| [1] Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281-297.
[2] German M A, Pillay M, Jeong D H, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nature Biotechnology, 2008, 26(8): 941-946.
[3] Lu T, Cui L, Zhou Y, et al. Transcriptome-wide investigation of circular RNAs in rice. RNA, 2015, 21(12): 2076-2087.
[4] Han R, Jian C, Lv J, et al. Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics, 2014, 15: 289.
[5] Barros-Carvalho G A, Paschoal A R, Marcelino-Guimaraes F C, et al. Prediction of potential novel microRNAs in soybean when in symbiosis. Genetics and Molecular Research, 2014, 13(4): 8519-8529.
[6] Long R C, Li M N, Kang J M, et al. Small RNA deep sequencing identifies novel and salt-stress-regulated microRNAs from roots of Medicago sativa and Medicago truncatula. Physiologia Plantarum, 2015, 154(1): 13-27.
[7] Ren Y, Sun F, Hou J, et al. Differential profiling analysis of miRNAs reveals a regulatory role in low N stress response of Populus. Functional & Integrative Genomics, 2015, 15(1): 93-105.
[8] Chen L N, Dong H P, Huang K X, et al. Transcriptomic analyses of nitrogen assimilation processes in a Chinese strain of Aureococcus anophagefferens. Genomics Data, 2015, 5: 344-345.
[9] Lee Y, Ahn C, Han J, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature, 2003, 425(6956): 415-419.
[10] Zeng Y, Wagner E J, Cullen B R. Both natural and designed microRNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Molecular Cell, 2002, 9(6): 1327-1333.
[11] Zeng Y, Yi R, Cullen B R. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(17): 9779-9784.
[12] Carrington J C, Ambros V. Role of microRNAs in plant and animal development. Science, 2003, 301(5631): 336-338.
[13] Hirsch J, Lefort V, Vankersschaver M, et al. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiology, 2006, 140(4): 1192-1204.
[14] Sunkar R, Zhu J K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell, 2004, 16(8): 2001-2019.
[15] Wang X J, Reyes J L, Chua N H, et al. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology, 2004, 5(9): R65.
[16] Chiou T J, Aung K, Lin S I, et al. Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. The Plant Cell, 2006, 18(2): 412-421.
[17] Schauer S E, Jacobsen S E, Meinke D W, et al. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends in Plant Science, 2002, 7(11): 487-491.
[18] Chen S, Lesnik E A, Hall T A, et al. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems, 2002, 65(2-3): 157-177.
[19] Jones-Rhoades M W, Bartel D P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell, 2004, 14(6): 787-799.
[20] Zhou X, Wang G, Sutoh K, et al. Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. 2008, 1779(11): 780-788.
[21] Fujii H, Chiou T J, Lin S I, et al. A miRNA involved in phosphate-starvation response in Arabidopsis. Current Biology, 2005, 15(22): 2038-2043.
[22] Lu S, Sun Y H, Chiang V L. Stress-responsive microRNAs in Populus. The Plant Journal, 2008, 55(1): 131-151.
[23] Zhao B, Liang R, Ge L, et al. Identification of drought-induced microRNAs in rice. Biochemical and Biophysical Research Communications, 2007, 354(2): 585-590.
[24] Navarro L, Dunoyer P, Jay F, et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science, 2006, 312(5772): 436-439.
[25] Fahlgren N, Howell M D, Kasschau K D, et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One, 2007, 2(2): e219.
[26] Lu S, Sun Y H, Amerson H, et al. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development. The Plant Journal, 2007, 51(6): 1077-1098.
[27] Usha S, Jyothi M N, Sharadamma N, et al. Identification of microRNAs and their targets in Finger millet by high throughput sequencing. Gene, 2015, 574(2): 210-216.
[28] Morton T, Petricka J, Corcoran D L, et al. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. The Plant Cell, 2014, 26(7): 2746-2760.
[29] Hieno A, Naznin H A, Hyakumachi M, et al. ppdb: plant promoter database version 3.0. Nucleic Acids Research, 2014, 42(Database issue): D1188-D1192.
[30] Yamamoto Y Y, Yoshitsugu T, Sakurai T, et al. Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. The Plant Journal, 2009, 60(2): 350-362.
[31] Kumari S, Ware D. Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PLoS One, 2013, 8(10): e79011.
[32] Liu Y, Wei L, Batzoglou S, et al. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research, 2004, 32(Web Server issue): W204-W207.
[33] Xie Z, Allen E, Fahlgren N, et al. Expression of Arabidopsis MIRNA genes. Plant Physiology, 2005, 138(4): 2145-2154.
[34] Megraw M, Baev V, Rusinov V, et al. MicroRNA promoter element discovery in Arabidopsis. RNA, 2006, 12(9): 1612-1619.
[35] Devi S J, Madhav M S, Kumar G R, et al. Identification of abiotic stress miRNA transcription factor binding motifs (TFBMs) in rice. Gene, 2013, 531(1): 15-22.
[36] Zeng H Q, Zhu Y Y, Huang S Q, et al. Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.). Journal of Plant Physiology, 2010, 167(15): 1289-1297.
[37] Goodstein D M, Shu S, Howson R, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 2012, 40(Database issue): D1178-D1186.
[38] Han Y Q, Hu Z, Zheng D F, et al. Analysis of promoters of microRNAs from a Glycine max degradome library. Journal of Zhejiang University Science B, 2014, 15(2): 125-132.
[39] Zhao X, Zhang H, Li L. Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis. Genomics, 2013, 101(3): 187-194.
[40] Devi S J, Madhav M S, Kumar G R, et al. Identification of abiotic stress miRNA transcription factor binding motifs (TFBMs) in rice. Gene, 2013, 531(1): 15-22.
[41] Zhao X, Li L. Comparative analysis of microRNA promoters in Arabidopsis and rice. Genomics, Proteomics & Bioinformatics. 2013, 11(1): 56-60.
[42] Kanjanawattanawong S, Tangphatsornruang S, Triwitayakorn K, et al. Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis. Molecular Genetics and Genomics, 2014, 289(5): 921-933.
[43] Higo K, Ugawa Y, Iwamoto M, et al. PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Research, 1998, 26(1): 358-359.
[44] Rombauts S, Dehais P, Van Montagu M, et al. PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Research, 1999, 27(1): 295-296.
[45] Okumura T, Makiguchi H, Makita Y, et al. Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Research, 2007, 35(Web Server issue): W227-W231.
[46] Lescot M, Dehais P, Thijs G, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 2002, 30(1): 325-327.
[47] Zhou M, Sun J, Wang Q H, et al. Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes. FEBS Journal, 2011, 278(6): 929-940.
[48] Schoof H, Ernst R, Nazarov V, et al. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Research, 2004, 32(Database issue): D373-D376.
[49] Wang Y, Hindemitt T, Mayer K F. Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs. Bioinformatics, 2006, 22(21): 2585-2589. |
