Identification of cold-inducible microRNAs in plants by transcriptome analysis

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1779, Issue 11, 2008, Pages 780-788

  Zhou, Xuefeng ^a   Wang, Guandong ^a   Sutoh, Keita ^c   Zhu, Jian Kang ^c   Zhang, Weixiong ^a,b  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cis elements; MicroRNAs; Post transcriptional regulation; Stress response; Transcriptome modeling

Indexed keywords

AUXIN; MICRORNA; TRANSCRIPTOME;

ABIOTIC STRESS; ARABIDOPSIS; ARTICLE; COLD; COLD STRESS; LOW TEMPERATURE; NONHUMAN; PLANT; PRIORITY JOURNAL; UPREGULATION;

ARABIDOPSIS; BASE SEQUENCE; COLD TEMPERATURE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; REGULATORY SEQUENCES, RIBONUCLEIC ACID; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; RNA, PLANT;

ARABIDOPSIS THALIANA;

EID: 55049118172     PISSN: 18749399     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2008.04.005     Document Type: Article

References (71)

1. Altman D.G. Practical Statistics for Medical Research (1991), Chapman & Hall/CRC
2. Arguello-Astorga G., and Herrera-Estrella L. Evolution of light-regulated plant promoters. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49 (Jun 1998) 525-555
3. Aukerman M.J., and Sakai H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15 11 (Nov 2003) 2730-2741
4. Axtell M.J., and Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 17 6 (Jun 2005) 1658-1673
5. Baima S., Possenti M., Matteucci A., Wisman E., Altamura M.M., Ruberti I., and Morelli G. The Arabidopsis ATHB-8 HD-zip protein acts as a differentiation-promoting transcription factor of the vascular meristems. Plant Physiol. 126 2 (Jun 2001) 643-655
6. Bari R., Datt Pant B., Stitt M., and Scheible W.R. Pho2, microrna399, and phr1 define a phosphate-signaling pathway in plants. Plant Physiol. 141 3 (Jul 2006) 988-999
7. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 2 (Jan 2004) 281-297
8. Beer M.A., and Tavazoie S. Predicting gene expression from sequence. Cell 117 2 (Apr 2004) 185-198
9. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 1 (Jan 2005) 21-24
10. Bussemaker H.J., Li H., and Siggia E.D. Regulatory element detection using correlation with expression. Nat. Genet. 27 2 (Feb 2001) 167-171
11. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303 5666 (Mar 2004) 2022-2025
12. Chiou T.-J., Aung K., Lin S.-I., Wu C.-C., Chiang S.-F., and Su C.l. Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 18 (2006) 412-421
13. Choi H., Hong J., Ha J., Kang J., and Kim S.Y. ABFs, a family of ABA-responsive element binding factors. J. Biol. Chem. 275 3 (Jan 2000) 1723-1730
14. Dharmasiri S., and Estelle M. The role of regulated protein degradation in auxin response. Plant Mol. Biol. 49 3-4 (Jun-Jul 2002) 401-409
15. Dong J., Chen C., and Chen Z. Expression profiles of the Arabidopsis WRKY gene super-family during plant defense response. Plant Mol. Biol. 51 1 (Jan 2003) 21-37
16. Edwards D., Murray J.A., and Smith A.G. Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiol. 117 3 (Jul 1998) 1015-1022
17. Finkelstein R.R., Gampala S.S., and Rock C.D. Abscisic acid signaling in seeds and seedlings. Plant Cell 14 Suppl (2002) S15-S45
18. Fujii H., Chiou T.J., and Zhu J.K. A miRNA involved in phosphate starvation response in Arabidopsis. Curr. Biol. 15 (2005) 2038-2043
19. Guiltinan M.J., Marcotte W.R., and Quatrano R.S. A plant leucine zipper protein that recognizes an abscisic acid response element. Science 250 4978 (Oct 1990) 267-271
20. Guo H.S., Xie Q., Fei J.F., and Chua N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17 5 (May 2005) 1376-1386
21. Guyon I., and Elisseeff A. An introduction to variable and feature selection. Mach. Learn. 3 (2003) 1157-1182
22. Hertel J., and Stadler P.F. Hairpins in a haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 22 14 (Jul 2006) e197-e202
23. Higo K., Ugawa Y., Iwamoto M., and Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27 1 (Jan 1999) 297-300
24. Hwang E.W., Kim K.A., Park S.C., Jeong M.J., Byun M.O., and Kwon H.B. Expression profiles of hot pepper (Capsicum annum) genes under cold stress conditions. J. Biosci. 30 5 (Dec 2005) 657-667
25. John B., Enright A.J., Aravin A., Tuschl T., Sander C., and Marks D.S. Human microRNA targets. PLoS Biol. 2 11 (Nov 2004) e363
26. Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 6 (Jun 2004) 787-799
27. Jones-Rhoades M.W., Bartel D.P., and Bartel B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57 (2006) 19-53
28. Kang J., and Dengler N. Cell cycling frequency and expression of the homeobox gene ATHB-8 during leaf vein development in Arabidopsis. Planta 216 2 (Dec 2002) 212-219
29. Kepinski S., and Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435 7041 (May 2005) 446-451
30. Kidner C.A., and Martienssen R.A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428 6978 (Mar 2004) 81-84
31. Kilian J., Whitehead D., Horak J., Wanke D., Weinl S., Batistic O., D'Angelo C., Bornberg-Bauer E., Kudla J., and Harter K. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50 2 (Apr. 2007) 347-363
32. Krek A., Grun D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., MacMenamin P., da Piedade I., Gunsalus K.C., Stoffel M., and Rajewsky N. Combinatorial microRNA target predictions. Nat. Genet. 37 5 (May 2005) 495-500
33. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 294 5543 (Oct 2001) 853-858
34. Lee J.Y., Colinas J., Wang J.Y., Mace D., Ohler U., and Benfey P.N. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl. Acad. Sci. U. S. A. 103 15 (Apr 2006) 6055-6060
35. Lee Y., Kim M., Han J., Yeom K.H., Lee S., Baek S.H., and Kim V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23 20 (Oct 2004) 4051-4060
36. Li Y., Lee K.K., Walsh S., Smith C., Hadingham S., Sorefan K., Cawley G., and Bevan M.W. Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine. Genome Res. 16 3 (Mar 2006) 414-427
37. Llave C., Xie Z., Kasschau K.D., and Carrington J.C. Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 5589 (Sep 2002) 2053-2056
38. Lu S., Sun Y.H., Shi R., Clark C., Li L., and Chiang V.L. Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17 8 (Aug 2005) 2186-2203
39. Narusaka Y., Nakashima K., Shinwari Z.K., Sakuma Y., Furihata T., Abe H., Narusaka M., Shinozaki K., and Yamaguchi-Shinozaki K. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34 (2003) 137-148
40. Narusaka Y., Narusaka M., Seki M., Umezawa T., Ishida J., Nakajima M., Enju A., and Shinozaki K. Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray. Plant Mol. Biol. 55 3 (May 2004) 327-342
41. Ng K.L., and Mishra S.K. De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics 23 11 (Jun 2007) 1321-1330
42. Palatnik J.F., Allen E., Wu X., Schommer C., Schwab R., Carrington J.C., and Weigel D. Control of leaf morphogenesis by microRNAs. Nature 425 6955 (Sep 2003) 257-263
43. Park W., Li J., Song R., Messing J., and Chen X. Carpel factory, a dicer homolog, and hen1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12 17 (Sep 2002) 1484-1495
44. Prigge M.J., Otsuga D., Alonso J.M., Ecker J.R., Drews G.N., and Clark S.E. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell 17 1 (Jan 2005) 61-76
45. Rose J.K., Braam J., Fry S.C., and Nishitani K. The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature. Plant Cell Physiol. 43 12 (Dec 2002) 1421-1435
46. Schlkopf B., and Smola A.J. Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond (2001), The MIT Press
47. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., and Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8 4 (Apr 2005) 517-527
48. Shalgi R., Lieber D., Oren M., and Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 3 7 (Jul 2007) e131
49. Shikata M., Matsuda Y., Ando K., Nishii A., Takemura M., Yokota A., and Kohchi T. Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family. J. Exp. Bot. 55 397 (Mar 2004) 631-639
50. Shinozaki K., Yamaguchi-Shinozaki K., and Seki M. Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6 5 (Oct 2003) 410-417
51. Sunkar R., and Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16 8 (Aug 2004) 2001-2019
52. Swindell W.R. The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana. Genetics 174 4 (Dec 2006) 1811-1824
53. Teakle G.R., and Kay S.A. The GATA-binding protein CGF-1 is closely related to GT-1. Plant Mol. Biol. 29 6 (Dec 1995) 1253-1266
54. Terzaghi W.B., and Cashmore A.R. Light-regulated transcription. Ann. Rev. Plant Physiol. Plant Mol. Biol. 46 (1995) 445-474
55. Tsang J., Zhu J., and van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 26 5 (Jun 2007) 753-767
56. Vaucheret H., Vazquez F., Crete P., and Bartel D.P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18 10 (May 2004) 1187-1197
57. Vissenberg K., Oyama M., Osato Y., Yokoyama R., Verbelen J.P., and Nishitani K. Differential expression of AtXTH17, AtXTH18, AtXTH19 and AtXTH20 genes in Arabidopsis roots. Physiological roles in specification in cell wall construction. Plant Cell Physiol. 46 1 (Jan 2005) 192-200
58. Walther D., Brunnemann R., and Selbig J. The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana. PLoS Genet. 3 2 (Feb 2007) e11
59. Wang G., Yu T., and Zhang W. WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Nucleic Acids Res. 33 (Jul 2005) W412-W416 (Web Server issue)
60. Wang G., and Zhang W. A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Genome Biol. 7 6 (2006) R49
61. Xie Q., Frugis G., Colgan D., and Chua N.H. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 14 23 (Dec 2000) 3024-3036
62. Xie Q., Guo H.S., Dallman G., Fang S., Weissman A.M., and Chua N.H. SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 419 6903 (Sep 2002) 167-170
63. Xie Z., Allen E., Fahlgren N., Calamar A., Givan S.A., and Carrington J.C. Expression of Arabidopsis MIRNA genes. Plant Physiol. 138 4 (Aug 2005) 2145-2154
64. Xie Z., Kasschau K.D., and Carrington J.C. Negative feedback regulation of Dicer-like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 13 9 (Apr 2003) 784-789
65. Xie Z., Zhang Z.L., Zou X., Huang J., Ruas P., Thompson D., and Shen Q.J. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol. 137 1 (Jan 2005) 176-189
66. Zhang J.Z., Creelman R.A., and Zhu J.K. From laboratory to field. Using information from Arabidopsis to engineer salt, cold, and drought tolerance in crops. Plant Physiol. 135 2 (Jun 2004) 615-621
67. Zhang W., Ruan J., Ho ThD., You Y., Yu T., and Quatrano R.S. Cis-regulatory element based targeted gene finding: genome-wide identification of aba- and abiotic stress-responsive genes in Arabidopsis thaliana. Bioinformatics 21 14 (2005) 3074-3081
68. Zhou X., Ruan J., Wang G., and Zhang W. Categorization and identification of microRNA core promoters in four model species. PLoS Comput. Biol. 3 3 (2007) e37
69. Zhou X., Wang G., and Zhang W. UV-B responsive microRNA genes in Arabidopsis thaliana. Mol. Syst. Biol. 3 (2007) 103
70. Zhou X., and Zhang W. Combinatory Circuits of miRNAs and Transcription Factors in Plant Gene Regulations. Proceeding of the Third Annual RECOMB Satellite Conference on Systems Biology (Nov 30-Dec 1 2007)
71. Zilberstein C.B., Ziv-Ukelson M., Pinter R.Y., and Yakhini Z. A high-throughput approach for associating MicroRNAs with their activity conditions. J. Comput. Biol. 13 2 (Mar 2006) 245-266