Spatial distribution of epigenetic modifications in Brachypodium distachyon embryos during seed maturation and germination

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Wolny, Elzbieta ^a   Braszewska Zalewska, Agnieszka ^a   Hasterok, Robert ^a  

^a UNIVERSITY OF SILESIA   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H4; HISTONE; STARCH; VEGETABLE PROTEIN;

ARTICLE; BRACHYPODIUM; CELL NUCLEUS; COLEORHIZA; CONTROLLED STUDY; DESICCATION; DNA MODIFICATION; EMBRYO DEVELOPMENT; EPIGENETICS; EPITHELIUM CELL; GENE EXPRESSION PROFILING; GENETIC MARKER; GERMINATION; HISTONE ACETYLATION; HISTONE METHYLATION; NONHUMAN; PLANT EMBRYO; PLANT LEAF; PLANT PARAMETERS; PLANT STRUCTURES; PLANT TISSUE; PRIMORDIUM; PROTEIN ANALYSIS; SCUTELLUM; SEED MATURATION; TISSUE SPECIFICITY; ACETYLATION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHYLATION; PHYSIOLOGY; PLANT SEED; PROTEIN PROCESSING;

ACETYLATION; BRACHYPODIUM; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GERMINATION; HISTONES; METHYLATION; PLANT PROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEEDS; STARCH;

EID: 84904103572     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0101246     Document Type: Article

References (66)

1. Bentsink L, Koornneef M (2008) Seed dormancy and germination. Arabidopsis Book 6: e0119.
2. Angelovici R, Galili G, Fernie AR, Fait A (2010) Seed desiccation: a bridge between maturation and germination. Trends Plant Sci 15: 211-218.
3. Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C (2007) Combined networks regulating seed maturation. Trends Plant Sci 12: 294-300. (Pubitemid 47031669)
4. Holdsworth MJ, Finch-Savage WE, Grappin P, Job D (2008) Post-genomics dissection of seed dormancy and germination. Trends Plant Sci 13: 7-13.
5. Nonogaki H, Bassel GW, Bewley JD (2010) Germination - Still a mystery. Plant Science 179: 574-581.
6. Bewley JD (1997) Seed dormancy and germination. Plant Cell 9: 1055-1066.
7. Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171: 501-523. (Pubitemid 44051305)
8. Finkelstein RR, Gampala SS, Rock CD (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 14 Suppl: S15-45. (Pubitemid 34609229)
9. Okamoto M, Kuwahara A, Seo M, Kushiro T, Asami T, et al. (2006) CYP707A1 and CYP707A2, which encode abscisic acid 89-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. Plant Physiol 141: 97-107. (Pubitemid 43956185)
10. Koornneef M, van der Veen JH (1980) Induction and analysis of gibberellin sensitive mutants in Arabidopsis thaliana (L.) Heynh. Theor Appl Genet 58: 257-263.
11. Yamauchi Y, Ogawa M, Kuwahara A, Hanada A, Kamiya Y, et al. (2004) Activation of gibberellin biosynthesis and response pathways by low temperature during imbibition of Arabidopsis thaliana seeds. Plant Cell 16: 367-378. (Pubitemid 38192696)
12. Ariizumi T, Hauvermale AL, Nelson SK, Hanada A, Yamaguchi S, et al. (2013) Lifting DELLA repression of Arabidopsis seed germination by nonproteolytic gibberellin signaling. Plant Physiol 162: 2125-2139.
13. Weitbrecht K, Muller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62: 3289-3309.
14. Muller K, Bouyer D, Schnittger A, Kermode AR (2012) Evolutionarily conserved histone methylation dynamics during seed life-cycle transitions. PLoS One 7: e51532.
15. van Zanten M, Koini MA, Geyer R, Liu Y, Brambilla V, et al. (2011) Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Proc Natl Acad Sci U S A 108: 20219-20224.
16. Cadman CS, Toorop PE, Hilhorst HW, Finch-Savage WE (2006) Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. Plant J 46: 805-822. (Pubitemid 43780627)
17. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080. (Pubitemid 32758077)
18. Hsieh TF, Fischer RL (2005) Biology of chromatin dynamics. Annu Rev Plant Biol 56: 327-351.
19. Deltour R (1985) Nuclear activation during early germination of the higher plant embryo. J Cell Sci 75: 43-83.
20. Fransz P, de Jong H (2011) From nucleosome to chromosome: a dynamic organization of genetic information. Plant J 66: 4-17.
21. van Zanten M, Carles A, Li Y, Soppe WJ (2012) Control and consequences of chromatin compaction during seed maturation in Arabidopsis thaliana. Plant Signal Behav 7: 338-341.
22. Fischer C, Neuhaus G (1996) lnfluence of auxin on the establishment of bilateral symmetry in monocots. Plant J 9: 659-669. (Pubitemid 126661047)
23. Fischer-Iglesias C, Sundberg B, Neuhaus G, Jones AM (2001) Auxin distribution and transport during embryonic pattern formation in wheat. Plant J 26: 115-129. (Pubitemid 32532720)
24. Barrero JM, Jacobsen JV, Talbot MJ, White RG, Swain SM, et al. (2012) Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon. New Phytol 193: 376-386.
25. Guillon F, Bouchet B, Jamme F, Robert P, Quemener B, et al. (2011) Brachypodium distachyon grain: characterization of endosperm cell walls. J Exp Bot 62: 1001-1015.
26. Guillon F, Larre C, Petipas F, Berger A, Moussawi J, et al. (2012) A comprehensive overview of grain development in Brachypodium distachyon variety Bd21. J Exp Bot 63: 739-755.
27. Opanowicz M, Hands P, Betts D, Parker ML, Toole GA, et al. (2011) Endosperm development in Brachypodium distachyon . J Exp Bot 62: 735-748.
28. Draper J, Mur LA, Jenkins G, Ghosh-Biswas GC, Bablak P, et al. (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol 127: 1539-1555. (Pubitemid 34050024)
29. Garvin DF, Gu YQ, Hasterok R, Hazen SP, Jenkins G, et al. (2008) Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Crop Sci 48: 69-84.
30. Mur LA, Allainguillaume J, Catalan P, Hasterok R, Jenkins G, et al. (2011) Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytol 191: 334-347.
31. Steedman HF (1957) Polyester wax; a new ribboning embedding medium for histology. Nature 179: 1345.
32. Braszewska-Zalewska A, Dziurlikowska A, Maluszynska J (2012) Histone H3 methylation patterns in Brassica nigra, Brassica juncea, and Brassica carinata species. Genome 55: 68-74.
33. Braszewska-Zalewska AJ, Wolny EA, Smialek L, Hasterok R (2013) Tissuespecific epigenetic modifications in root apical meristem cells of Hordeum vulgare. PLoS One 8: e69204.
34. Braszewska-Zalewska A, Bernas T, Maluszynska J (2010) Epigenetic chromatin modifications in Brassica genomes. Genome 53: 203-210.
35. Andriotis VM, Pike MJ, Kular B, Rawsthorne S, Smith AM (2010) Starch turnover in developing oilseed embryos. New Phytol 187: 791-804.
36. Benoit M, Layat E, Tourmente S, Probst AV (2013) Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci. Gene 526: 39-45.
37. Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, et al. (2009) PHYTOCHROME B and HISTONE DEACETYLASE 6 control lightinduced chromatin compaction in Arabidopsis thaliana. PLoS Genet 5: e1000638.
38. Pecinka A, Dinh HQ, Baubec T, Rosa M, Lettner N, et al. (2010) Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis . Plant Cell 22: 3118-3129.
39. Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, et al. (2007) Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci 120: 1200-1208. (Pubitemid 46711838)
40. Douet J, Blanchard B, Cuvillier C, Tourmente S (2008) Interplay of RNA Pol IV and ROS1 during post-embryonic 5S rDNA chromatin remodeling. Plant Cell Physiol 49: 1783-1791.
41. Mathieu O, Jasencakova Z, Vaillant I, Gendrel AV, Colot V, et al. (2003) Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 15: 2929-2939. (Pubitemid 37546261)
42. Tessadori F, Schulkes RK, van Driel R, Fransz P (2007) Light-regulated largescale reorganization of chromatin during the floral transition in Arabidopsis. Plant J 50: 848-857. (Pubitemid 46855032)
43. Zhang H, Ogas J (2009) An epigenetic perspective on developmental regulation of seed genes. Mol Plant 2: 610-627.
44. Zhang L, Qiu Z, Hu Y, Yang F, Yan S, et al. (2011) ABA treatment of germinating maize seeds induces VP1 gene expression and selective promoterassociated histone acetylation. Physiol Plant 143: 287-296.
45. Zhang L, Hu Y, Yan S, Li H, He S, et al. (2012) ABA-mediated inhibition of seed germination is associated with ribosomal DNA chromatin condensation, decreased transcription, and ribosomal RNA gene hypoacetylation. Plant Mol Biol 79: 285-293.
46. Braszewska-Zalewska A, Hasterok R (2013) Epigenetic modifications of nuclei differ between root meristematic tissues of Hordeum vulgare. Plant Signal Behav 9: e26711.
47. Vicente-Carbajosa J, Carbonero P (2005) Seed maturation: developing an intrusive phase to accomplish a quiescent state. Int J Dev Biol 49: 645-651. (Pubitemid 41615616)
48. Liu Y, Koornneef M, Soppe WJ (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. (Pubitemid 46941669)
49. Zheng J, Chen F, Wang Z, Cao H, Li X, et al. (2012) A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. New Phytol 193: 605-616.
50. Willmann MR, Mehalick AJ, Packer RL, Jenik PD (2011) MicroRNAs regulate the timing of embryo maturation in Arabidopsis. Plant Physiol 155: 1871-1884.
51. Long JA, Ohno C, Smith ZR, Meyerowitz EM (2006) TOPLESS regulates apical embryonic fate in Arabidopsis . Science 312: 1520-1523. (Pubitemid 43865890)
52. Servet C, Conde e Silva N, Zhou DX (2010) Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Mol Plant 3: 670-677.
53. van Zanten M, Liu Y, Soppe WJ (2013) Epigenetic signalling during life of seeds. In: Grafi G, Ohad N, editors. Epigenetic memory and control in plants. Berlin Heidelberg: Springer-Verlag. 261.
54. Leubner-Metzger G (2005) beta-1,3-Glucanase gene expression in low-hydrated seeds as a mechanism for dormancy release during tobacco after-ripening. Plant J 41: 133-145.
55. Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E (2005) Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J 41: 697-709. (Pubitemid 40336001)
56. Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, et al. (2012) Seed germination and vigor. Annu Rev Plant Biol 63: 507-533.
57. Bino RJ, Lanteri S, Verhoeven HA, Kraak HL (1993) Flow cytometric deterination of nuclear replication stages in seeds tissues. Ann Bot 72: 181-187.
58. Osborne DJ, Boubriak I, Leprince O (2002) Rehydration of dry systems: membranes and the nuclear genome. In: Black M, Pritchard HW, editors. Desiccation and survival in plants, drying without dying. Wallingford, UK: CABI Publishing. 350-354.
59. Comai L, Harada JJ (1990) Transcriptional activities in dry seed nuclei indicate the timing of the transition from embryogeny to germination. Proc Natl Acad Sci U S A 87: 2671-2674.
60. North H, Baud S, Debeaujon I, Dubos C, Dubreucq B, et al. (2010) Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research. Plant J 61: 971-981.
61. Zhang M, Xu C, von Wettstein D, Liu B (2011) Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum. Plant Physiol 156: 1955-1966.
62. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451.
63. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451-1454.
64. Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107: 18729-18734.
65. Lauria M, Rupe M, Guo M, Kranz E, Pirona R, et al. (2004) Extensive maternal DNA hypomethylation in the endosperm of Zea mays . Plant Cell 16: 510-522. (Pubitemid 38192706)
66. Kapazoglou A, Drosou V, Argiriou A, Tsaftaris AS (2013) The study of a barley epigenetic regulator, HvDME, in seed development and under drought. BMC Plant Biol 13: 172.