Identification of conserved Aquilegia coerulea microRNAs and their targets

Gene

Volumn 448, Issue 1, 2009, Pages 46-56

  Puzey, Joshua R ^a   Kramer, Elena M ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Angiosperm; Aquilegia; Evolution; microRNA

Indexed keywords

AUXIN; MICRORNA; TRANSCRIPTION FACTOR;

AQUILEGIA; AQUILEGIA COERULEA; ARTICLE; CELL TRANSPORT; CONTROLLED STUDY; GENE FUNCTION; GENE LOCUS; GENE TARGETING; GENOMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PLANT GENETICS; PLANT METABOLISM; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STRESS;

AQUILEGIA; BASE SEQUENCE; CARBOHYDRATE CONFORMATION; DATABASES, NUCLEIC ACID; GENOME, PLANT; MICRORNAS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, PLANT;

AQUILEGIA; AQUILEGIA COERULEA; ARABIDOPSIS; MAGNOLIOPHYTA; ORYZA;

EID: 70349786509     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.08.005     Document Type: Article

References (58)

1. 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 (2003) 2730-2741
2. Axtell M.J., and Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 17 (2005) 1658-1673
3. Axtell M.J., and Bowman J.L. Evolution of plant microRNAs and their targets. Trends Plant Sci. 13 (2008) 343-349
4. Axtell M.J., Snyder J.A., and Bartel D.P. Common functions for diverse small RNAs of land plants. Plant Cell 19 (2007) 1750-1769
5. Barakat A., Wall P.K., Diloreto S., Depamphilis C.W., and Carlson J.E. Conservation and divergence of microRNAs in Populus. BMC Genomics 8 (2007) 481
6. Barakat A., Wall K., Leebens-Mack J., Wang Y.J., Carlson J.E., and Depamphilis C.W. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J. 51 (2007) 991-1003
7. Boualem A., et al. MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J. 54 (2008) 876-887
8. Cartolano M., et al. A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity. Nat. Genet. 39 (2007) 901-905
9. Chaw S.M., Chang C.C., Chen H.L., and Li W.H. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol. Evol. 58 (2004) 424-441
10. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303 (2004) 2022-2025
11. Ding D., Zhang L., Wang H., Liu Z., Zhang Z., and Zheng Y. Differential expression of miRNAs in response to salt stress in maize roots. Ann. Bot. (Lond.) 103 (2009) 29-38
12. Fahlgren N., et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE e219 (2007) 2
13. Gandikota M., Birkenbihl R.P., Hohmann S., Cardon G.H., Saedler H., and Huijser P. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 49 (2007) 683-693
14. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 32 (2004) D109-D111
15. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., and Enright A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34 (2006) D140-D144
16. Griffiths-Jones S., Saini H.K., van Dongen S., and Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (2008) D154-D158
17. Guo A.Y., Zhu Q.H., Gu X., Ge S., Yang J., and Luo J. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 418 (2008) 1-8
18. Hodges S.A., and Arnold M.L. Columbines-a geographically widespread species flock. Proc. Natl. Acad. Sci. 91 (1994) 5129-5132
19. Hodges S.A., and Arnold M.L. Floral and ecological isolation between Aquilegia formosa and Aquilegia pubescens. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 2493-2496
20. Hodges S.A., and Kramer E.M. Columbines. Curr. Biol. 17 (2007) R992-R994
21. Hodges S.A., Fulton M., Yang J.Y., and Whittal JB. Verne Grant and evolutionary studies of Aquilegia. New Phytologist (2003) 113-120
22. Jaillon O., et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
23. Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 (2004) 787-799
24. 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
25. Lauter N., Kampani A., Carlson S., Goebel M., and Moose S.P. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 9412-9417
26. Liu B., et al. Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol. 139 (2005) 296-305
27. 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 (2005) 2186-2203
28. Lu S., Sun Y.H., Amerson H., and Chiang V.L. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development. Plant J. 51 (2007) 1077-1098
29. Lu S., Sun Y.H., and Chiang V.L. Stress-responsive microRNAs in Populus. Plant J. 55 (2008) 131-151
30. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
31. Meyers B.C., et al. Criteria for annotation of plant MicroRNAs. Plant Cell (2008)
32. Mi S., et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 133 (2008) 116-127
33. Montgomery T.A., et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133 (2008) 128-141
34. Moore M.J., Bell C.D., Soltis P.S., and Soltis D.E. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc. Natl. Acad. Sci. 104 (2007) 19363-19368
35. Palatnik J.F., et al. Control of leaf morphogenesis by microRNAs. Nature 425 (2003) 257-263
36. Palatnik J.F., et al. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13 (2007) 115-125
37. Paterson A.H., et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457 (2009) 551-556
38. Qiu Y.L., et al. A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes. Int'l J. Plant Sci. 168 (2007) 691-708
39. Rensing S.A., et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319 (2008) 64-69
40. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., and Bartel D.P. Prediction of plant microRNA targets. Cell 110 (2002) 513-520
41. Sanderson M.J. Molecular data from 27 proteins do not support a Precambrian origin of land plants. Am. J. Bot. 90 (2003) 954-956
42. Sanderson M.J., Thorne J.L., Wikstrom N., and Bremer K. Molecular evidence on plant divergence times. Am. J. Bot. 91 (2004) 1656-1665
43. 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 (2005) 517-527
44. Schwab R., Ossowski S., Riester M., Warthmann N., and Weigel D. Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18 (2006) 1121-1133
45. Shukla L.I., Chinnusamy V., and Sunkar R. The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim. Biophys. Acta 1779 (2008) 743-748
46. Sunkar K., and Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 8 (2008) 37
47. Sunkar R., Zhou X., Zheng Y., Zhang W., and Zhu J.K. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 8 (2008) 25
48. Takeda A., Iwasaki S., Watanabe T., Utsumi M., and Watanabe Y. The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol. 49 (2008) 493-500
49. Usami T., Horiguchi G., Yano S., and Tsukaya H. The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty. Development 136 (2009) 955-964
50. Wang J.W., Schwab R., Czech B., Mica E., and Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 20 (2008) 1231-1243
51. Willmann M.R., and Poethig R.S. Conservation and evolution of miRNA regulatory programs in plant development. Curr. Opin. Plant Biol. 10 (2007) 503-511
52. Wu M.F., Tian Q., and Reed J.W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133 (2006) 4211-4218
53. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., and Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci. 63 (2006) 246-254
54. Zhang B., Pan X., Cannon C.H., Cobb G.P., and Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 46 (2006) 243-259
55. Zhang B., et al. Identification of cotton microRNAs and their targets. Gene 397 (2007) 26-37
56. Zhang B., Pan X., and Stellwag E.J. Identification of soybean microRNAs and their targets. Planta 229 (2008) 161-182
57. Zhang J.F., Yuan L.J., Shao Y., Du W., Yan D.W., and Lu Y.T. The disturbance of small RNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis. Plant Cell Environ. 31 (2008) 562-574
58. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415