Analysis of global changes in gene expression during activity-dormancy cycle in hybrid aspen apex

Plant Biotechnology

Volumn 27, Issue 1, 2010, Pages 1-16

  Karlberg, Anna ^a   Englund, Madeleine ^a   Petterle, Anna ^a   Molnar, Gergely ^a   Sjödin, Andreas ^b   Bako, Laszlo ^b   Bhalerao, Rishikesh P ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UMEÅ UNIVERSITY   (Sweden)

Author keywords

Cell cycle; Dormancy; Hormone; Microarray; Poplar

Indexed keywords

EID: 77952927736     PISSN: 13424580     EISSN: 13476114     Source Type: Journal    
DOI: 10.5511/plantbiotechnology.27.1     Document Type: Article

References (62)

1. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucl Acids Res 35: D760-D765
2. Bastow R, Mylne J.S, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164-167
3. Benedict C, Skinner JS, Meng R, Chang YJ, Bhalerao R, Huner NPA, Finn CE, Chen THH, Hurry V (2006) The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp. Plant Cell Environ 29: 1259-1272
4. Bohlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O (2006) CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312: 1040-1043
5. Cao X, Jacobsen S (2002) Role of the Arabidopsis DRM methyltransferase in de novo methylation and gene silencing. Curr Biol 12: 1138-1144
6. Doherty CJ, Van Buskirk HA, Myers SJ, Thomashow MF (2009) Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 21: 972-984
7. Druart N, Johansson A, Baba K, Schrader J, Sjodin A, Bhalerao RR, Resman L, Trygg J, Moritz T, Bhalerao RP (2007) Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant J 50: 557-573
8. Eriksson ME, Moritz T (2002) Daylength and spatial expression of a gibberellin 20-oxidase isolated from hybrid aspen (Populus tremula L. x P-tremuloides Michx.). Planta 214: 920-930
9. Eriksson ME, Israelsson M, Olsson O, Moritz T (2000) Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length. Nat Biotechnol 18: 784-788
10. Espinosa-Ruiz A, Saxena S, Schmidt J, Mellerowicz E, Miskolczi P, Bako L, Bhalerao RP (2004) Differential stage-specific regulation of cyclin-dependent kinases during cambial dormancy in hybrid aspen. Plant J 38: 603-615
11. Fowler DB, Breton G, Limin AE, Mahfoozi S, Sarhan F (2001) Photoperiod and temperature interactions regulate low-temperature-induced gene expression in barley. Plant Physiol 127: 1676-1681
12. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 93: 8449-8454
13. Gehring M, Huh, JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506
14. Gonzalez-Guzman M, Apostolova N, Belles JM, Barrero JM, Piqueras P, Ponce MR, Micol JL, Serrano R, Rodriguez PL (2002) The short-chain alcohol dehydrogenase ABA2 catalyzes the conversion of xanthoxin to abscisic aldehyde. Plant Cell 14: 1833-1846
15. Grant PA, Duggan L, Cote J, Roberts SM, Brownell JE, et al. (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: Characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev 11: 1640-1650
16. Hedden P, Proebsting, WM (1999) Genetic analysis of gibberellin biosynthesis. Plant Physiol 119: 365-370
17. Hemerly A, Ferreira P, Engler J, Engler G, Inze D, Vanmontagu M (1993) The control of cell-cycle in Arabidopsis plant-cell cultures. J Plant Res 3: 51-56
18. Hill K, Wang H, Perry SE (2008) A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. Plant J 53: 172-185
19. Hsu CY, Liu YX, Luthe DS, Yuceer C (2006) Poplar FT2 shortens the juvenile phase and promotes seasonal flowering. Plant Cell 18:1846-1861
20. Iuchi S, Kobayashi M, Taji T, Naramoto M, Seki M, Kato T, Tabata S, Kakubari Yamaguchi-Shinozaki K, Shinozaki K (2001) Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis. Plant J 27: 325-333
21. Junttila O, Jensen E (1988) Gibberellins and photoperiodic control of shoot elongation in salix. Physiol Plant 74: 371-376.
22. Kim HJ, Hyun Y, Park JY, Park MJ, Park MK, Kim MD, Lee MH, Moon J, Lee I, Kim J (2004) A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nat Genet 36: 167-171
23. Kinoshita T, Miura A, Choi YH, Kinoshita Y, Cao XF, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523
24. Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705
25. Kushiro T, Okamoto M, Nakabayashi K, Yamagishi K, Kitamura S, Asami T, Hirai N, Koshiba T, Kamiya Y, Nambara E (2004) The Arabidopsis cytochrome P450CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism. EMBO J 23: 1647-1656
26. Law RD, Suttle JC (2004) Changes in histone H3 and H4 multiacetylation during natural and forced dormancy break in potato tubers. Physiol Plant 120: 642-649
27. Little CHA, Bonga, JM (1974) Rest in cambium of abiesbalsamea. Can J Bot52: 1723-1730
28. Liu YX, Koornneef M, Soppe WJJ (2007) The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19: 433-444
29. Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y, Christmann A, Grill E (2009) Regulators of PP2C phosphatase activity function as Abscisic Acid sensors. Science 324: 1064-1068
30. Menges M, de Jager SM, Gruissem W, Murray, JAH (2005) Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control. Plant J 41: 546-566
31. Michael WM, Newport J (1998) Coupling of mitosis to the completion of S phase through Cdc34-mediated degradation of Wee 1. Science 282: 1886-1889
32. Mitchum MG, Yamaguchi S, Hanada A, Kuwahara A, Yoshioka Y, Kato T, Tabata S, Kamiya Y, Sun, TP (2006) Distinct and overlapping roles of two gibberellin 3-oxidases in Arabidopsis development. Plant J 45: 804-818
33. Nitsch JP (1957) Photoperiodism in woody plants. Proc Am Soc Hortic Sci 70: 526-544
34. Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in, stress tolerance in Arabidopsis. Proc Natl Acad Sci USA 101: 3985-3990
35. Okamoto M, Kuwahara A, Seo M, Kushiro T, Asami T, Hirai N, Kamiya Y, Koshiba T, Nambara E (2006) CYP707A1 and CYP707A2, which encode abscisic acid 8'-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. Plant Physiol 141: 97-107
36. Olsen JE, Junttila O, Nilsen J, Eriksson ME, Martinussen I, Olsson O, Sandberg G, Moritz T (1997) Ectopic expression of oat phytochrome A in hybrid aspen changes critical daylength for growth and prevents cold acclimatization. Plant J 12: 1339-1350
37. Parker LL, Athertonfessler S, Lee MS, Ogg S, Falk JL, Swenson KI, Piwnicaworms H (1991) Cyclin promotes the tyrosine phosphorylation of P34CDC2 in a WEE1 + dependent manner. EMBO J 10: 1255-1263
38. Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the polycomb and trithorax group proteins. Annu Rev Genet 38: 413-443
39. Rinne PLH, Kaikuranta PM, van der Schoot C (2001) The shoot apical meristem restores its symplasmic organization during chilling-induced release from dormancy. Plant J 26: 249-264
40. Rohde A, Bhalerao RP (2007) Plant dormancy in the perennial context. Trends Plant Sci 12: 217-223
41. Rohde A, Prinsen E, De Rycke R, Engler G, Van Montagu M, Boerjan W (2002) PtABI3 impinges on the growth and differentiation of embryonic leaves during bud set in poplar. Plant Cell 14: 2975-2975
42. Ruttink T, Arend M, Morreel K, Storme V, Rombauts S, Fromm J, Bhalerao RP, Boerjan W, Rohde A (2007) A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19: 2370-2390
43. Saito S, Hirai N, Matsumoto C, Ohigashi H, Ohta D, Sakata K, Mizutani M (2004) Arabidopsis CYP707As encode (+)-abscisic acid 8'-hydroxylase, a key enzyme in the oxidative catabolism of abscisic acid. Plant Physiol 134: 1439-1449
44. Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J, Nilsson P, Bhalerao RP (2004) Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J 40: 173-187
45. Schwartz SH, Tan BC, Gage DA, Zeevaart JAD, McCarty DR (1997) Specific oxidative cleavage of carotenoids by VP14 of maize. Science 276: 1872-1874
46. Seo M, Hanada A, Kuwahara A, Endo A, Okamoto M, et al. (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J 48: 354-366
47. Shindo C, Lister C, Crevillen P, Nordborg M, Dean C (2006) Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Dev 20: 3079-3083
48. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman VCR, Dudoit S, Irizarry R, Huber W (eds) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp 397-420
49. Sterky F, Bhalerao RR, Unneberg P, Segerman B, Nilsson P, et al. (2004) A Populus EST resource for plant functional genomics. Proc Natl Acad Sci USA 101: 13951-13956
50. Sung S, Amasino, RM (2005) Remembering winter: Toward a molecular understanding of vernalization. Annu Rev Plant Biol 56:491-508
51. Sung SB, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159-164
52. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucl Acids Res 36: D1009-D1014
53. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604
54. Waterborg JH (1990) Sequence-analysis of acetylation and methylation in 2 histone-H3 variants of alfalfa. J Biol Chem 265:17157-17161
55. Weiser C (1970) Cold resistance and injury in woody plants: knowledge of hardy plant adaptations to freezing stress may help us to reduce winter damage. Science 169: 1269
56. Welling A, Moritz T, Palva ET, Junttila O (2002) Independent activation of cold acclimation by low temperature and short photoperiod in hybrid aspen. Plant Physiol 129: 1633-1641
57. Vlachonasios KE, Thomashow MF, Triezenberg, SJ (2003) Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15: 626-638
58. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41: 195-211
59. Xu YL, Li L, Wu KQ, Peeters AJM, Gage DA, Zeevaart JAD (1995) The GA5 locus of Arabidopsis Thaliana encodes a multifunctional gibberellin 20-oxidase-molecular- cloning and functional expression. Proc Natl Acad Sci USA 92: 6640-6644
60. Xu ZJ, Nakajima M, Suzuki Y, Yamaguchi I (2002) Cloning and characterization of the abscisic acid-specific glucosyltransferase gene from adzuki bean seedlings. Plant Physiol 129: 1285-1295
61. Yamauchi Y, Ogawa M, Kuwahara A, Hanada A, Kamiya Y, Yamaguchi S (2004) Activation of Gibberellin biosynthesis and response pathways by low temperature during imbibition of Arabidopsis thaliana seeds. Plant Cell 16: 367-378
62. Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, et al. (2008) Genomewide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371: 468-474