Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Meng, Yijun ^a   Shao, Chaogang ^b   Wang, Huizhong ^a   Jin, Yongfeng ^c  

^a HANGZHOU NORMAL UNIVERSITY   (China)

^b HUZHOU UNIVERSITY   (China)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

Arabidopsis (Arabidopsis thaliana); Degradome; MicroRNA; Network; Rice (Oryza sativa); Subnetwork; Target mimic

Indexed keywords

MICRORNA; PLANT RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; BIOINFORMATICS; COMPUTER PREDICTION; CONTROLLED STUDY; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CONSERVATION; RICE; RNA ANALYSIS; RNA SEQUENCE;

ARABIDOPSIS; DATABASES, GENETIC; GENE REGULATORY NETWORKS; MICRORNAS; OPEN READING FRAMES; ORYZA SATIVA; RNA, PLANT; SOFTWARE; UNTRANSLATED REGIONS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA;

EID: 84861216292     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-197     Document Type: Article

References (50)

1. Chen X. Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 2009, 25:21-44. 10.1146/annurev.cellbio.042308.113417, 19575669.
2. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 2006, 57:19-53. 10.1146/annurev.arplant.57.032905.105218, 16669754.
3. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23:4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
4. Meng Y, Huang F, Shi Q, Cao J, Chen D, Zhang J, Ni J, Wu P, Chen M. Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant. Planta 2009, 230:883-898. 10.1007/s00425-009-0994-3, 19655164.
5. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiol 2005, 138:2145-2154. 10.1104/pp.105.062943, 1183402, 16040653.
6. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687. 10.1016/j.cell.2009.01.046, 19239888.
7. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 2007, 39:1033-1037. 10.1038/ng2079, 17643101.
8. Ivashuta S, Banks IR, Wiggins BE, Zhang Y, Ziegler TE, Roberts JK, Heck GR. Regulation of gene expression in plants through miRNA inactivation. PLoS One 2011, 6:e21330. 10.1371/journal.pone.0021330, 3121747, 21731706.
9. Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet 2010, 6:e1001031. 10.1371/journal.pgen.1001031, 2908682, 20661442.
10. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34:D140-144. 10.1093/nar/gkj112, 1347474, 16381832.
11. Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, et al. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001, 29:102-105. 10.1093/nar/29.1.102, 29827, 11125061.
12. Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 2003, 31:229-233. 10.1093/nar/gkg059, 165506, 12519988.
13. Pearson WR. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 1991, 11:635-650. 10.1016/0888-7543(91)90071-L, 1774068.
14. Pearson WR. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000, 132:185-219.
15. Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009, 37:D93-97. 10.1093/nar/gkn787, 2686519, 18984615.
16. He S, Liu C, Skogerbo G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 2008, 36:D170-172. 10.1093/nar/gkn294, 2238973, 18000000.
17. Liu C, Bai B, Skogerbo G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 2005, 33:D112-115. 10.1093/nar/gni113, 539995, 15608158.
18. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190. 10.1101/gr.849004, 419797, 15173120.
19. Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100. 10.1093/nar/18.20.6097, 332411, 2172928.
20. Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010, 38:W64-70. 10.1093/nar/gkq310, 2896167, 20435677.
21. Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 2011, 39:W155-159. 10.1093/nar/gkr319, 3125753, 21622958.
22. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005, 33:W701-704. 10.1093/nar/gki383, 1160144, 15980567.
23. Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M. PmiRKB: a plant microRNA knowledge base. Nucleic Acids Res 2011, 39:D181-187. 10.1093/nar/gkq721, 3013752, 20719744.
24. Meng Y, Gou L, Chen D, Wu P, Chen M. High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism. J Exp Bot 2010, 61:3833-3837. 10.1093/jxb/erq209, 20643809.
25. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
26. Nilsson L, Muller R, Nielsen TH. Dissecting the plant transcriptome and the regulatory responses to phosphate deprivation. Physiol Plant 2010, 139:129-143. 10.1111/j.1399-3054.2010.01356.x, 20113436.
27. Bari R, Datt Pant B, Stitt M, Scheible WR. PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 2006, 141:988-999. 10.1104/pp.106.079707, 1489890, 16679424.
28. Guo HS, Xie Q, Fei JF, Chua NH. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 2005, 17:1376-1386. 10.1105/tpc.105.030841, 1091761, 15829603.
29. Kawashima CG, Matthewman CA, Huang S, Lee BR, Yoshimoto N, Koprivova A, Rubio-Somoza I, Todesco M, Rathjen T, Saito K, et al. Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis. Plant J 2011, 66:863-876. 10.1111/j.1365-313X.2011.04547.x, 21401744.
30. Kawashima CG, Yoshimoto N, Maruyama-Nakashita A, Tsuchiya YN, Saito K, Takahashi H, Dalmay T. Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J 2009, 57:313-321. 10.1111/j.1365-313X.2008.03690.x, 18801012.
31. Koyama T, Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M. TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell 2010, 22:3574-3588. 10.1105/tpc.110.075598, 3015130, 21119060.
32. Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, Rodriguez R, Warthmann N, Allen E, Dezulian T, Huson D, et al. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev Cell 2007, 13:115-125. 10.1016/j.devcel.2007.04.012, 17609114.
33. Jia X, Ren L, Chen QJ, Li R, Tang G. UV-B-responsive microRNAs in Populus tremula. J Plant Physiol 2009, 166:2046-2057. 10.1016/j.jplph.2009.06.011, 19628301.
34. Nikovics K, Blein T, Peaucelle A, Ishida T, Morin H, Aida M, Laufs P. The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 2006, 18:2929-2945. 10.1105/tpc.106.045617, 1693934, 17098808.
35. Pulido A, Laufs P. Co-ordination of developmental processes by small RNAs during leaf development. J Exp Bot 2010, 61:1277-1291. 10.1093/jxb/erp397, 20097843.
36. Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Hoefgen R. Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J 2003, 33:633-650. 10.1046/j.1365-313X.2003.01657.x, 12609038.
37. Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741. 10.1105/tpc.016238, 280575, 14555699.
38. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025. 10.1126/science.1088060, 12893888.
39. Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 2010, 16:43-56. 10.1261/rna.1972910, 2802036, 19917635.
40. Meng Y, Shao C, Gou L, Jin Y, Chen M. Construction of microRNA- and microRNA*-mediated regulatory networks in plants. RNA Biol 2011, 8:1124-1148. 10.4161/rna.8.6.17743, 21955495.
41. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC. The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol 2008, 15:354-363. 10.1038/nsmb.1409, 2698667, 18376413.
42. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC. Widespread regulatory activity of vertebrate microRNA* species. RNA 2011, 17:312-326. 10.1261/rna.2537911, 3022280, 21177881.
43. Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 2007, 354:585-590. 10.1016/j.bbrc.2007.01.022, 17254555.
44. Zhao M, Ding H, Zhu JK, Zhang F, Li WX. Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol 2011, 190:906-915. 10.1111/j.1469-8137.2011.03647.x, 21348874.
45. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37:D885-890. 10.1093/nar/gkn764, 2686538, 18940857.
46. Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 2006, 34:D731-735. 10.1093/nar/gkj077, 1347440, 16381968.
47. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
48. Meng Y, Shao C, Chen M. Toward microRNA-mediated gene regulatory networks in plants. Brief Bioinform 2011, 12:645-659. 10.1093/bib/bbq091, 21262742.
49. German MA, Luo S, Schroth G, Meyers BC, Green PJ. Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 2009, 4:356-362. 10.1038/nprot.2009.8, 19247285.
50. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26:941-946. 10.1038/nbt1417, 18542052.