Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in Phalaenopsis Orchid

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  An, Feng Ming ^a,b   Hsiao, Shuan Rung ^a,b   Chan, Ming Tsair ^a,b,c  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b Academia Sinica Biotechnology Center in Southern Taiwan   (Taiwan)

^c AGRICULTURAL BIOTECHNOLOGY RESEARCH CENTER   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 156; MICRORNA 162; MICRORNA 528; MICRORNA 535; PLANT RNA; SMALL UNTRANSLATED RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; COLD ACCLIMATIZATION; CONTROLLED STUDY; ENVIRONMENTAL TEMPERATURE; FLOWERING; GENE FUNCTION; GENE IDENTIFICATION; LOW TEMPERATURE; NONHUMAN; ORCHIDACEAE; PHALAENOPSIS APHRODITE; PLANT GENOME; PLANT REPRODUCTION; PLANT RESPONSE; RNA ANALYSIS; RNA HYBRIDIZATION; RNA SEQUENCE; TEMPERATURE SENSE; TISSUE SPECIFICITY; TRANSCRIPTOMICS; VEGETATIVE STAGE; GENE EXPRESSION REGULATION; GENETICS; TEMPERATURE;

ORCHIDACEAE; PHALAENOPSIS; PHALAENOPSIS APHRODITE SUBSP. FORMOSANA;

GENE EXPRESSION REGULATION, PLANT; MICRORNAS; ORCHIDACEAE; RNA, PLANT; TEMPERATURE;

EID: 79955841150     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018937     Document Type: Article

References (43)

1. Sun W, Julie Li YS, Huang HD, Shyy JY, Chien S, (2010) microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng 12: 1-27.
2. Padmanabhan C, Zhang X, Jin H, (2009) Host small RNAs are big contributors to plant innate immunity. Curr Opin Plant Biol 12: 465-472.
3. Jamalkandi SA, Masoudi-Nejad A, (2009) Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway. Funct Integr Genomics 9: 419-432.
4. Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
5. Blanchard MG, Runkle ES, (2006) Temperature during the day, but not during the night, controls flowering of Phalaenopsis orchids. J Exp Bot 57: 4043-4049.
6. Chen WH, Tseng YC, Liu YC, Chuo CM, Chen PT, et al. (2008) Cool-night temperature induces spike emergence and affects photosynthetic efficiency and metabolizable carbohydrate and organic acid pools in Phalaenopsis aphrodite. Plant Cell Rep 27: 1667-1675.
7. Sunkar R, Kapoor A, Zhu JK, (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065.
8. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC, (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14: 836-843.
9. Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W, (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779: 780-788.
10. Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, et al. (2006) Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell 18: 412-421.
11. Kawashima CG, Yoshimoto N, Maruyama-Nakashita A, Tsuchiya YN, Saito K, et al. (2009) Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J 57: 313-321.
12. Liang G, Yang F, Yu D, (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. Plant J 62: 1046-1057.
13. Lee H, Yoo SJ, Lee JH, Kim W, Yoo SK, et al. (2010) Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis. Nucleic Acids Res 38: 3081-3093.
14. Glazinska P, Zienkiewicz A, Wojciechowski W, Kopcewicz J, (2009) The putative miR172 target gene InAPETALA2-like is involved in the photoperiodic flower induction of Ipomoea nil. J Plant Physiol 166: 1801-1813.
15. Mathieu J, Yant LJ, Murdter F, Kuttner F, Schmid M, (2009) Repression of flowering by the miR172 target SMZ. PLoS Biol 7: e1000148.
16. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136-140.
17. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL, (2007) GenBank. Nucleic Acids Res 35: D21-25.
18. Xie F, Frazier TP, Zhang B, (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232: 417-434.
19. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA, (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
20. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL, (2008) The Vienna RNA websuite. Nucleic Acids Res 36: W70-74.
21. Aukerman MJ, Sakai H, (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
22. Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LE, da Silva MJ, et al. (2010) Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biol 10: 260.
23. Liu B, Li P, Li X, Liu C, Cao S, et al. (2005) Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol 139: 296-305.
24. Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, et al. (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5: e1000716.
25. Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, et al. (2005) Cloning and characterization of micro-RNAs from moss. Plant J 43: 837-848.
26. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
27. Cheng Y, Kato N, Wang W, Li J, Chen X, (2003) Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana. Dev Cell 4: 53-66.
28. Deal RB, Topp CN, McKinney EC, Meagher RB, (2007) Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 19: 74-83.
29. Risseeuw EP, Daskalchuk TE, Banks TW, Liu E, Cotelesage J, et al. (2003) Protein interaction analysis of SCF ubiquitin E3 ligase subunits from Arabidopsis. Plant J 34: 753-767.
30. Wu G, Park MY, Conway SR, Wang JW, Weigel D, et al. (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138: 750-759.
31. Chen X, (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
32. Jung JH, Seo YH, Seo PJ, Reyes JL, Yun J, et al. (2007) The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19: 2736-2748.
33. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, et al. (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
34. Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, et al. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32: e175.
35. Yang H, Schmuke JJ, Flagg LM, Roberts JK, Allen EM, et al. (2009) A novel real-time polymerase chain reaction method for high throughput quantification of small regulatory RNAs. Plant Biotechnol J 7: 621-630.
36. Barlow JJ, Mathias AP, Williamson R, Gammack DB, (1963) A Simple Method for the Quantitative Isolation of Undegraded High Molecular Weight Ribonucleic Acid. Biochem Biophys Res Commun 13: 61-66.
37. Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, et al. (2010) 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107: 15269-15274.
38. Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, et al. (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17: 997-1003.
39. Hsu CC, Chung YL, Chen TC, Lee YL, Kuo YT, et al. (2011) An overview of the Phalaenopsis orchid genome through BAC end sequence analysis. BMC Plant Biol 11: 3.
40. Lau NC, Lim LP, Weinstein EG, Bartel DP, (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
41. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
42. Dai X, Zhuang Z, Zhao PX, (2010) Computational analysis of miRNA targets in plants: current status and challenges. Brief Bioinform.
43. Llave C, Xie Z, Kasschau KD, Carrington JC, (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.