, Wang Y, Zhan Y, Li Y, Kawabata S. Chalcone synthase family genes have redundant roles in anthocyanin biosynthesis and in response to blue/UV-A light in turnip (Brassica rapa; Brassicaceae). Am J Bot. 2013;100(12):2458–67.
Article
CAS
PubMed
Google Scholar
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. Criteria for annotation of plant MicroRNAs. Plant Cell. 2008;20(12):3186–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang H, He H, Wang X, Yang X, Li L, Deng XW. Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J. 2011;65(3):346–58.
Article
CAS
PubMed
Google Scholar
Wang JW. Regulation of flowering time by the miR156-mediated age pathway. J Exp Bot. 2014;65(17):4723–30.
Article
CAS
PubMed
Google Scholar
Zhou X, Wang G, Zhang W. UV-B responsive microRNA genes in Arabidopsis thaliana. Mol Syst Biol. 2007;3:103.
Article
PubMed
PubMed Central
Google Scholar
Montgomery BL. Sensing the light: photoreceptive systems and signal transduction in cyanobacteria. Mol Microbiol. 2007;64(1):16–27.
Article
CAS
PubMed
Google Scholar
Wei N, Kwok SF, von Arnim AG, Lee A, McNellis TW, Piekos B, Deng XW. Arabidopsis COP8, COP10, and COP11 genes are involved in repression of photomorphogenic development in darkness. Plant Cell. 1994;6(5):629–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nakamura M, Satoh T, Tanaka S, Mochizuki N, Yokota T, Nagatani A. Activation of the cytochrome P450 gene, CYP72C1, reduces the levels of active brassinosteroids in vivo. J Exp Bot. 2005;56(413):833–40.
Article
CAS
PubMed
Google Scholar
Zhang H, Yin W, Xia X. Shaker-like potassium channels in Populus, regulated by the CBL-CIPK signal transduction pathway, increase tolerance to low-K+ stress. Plant Cell Rep. 2010;29(9):1007–12.
Article
CAS
PubMed
Google Scholar
Yang L, Xu M, Koo Y, He J, Poethig RS. Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C. Elife. 2013;2:e00260.
PubMed
PubMed Central
Google Scholar
Yu S, Cao L, Zhou CM, Zhang TQ, Lian H, Sun Y, Wu J, Huang J, Wang G, Wang JW. Sugar is an endogenous cue for juvenile-to-adult phase transition in plants. Elife. 2013;2:e00269.
PubMed
PubMed Central
Google Scholar
Wang H. The miR156/SPL Module, a Regulatory Hub and Versatile Toolbox, Gears up Crops for Enhanced Agronomic Traits. Mol Plant. 2015;8(5):677–88.
Article
CAS
PubMed
Google Scholar
Chen X, Zhang Z, Liu D, Zhang K, Li A, Mao L. SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J Integr Plant Biol. 2010;52(11):946–51.
Article
CAS
PubMed
Google Scholar
Xie K, Shen J, Hou X, Yao J, Li X, Xiao J, Xiong L. Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiol. 2012;158(3):1382–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang JW, Czech B, Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell. 2009;138(4):738–49.
Article
CAS
PubMed
Google Scholar
Wu G, Park MY, Conway SR, Wang JW, Weigel D, Poethig RS. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell. 2009;138(4):750–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo AY, Zhu QH, Gu X, Ge S, Yang J, Luo J. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene. 2008;418(1–2):1–8.
Article
CAS
PubMed
Google Scholar
Schwarz S, Grande AV, Bujdoso N, Saedler H, Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol. 2008;67(1–2):183–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu C, Sunkar R, Zhou C, Shen H, Zhang JY, Matts J, Wolf J, Mann DG, Stewart Jr CN, Tang Y, et al. Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production. Plant Biotechnol J. 2012;10(4):443–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei S, Gruber MY, Yu B, Gao MJ, Khachatourians GG, Hegedus DD, Parkin IA, Hannoufa A. Arabidopsis mutant sk156 reveals complex regulation of SPL15 in a miR156-controlled gene network. BMC Plant Biol. 2012;12:169.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei S, Yu B, Gruber MY, Khachatourians GG, Hegedus DD, Hannoufa A. Enhanced seed carotenoid levels and branching in transgenic Brassica napus expressing the Arabidopsis miR156b gene. J Agric Food Chem. 2010;58(17):9572–8.
Article
CAS
PubMed
Google Scholar
Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011;23(4):1512–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petroni K, Tonelli C. Recent advances on the regulation of anthocyanin synthesis in reproductive organs. Plant Sci. 2011;181(3):219–29.
Article
CAS
PubMed
Google Scholar
Guo N, Cheng F, Wu J, Liu B, Zheng S, Liang J, Wang X. Anthocyanin biosynthetic genes in Brassica rapa. BMC Genomics. 2014;15:426.
Article
PubMed
PubMed Central
Google Scholar
Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics. 2010;11:431.
Article
PubMed
PubMed Central
Google Scholar
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24(5):713–4.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Griffiths-Jones S. miRBase: the microRNA sequence database. Methods Mol Biol. 2006;342:129–38.
CAS
PubMed
Google Scholar
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008;36(Database issue):D154–158.
CAS
PubMed
PubMed Central
Google Scholar
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fan P, ZHOU B, Li Y. A Safer Method for Northern Blot Analysis of MicroRNAs in Turnip Brassica rapa ‘Tsuda’. Fenzi Zhiwu Yuzhong (online) (Molecular Plant Breeding). 2013;11(28):1206–10.
Google Scholar
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005;33(20):e179.
Article
PubMed
PubMed Central
Google Scholar
Gao ZH, Wei JH, Yang Y, Zhang Z, Xiong HY, Zhao WT. Identification of conserved and novel microRNAs in Aquilaria sinensis based on small RNA sequencing and transcriptome sequence data. Gene. 2012;505(1):167–75.
Article
CAS
PubMed
Google Scholar
Lao K, Xu NL, Yeung V, Chen C, Livak KJ, Straus NA. Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Commun. 2006;343(1):85–9.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) Method. Methods. 2001;25(4):402–8.
Article
CAS
PubMed
Google Scholar