Ethylene-responsive miRNAs in roots of Medicago truncatula identified by high-throughput sequencing at whole genome level

Plant Science

Volumn 184, Issue , 2012, Pages 14-19

  Chen, Lei ^a,b   Wang, Tianzuo ^a,b   Zhao, Mingui ^a   Zhang, Wenhao ^a  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Ethylene; High throughput sequencing; Medicago truncatula; MicroRNA

Indexed keywords

1 AMINOCYCLOPROPANECARBOXYLIC ACID; 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID; AMINO ACID; ETHYLENE; ETHYLENE DERIVATIVE; MICRORNA;

ARTICLE; BARREL MEDIC; CHEMISTRY; CONFORMATION; DRUG EFFECT; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENOME; PLANT ROOT; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SEEDLING;

AMINO ACIDS, CYCLIC; BASE SEQUENCE; ETHYLENES; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MEDICAGO TRUNCATULA; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLANT ROOTS; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEEDLING;

MEDICAGO TRUNCATULA;

EID: 84855161443     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2011.11.007     Document Type: Article

References (42)

1. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
2. Lee R.C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294:862-864.
3. Llave C., Kasschau K.D., Rector M.A., Carrington J.C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 2002, 14:1605-1619.
4. Lee H.C., Li L., Gu W., Xue Z., Crosthwaite S.K., Pertsemlidis A., Lewis Z.A., Freitag M., Selker E.U., Mello C.C., Liu Y. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol. Cell 2010, 38:803-814.
5. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
6. Liu D., Song Y., Chen Z., Yu D. Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol. Plant 2009, 136:223-236.
7. Reyes J.L., Chua N.H. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J. 2007, 49:592-606.
8. Subramanian S., Fu Y., Sunkar R., Barbazuk W.B., Zhu J.K., Yu O. Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics 2008, 9:160.
9. Wang J.W., Wang L.J., Mao Y.B., Cai W.J., Xue H.W., Chen X.Y. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 2005, 17:2204-2216.
10. Chen L., Wang T., Zhao M., Tian Q., Zhang W.H. Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. Planta 2011, 10.1007/s00425-011-1514-9.
11. Jian X., Zhang L., Li G., Wang X., Cao X., Fang X., Chen F. Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 2010, 95:47-55.
12. Li W.X., Oono Y., Zhu J., He X.J., Wu J.M., Iida K., Lu X.Y., Cui X., Jin H., Zhu J.K. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 2008, 20:2238-2251.
13. Liu H.H., Tian X., Li Y.J., Wu C.A., Zheng C.C. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 2008, 14:836-843.
14. Wang T., Chen L., Zhao M., Tian Q., Zhang W.H. Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 2011, 12:367.
15. 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.
16. Achard P., Herr A., Baulcombe D.C., Harberd N.P. Modulation of floral development by a gibberellin-regulated microRNA. Development 2004, 131:3357-3365.
17. Wang K.L., Li H., Ecker J.R. Ethylene biosynthesis and signaling networks. Plant Cell 2002, 14(Suppl.):S131-S151.
18. Swarup R., Perry P., Hagenbeek D., Van Der Straeten D., Beemster G.T., Sandberg G., Bhalerao R., Ljung K., Bennett M.J. Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 2007, 19:2186-2196.
19. Sun P., Tian Q.Y., Zhao M.G., Dai X.Y., Huang J.H., Li L.H., Zhang W.H. Aluminum-induced ethylene production is associated with inhibition of root elongation in Lotus japonicus L. Plant Cell Physiol. 2007, 48:1229-1235.
20. Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 2006, 57:19-53.
21. Cook D.R. Medicago truncatula-a model in the making!. Curr. Opin. Plant Biol. 1999, 2:301-304.
22. Lelandais-Briere C., Sorin C., Declerck M., Benslimane A., Crespi M., Hartmann C. Small RNA diversity in plants and its impact in development. Curr. Genomics 2010, 11:14-23.
23. Zhang J., Xu Y., Huan Q., Chong K. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 2009, 10:449.
24. Axtell M.J., Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 2005, 17:1658-1673.
25. Fahlgren N., Howell M.D., Kasschau K.D., Chapman E.J., Sullivan C.M., Cumbie J.S., Givan S.A., Law T.F., Grant S.R., Dangl J.L., Carrington J.C. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2007, 2:e219.
26. Sunkar R., Zhou X., Zheng Y., Zhang W., Zhu J.K. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 2008, 8:25.
27. Szittya G., Moxon S., Santos D.M., Jing R., Fevereiro M.P., Moulton V., Dalmay T. High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 2008, 9:593.
28. Li R., Li Y., Kristiansen K., Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714.
29. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.
30. Allen E., Xie Z., Gustafson A.M., Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221.
31. Dai X., Zhao P.X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011, 39:W155-W159.
32. Meyers B.C., Axtell M.J., Bartel B., Bartel D.P., Baulcombe D., Bowman J.L., Cao X., Carrington J.C., Chen X., Green P.J., Griffiths-Jones S., Jacobsen S.E., Mallory A.C., Martienssen R.A., Poethig R.S., Qi Y., Vaucheret H., Voinnet O., Watanabe Y., Weigel D., Zhu J.K. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20:3186-3190.
33. Guo H.S., Xie Q., Fei J.F., Chua N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 2005, 17:1376-1386.
34. Marin E., Jouannet V., Herz A., Lokerse A.S., Weijers D., Vaucheret H., Nussaume L., Crespi M.D., Maizel A. miR390, Arabidopsis TAS3 tasiRNAs, and their auxin response factor targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 2010, 22:1104-1117.
35. Palatnik J.F., Allen E., Wu X.L., Schommer C., Schwab R., Carrington J.C., Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003, 425:257-263.
36. Nag A., King S., Jack T. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:22534-22539.
37. Sunkar R., Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004, 16:2001-2019.
38. Yoon E.K., Yang J.H., Lim J., Kim S.H., Kim S.K., Lee W.S. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res. 2010, 38:1382-1391.
39. Rodriguez R.E., Mecchia M.A., Debernardi J.M., Schommer C., Weigel D., Palatnik J.F. Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 2010, 137:103-112.
40. Xie Q., Frugis G., Colgan D., Chua N.H. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 2000, 14:3024-3036.
41. Schommer C., Palatnik J.F., Aggarwal P., Chetelat A., Cubas P., Farmer E.E., Nath U., Weigel D. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 2008, 6:1991-2001.
42. Palatnik J.F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Huson D., Carrington J.C., Weigel D. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 2007, 13:115-125.