MicroRNA misregulation: An overlooked factor generating somaclonal variation?

Trends in Plant Science

Volumn 16, Issue 5, 2011, Pages 242-248

  Rodriguez Enriquez, J ^a   Dickinson, H G ^b   Grant Downton, R T ^b  

^a UNIVERSIDAD DE LA LAGUNA   (Spain)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; PHENOTYPE; PHYSIOLOGY; PLANT; PLANT GENOME; PLANT PHYSIOLOGY; REVIEW; TISSUE CULTURE TECHNIQUE;

EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENETIC VARIATION; GENOME, PLANT; MICRORNAS; MODELS, GENETIC; PHENOTYPE; PLANT PHYSIOLOGICAL PHENOMENA; PLANTS; TISSUE CULTURE TECHNIQUES; TRANSCRIPTION, GENETIC;

EID: 79955709391     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2011.03.002     Document Type: Review

References (72)

1. Skirvin R.M. Natural and induced variation in tissue culture. Euphytica 1978, 27:241-266.
2. Gautheret R.J. Plant tissue culture: a history. Bot. Mag. 1983, 96:393-410.
3. Smulders M.J.M., de Klerk G.J. Epigenetics in plant tissue culture. Plant Growth Regul. 2011, 63:137-146.
4. Evans D.A. Somaclonal variation - genetic basis and breeding applications. Trends Genet. 1989, 5:46-50.
5. Kaeppler S.M., et al. Epigenetic aspects of somaclonal variation in plants. Plant Mol. Biol. 2000, 43:179-188.
6. Hirochika H., et al. Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:7783-7788.
7. Chiu L.W., et al. The purple cauliflower arises from activation of a MYB transcription factor. Plant Physiol. 2010, 154:1470-1480.
8. Lisch D. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 2009, 60:43-66.
9. Tanurdzic M., et al. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 2008, 6:2880-2895.
10. Berdasco M., et al. Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS ONE 2008, 3:e3306.
11. Zhang M., et al. Limited tissue culture-induced mutations and linked epigenetic modifications in F hybrids of sorghum pure lines are accompanied by increased transcription of DNA methyltransferases and 5-methylcytosine glycosylases. Plant J. 2009, 57:666-679.
12. Mallory A., Vaucheret H. Form, function and regulation of ARGONAUTE proteins. Plant Cell 2010, 22:3879-3889.
13. Harvey J.J.W., et al. An antiviral defense role of AGO2 in plants. PLoS ONE 2011, 6:e14639.
14. Matzke A.J.M., Matzke M.A. Epigenetic silencing of plant transgenes as a consequence of diverse cellular responses. Cell. Mol. Life Sci. 1998, 54:94-103.
15. Fojtova M., et al. Epigenetic switch from posttranscriptional to transcriptional silencing is correlated with promoter hypermethylation. Plant Physiol. 2003, 133:1240-1250.
16. Krizova K., et al. Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles. Plant Physiol. 2009, 149:1493-1504.
17. Mitsuhara I., et al. Release from post-transcriptional gene silencing by cell proliferation in transgenic tobacco plants: possible mechanism for noninheritance of the silencing. Genetics 2002, 160:343-352.
18. Rhee Y., et al. Tissue culture-induced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize. Genetics 2010, 186:843-855.
19. Tessadori F., et al. Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J. Cell Sci. 2007, 120:1200-1208.
20. Vaucheret H. Post-transcriptional small RNA pathways in plants - mechanisms and regulation. Genes Dev. 2006, 20:759-771.
21. Brodersen P., et al. Widespread translational inhibition by plant microRNAs and siRNAs. Science 2008, 320:1185-1190.
22. Bao N., et al. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell 2004, 7:653-662.
23. Chellappan P., et al. siRNAs from microRNA sites mediate DNA methylation of target genes. Nucleic Acids Res. 2010, 38:6883-6894.
24. Khraiwesh B., et al. Transcriptional control of gene expression by microRNAs. Cell 2010, 140:111-122.
25. Wu L., et al. DNA methylation mediated by a microRNA pathway. Mol. Cell 2010, 38:465-475.
26. Grant-Downton R.T., et al. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. BMC Genomics 2009, 10:643.
27. Zhan S., Lukens L. Identification of novel microRNAs and microRNA dependent developmental shifts of genes expression in Arabidopsis thaliana. PLoS ONE 2010, 5:e10157.
28. Allen E., Howell M.D. microRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin. Cell Dev. Biol. 2010, 21:798-804.
29. Cuperus J.T., et al. Unique functionality of 22-nt microRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat. Struct. Mol. Biol. 2010, 17:997-1003.
30. Chen H.-M., et al. 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:15269-15274.
31. Vazquez F., et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res. 2008, 36:6429-6438.
32. Ebhardt, et al. Naturally occurring variations in sequence length create microRNA isoforms that vary in argonaute effector complex specificity. Silence 2010, 1:12.
33. Zhang W., et al. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol. 2010, 11:R81.
34. Poethig R.S. Small RNAs and developmental timing in plants. Curr. Opin. Genet. Dev. 2009, 19:374-378.
35. Peragine A., et al. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 2004, 18:2368-2379.
36. Brink R.A. Phase changes in higher plants and somatic cell heredity. Q. Rev. Biol. 1962, 37:1-22.
37. von Aderkas P., Bonga J.M. Influencing micropropagation and somatic embryogenesis in mature trees by manipulation of phase change, stress and culture environment. Tree Physiol. 2000, 20:921-928.
38. Huang L.-C., et al. Restoration of vigor and rooting competence in stem tissues of mature Citrus by repeated grafting of their shoot apices onto freshly germinated seedlings in vitro. In Vitro Cell Dev. Biol. Plant 1992, 28:30-32.
39. Angeles Revilla M., et al. In vitro reinvigoration of mature olive trees (Olea europea L.) through micrografting. In Vitro Cell Dev. Biol. Plant 1996, 32:257-261.
40. Zalewska M., et al. Effect of in vitro topophysis on the growth, development, and rooting of chrysanthemum explants (Chrysanthemum x grandiflorum Ramat./Kitam.). J. Hort. Sci. Biotechnol. 2010, 85:362-366.
41. Sunkar R. MicroRNAs with macro-effects on plant stress responses. Semin. Cell Dev. Biol. 2010, 21:805-811.
42. Luo Y.C., et al. Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development. FEBS Lett. 2006, 580:5111-5116.
43. Zhang S., et al. Four abiotic stress-induced microRNA families differentially regulated in the embryogenic and non-embryogenic callus tissues of Larix leptolepis. Biochem. Biophys. Res. Commun. 2010, 398:355-360.
44. Tang G. Plant microRNAs: an insight into their gene structure and evolution. Semin. Cell. Dev. Biol. 2010, 21:782-789.
45. Allen E., et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 2004, 36:1282-1290.
46. Fahlgren N., et al. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 2010, 22:1074-1089.
47. Arteaga-Vazquez M., et al. RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:12986-12991.
48. Vaistij F.E., et al. Suppression of microRNA accumulation via RNA interference in Arabidopsis thaliana. Plant Mol. Biol. 2010, 73:391-397.
49. Li H., et al. MicroRNA expression profiles in conventional and micropropagated strawberry (Fragaria x ananassa Duch.) plants. Plant Cell Rep. 2009, 28:91-902.
50. Xie Z., et al. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 2003, 13:784-789.
51. Rajagopalan R., et al. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 2006, 20:3407-3425.
52. Mallory A., Vaucheret H. ARGONAUTE1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep. 2009, 10:521-526.
53. Mi S., et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 2008, 133:116-127.
54. Parry G., et al. Complex regulation of the TIR1/AFB family of auxin receptors. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:22540-22545.
55. Marin E., et al. 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.
56. Chakrabarty D., et al. Differential transcriptional expression following thidiazuron-induced callus differentiation developmental shifts in rice. Plant Biol. (Stuttg) 2009, 12:46-59.
57. Gautheret R.J. Hétér-auxines et cultures de tissus végétaux. Bull. Soc. Chim. Biol. (Paris) 1942, 24:13-47.
58. Meins F. Habituation: heritable variation in the requirement of cultured plant cells for hormones. Annu. Rev. Genet. 1989, 23:395-408.
59. Spencer D.F., Kimmins W.C. Presence of plasmodesmata in callus cultures of tobacco and carrot. Can. J. Bot. 1969, 47:2049-2050.
60. Chitwood D., et al. Pattern formation via small RNA mobility. Genes Dev. 2009, 23:549-554.
61. Dunoyer P., et al. Small RNA duplexes function as mobile silencing signals between plant cells. Science 2010, 328:912-916.
62. Lelandais-Brière C., et al. Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 2009, 21:2780-2796.
63. Zhang S., et al. The phloem-delivered RNA pool contains small non-coding RNAs and interferes with translation. Plant Physiol. 2009, 150:378-387.
64. Molnar A., et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010, 328:872-875.
65. Pant B.D., et al. MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J. 2008, 53:731-738.
66. Tucker M.R., et al. Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo. Development 2008, 135:2839-2843.
67. Mallory A., et al. Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS Genet. 2009, 5:e1000646.
68. Newman K., et al. Regulation of axis determinacy by the Arabidopsis PINHEAD gene. Plant Cell 2002, 14:3029-3042.
69. Teixera F.P., et al. A role for RNAi in the selective correction of DNA methylation defects. Science 2009, 322:1600-1604.
70. Liu X., et al. The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression. Plant J. 2010, 62:416-418.
71. Franco-Zorrilla J.M., et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 2007, 39:1033-1037.
72. Mallory A.C., et al. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 2005, 17:1360-1375.