Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon

Nucleic Acids Research

Volumn 40, Issue 17, 2012, Pages 8240-8254

  Mönke, Gudrun ^a   Seifert, Michael ^a   Keilwagen, Jens ^a   Mohr, Michaela ^b   Grosse, Ivo ^c   Hähnel, Urs ^a   Junker, Astrid ^a   Weisshaar, Bernd ^d   Conrad, Udo ^a   Bäumlein, Helmut ^a   Altschmied, Lothar ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b GWDG Gesellschaft für wissenschaftliche Datenverarbeitung GmbH Göttingen   (Germany)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^d BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABSCISIC ACID; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ABSCISIC ACID INSENSITIVE3; TRANSCRIPTION FACTOR B3 DOMAIN CONTAINING FUS3; TRANSCRIPTION FACTOR B3 DOMAIN CONTAINING LEC2; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; ASSAY; CHROMATIN IMMUNOPRECIPITATION; DESICCATION; EMBRYONIC STRUCTURES; EPIGENETICS; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; MOLECULAR RECOGNITION; NONHUMAN; PLANT SEED; PRIORITY JOURNAL; PROMOTER REGION; PROTECTION; REGULON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEED DEVELOPMENT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN IMMUNOPRECIPITATION; DNA, PLANT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; NUCLEOTIDE MOTIFS; PROMOTER REGIONS, GENETIC; REGULON; SEEDS; TRANSCRIPTION FACTORS;

ARABIDOPSIS THALIANA;

EID: 84866902488     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks594     Document Type: Article

References (96)

1. Gutierrez, L., Van Wuytswinkel, O., Castelain, M. and Bellini, C. (2007) Combined networks regulating seed maturation. Trends Plant Sci., 12, 294-300. (Pubitemid 47031669)
2. Santos-Mendoza, M., Dubreucq, B., Baud, S., Parcy, F., Caboche, M. and Lepiniec, L. (2008) Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J., 54, 608-620. (Pubitemid 351678046)
3. Vicente-Carbajosa, J. and Carbonero, P. (2005) Seed maturation: developing an intrusive phase to accomplish a quiescent state. Int. J. Dev. Biol., 49, 645-651. (Pubitemid 41615616)
4. Lotan, T., Ohto, M., Yee, K.M., West, M.A., Lo, R., Kwong, R.W., Yamagishi, K., Fischer, R.L., Goldberg, R.B. and Harada, J.J. (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell, 93, 1195-1205.
5. Gazzarrini, S. and McCourt, P. (2003) Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us. Ann. Bot. (Lond), 91, 605-612. (Pubitemid 41295103)
6. Ng, D.W., Chandrasekharan, M.B. and Hall, T.C. (2004) The 50 UTR negatively regulates quantitative and spatial expression from the ABI3 promoter. Plant Mol. Biol., 54, 25-38. (Pubitemid 39001404)
7. Zhang, X., Garreton, V. and Chua, N.H. (2005) The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev., 19, 1532-1543. (Pubitemid 41002997)
8. Berger, N., Dubreucq, B., Roudier, F., Dubos, C. and Lepiniec, L. (2011) Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell, 23, 4065-4078.
9. Ng, D.W., Chandrasekharan, M.B. and Hall, T.C. (2006) Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell, 18, 119-132. (Pubitemid 43951319)
10. Rider, D.S. Jr, Henderson, J.T., Jerome, R.E., Edenberg, H.J., Romero-Severson, J. and Ogas, J. (2003) Coordinate repression of regulators of embryonic identity by PICKLE during germination in Arabidopsis. Plant J., 35, 33-43. (Pubitemid 36821103)
11. Suzuki, M., Wang, H.H. and McCarty, D.R. (2007) Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol., 143, 902-911. (Pubitemid 46940987)
12. Perruc, E., Kinoshita, N. and Lopez-Molina, L. (2007) The role of chromatin-remodeling factor PKL in balancing osmotic stress responses during Arabidopsis seed germination. Plant J., 52, 927-936. (Pubitemid 350157758)
13. Sugliani, M., Brambilla, V., Clerkx, E.J., Koornneef, M. and Soppe, W.J. (2010) The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis. Plant Cell, 22, 1936-1946.
14. Braybrook, S.A., Stone, S.L., Park, S., Bui, A.Q., Le, B.H., Fischer, R.L., Goldberg, R.B. and Harada, J.J. (2006) Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. Proc. Natl Acad. Sci. USA, 103, 3468-3473. (Pubitemid 43346492)
15. Parcy, F., Valon, C., Raynal, M., Gaubier-Comella, P., Delseny, M. and Giraudat, J. (1994) Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of endogenous abscisic acid. Plant Cell, 6, 1567-1582. (Pubitemid 24986211)
16. Suzuki, M., Ketterling, M.G., Li, Q.B. and McCarty, D.R. (2003) Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling. Plant Physiol., 132, 1664-1677. (Pubitemid 36872913)
17. Yamamoto, A., Kagaya, Y., Usui, H., Hobo, T., Takeda, S. and Hattori, T. (2010) Diverse roles and mechanisms of gene regulation by the Arabidopsis seed maturation master regulator FUS3 revealed by microarray analysis. Plant Cell Physiol., 51, 2031-2046.
18. Baumlein, H., Nagy, I., Villarroel, R., Inze, D. and Wobus, U. (1992) Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within the legumin box is essential for tissue-specific expression of a legumin gene. Plant J., 2, 233-239.
19. Monke, G., Altschmied, L., Tewes, A., Reidt, W., Mock, H.P., Baumlein, H. and Conrad, U. (2004) Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA. Planta, 219, 158-166. (Pubitemid 38642146)
20. Reidt, W., Wohlfarth, T., Ellerströ m, M., Czihal, A., Tewes, A., Ezcurra, I., Rask, L. and Bä umlein, H. (2000) Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product. Plant J., 21, 1-8.
21. Marella, H.H., Sakata, Y. and Quatrano, R.S. (2006) Characterization and functional analysis of ABSCISIC ACID INSENSITIVE3-like genes from Physcomitrella patens. Plant J., 46, 1032-1044.
22. Schallau, A., Kakhovskaya, I., Tewes, A., Czihal, A., Tiedemann, J., Mohr, M., Grosse, I., Manteuffel, R. and Baumlein, H. (2008) Phylogenetic footprints in fern spore-and seed-specific gene promoters. Plant J., 53, 414-424. (Pubitemid 351172018)
23. Khandelwal, A., Cho, S.H., Marella, H., Sakata, Y., Perroud, P.F., Pan, A. and Quatrano, R.S. (2010) Role of ABA and ABI3 in desiccation tolerance. Science, 327, 546.
24. Rohde, A., Prinsen, E., De Rycke, R., Engler, G., Van Montagu, M. and Boerjan, W. (2002) PtABI3 impinges on the growth and differentiation of embryonic leaves during bud set in poplar. Plant Cell, 14, 1885-1901. (Pubitemid 35002941)
25. Rohde, A., Ruttink, T., Hostyn, V., Sterck, L., Van Driessche, K. and Boerjan, W. (2007) Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar. J. Exp. Bot., 58, 4047-4060. (Pubitemid 351323604)
26. Ezcurra, I., Wycliffe, P., Nehlin, L., Ellerstrom, M. and Rask, L. (2000) Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box. Plant J., 24, 57-66.
27. Giraudat, J., Hauge, B.M., Valon, C., Smalle, J., Parcy, F. and Goodman, H.M. (1992) Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell, 4, 1251-1261.
28. Hill, A., Nantel, A., Rock, C.D. and Quatrano, R.S. (1996) A conserved domain of the viviparous-1 gene product enhances the DNA binding activity of the bZIP protein EmBP-1 and other transcription factors. J. Biol. Chem., 271, 3366-3374. (Pubitemid 26065640)
29. Lara, P., Onate-Sanchez, L., Abraham, Z., Ferrandiz, C., Diaz, I., Carbonero, P. and Vicente-Carbajosa, J. (2003) Synergistic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2. J. Biol. Chem., 278, 21003-21011. (Pubitemid 36806410)
30. Nakamura, S., Lynch, T.J. and Finkelstein, R.R. (2001) Physical interactions between ABA response loci of Arabidopsis. Plant J., 26, 627-635. (Pubitemid 32692905)
31. Suzuki, M., Kao, C.Y. and McCarty, D.R. (1997) The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell, 9, 799-807. (Pubitemid 28104508)
32. Finkelstein, R.R. and Somerville, C.R. (1990) Three classes of abscisic acid (ABA)-insensitive mutations of Arabidopsis define genes that control overlapping subsets of ABA responses. Plant Physiol., 94, 1172-1179. (Pubitemid 120015675)
33. Nakashima, K., Fujita, Y., Katsura, K., Maruyama, K., Narusaka, Y., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2006) Transcriptional regulation of ABI3-and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis. Plant Mol. Biol., 60, 51-68. (Pubitemid 43194442)
34. Parcy, F., Valon, C.h., Kohara, A., Misera, S. and Giraudat, J. (1997) The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Plant Cell, 9, 1265-1277. (Pubitemid 28174108)
35. Kagaya, Y., Toyoshima, R., Okuda, R., Usui, H., Yamamoto, A. and Hattori, T. (2005) LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3. Plant Cell Physiol., 46, 399-406.
36. Collas, P. (2010) The current state of chromatin immunoprecipitation. Mol. Biotechnol., 45, 87-100.
37. Solomon, M.J., Larsen, P.L. and Varshavsky, A. (1988) Mapping protein DNA interactions in vivo with formaldehyde-evidence that histone-H4 is retained on a highly transcribed gene. Cell, 53, 937-947.
38. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M. and Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538. (Pubitemid 32144361)
39. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804. (Pubitemid 35231527)
40. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309. (Pubitemid 32041573)
41. Benhamed, M., Martin-Magniette, M.L., Taconnat, L., Bitton, F., Servet, C., De Clercq, R., De Meyer, B., Buysschaert, C., Rombauts, S., Villarroel, R. et al. (2008) Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J., 56, 493-504.
42. Kaufmann, K., Muino, J.M., Jauregui, R., Airoldi, C.A., Smaczniak, C., Krajewski, P. and Angenent, G.C. (2009) Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol., 7, e1000090.
43. Lee, J., He, K., Stolc, V., Lee, H., Figueroa, P., Gao, Y., Tongprasit, W., Zhao, H.Y., Lee, I. and Deng, X. (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell, 19, 731-749. (Pubitemid 46953224)
44. Oh, E., Kang, H., Yamaguchi, S., Park, J., Lee, D., Kamiya, Y. and Choi, G. (2009) Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell, 21, 403-419.
45. Roccaro, M. and Somssich, I.E. (2011) Chromatin immunoprecipitation to identify global targets of WRKY transcription factor family members involved in plant immunity. Methods Mol. Biol., 712, 45-58.
46. Tao, Z., Shen, L., Liu, C., Liu, L., Yan, Y. and Yu, H. (2012) Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis. Plant J., 70, 549-561.
47. Thibaud-Nissen, F., Wu, H., Richmond, T., Redman, J.C., Johnson, C., Green, R., Arias, J. and Town, C.D. (2006) Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J., 47, 152-162. (Pubitemid 43883021)
48. Zheng, Y., Ren, N., Wang, H., Stromberg, A.J. and Perry, S.E. (2009) Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. Plant Cell, 21, 2563-2577.
49. Baudry, A., Heim, M.A., Dubreucq, B., Caboche, M., Weisshaar, B. and Lepiniec, L. (2004) TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J., 39, 366-380. (Pubitemid 39040142)
50. Bent, A. (2006) Arabidopsis thaliana floral dip transformation method. Methods Mol. Biol., 343, 87-103.
51. Wan, C.Y. and Wilkins, T.A. (1994) A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L). Anal. Biochem., 223, 7-12. (Pubitemid 24356684)
52. Czechowski, T., Bari, R.P., Stitt, M., Scheible, W.R. and Udvardi, M.K. (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root-and shoot-specific genes. Plant J., 38, 366-379. (Pubitemid 38503736)
53. Junker, A., Monke, G., Rutten, T., Keilwagen, J., Seifert, M., Thi, T.M., Renou, J.P., Balzergue, S., Viehover, P., Hahnel, U. et al. (2012) Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. Plant J., 71, 427-442.
54. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193. (Pubitemid 36181903)
55. Seifert, M., Keilwagen, J., Strickert, M. and Grosse, I. (2009) Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. Bioinformatics, 25, 2118-2125.
56. Rabiner, L.R. (1989) A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc. IEEE, 77, 257-283.
57. Breitling, F. and Herzyk, P. (2005) Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data. J. Bioinf. Comp. Biol., 3, 1178-1189.
58. Hong, F., Breitling, R., McEntee, C.W., Wittner, B.S., Nemhauser, J.L. and Chory, J. (2006) RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics, 22, 2825-2827. (Pubitemid 44742407)
59. Stalberg, K., Ellerstrom, M., Josefsson, L.G. and Rask, L. (1993) Deletion analysis of a 2S seed storage protein promoter of Brassica napus in transgenic tobacco. Plant Mol. Biol., 23, 671-683. (Pubitemid 2021189)
60. Kleindt, C.K., Stracke, R., Mehrtens, F. and Weisshaar, B. (2010) Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Res. Notes, 3, 255.
61. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol., 136, 2621-2632. (Pubitemid 41071302)
62. Keilwagen, J., Grau, J., Paponov, I.A., Posch, S., Strickert, M. and Grosse, I. (2011) De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput. Biol., 7, e1001070.
63. Aoyama, T. and Chua, N.H. (1997) A glucocorticoid-mediated transcriptional induction system in transgenic plants. Plant J., 11, 605-612. (Pubitemid 27158965)
64. Suzuki, M., Kao, C.Y., Cocciolone, S. and McCarty, D.R. (2001) Maize VP1 complements Arabidopsis abi3 and confers a novel ABA/auxin interaction in roots. Plant J., 28, 409-418. (Pubitemid 34045588)
65. Ivanov, R., Tiedemann, J., Czihal, A., Schallau, A., Diep, l.H., Mock, H.P., Claus, B., Tewes, A. and Baumlein, H. (2008) EFFECTOR OF TRANSCRIPTION2 is involved in xylem differentiation and includes a functional DNA single strand cutting domain 8. Dev. Biol., 313, 93-106. (Pubitemid 350298303)
66. Carbon, S., Ireland, A., Mungall, C.J., Shu, S., Marshall, B. and Lewis, S. (2011) AmiGO: online access to ontology and annotation data. Bioinformatics, 25, 288-289.
67. Dunwell, J.M., Purvis, A. and Khuri, S. (2004) Cupins: the most functionally diverse protein superfamily? Phytochemistry, 65, 7-17. (Pubitemid 38155888)
68. Kreis, M., Forde, B.G., Rahman, S., Miflin, B.J. and Shewry, P.R. (1985) Molecular evolution of the seed storage proteins of barley, rye and wheat. J. Mol. Biol., 183, 499-502.
69. Tunnacliffe, A. and Wise, M.J. (2007) The continuing conundrum of the LEA proteins. Naturwissenschaften, 94, 791-812. (Pubitemid 47367664)
70. Capuano, F., Beaudoin, F., Napier, J.A. and Shewry, P.R. (2007) Properties and exploitation of oleosins. Biotechnol. Adv., 25, 203-206. (Pubitemid 46149226)
71. Guiltinan, M.J., Marcotte, W.R. Jr and Quatrano, R.S. (1990) A plant leucine zipper protein that recognizes an abscisic acid response element. Science, 250, 267-271. (Pubitemid 120031749)
72. Hattori, T., Totsuka, M., Hobo, T., Kagaya, Y. and Yamamoto-Toyoda, A. (2002) Experimentally determined sequence requirement of ACGT-containing abscisic acid response element. Plant Cell Physiol., 43, 136-140. (Pubitemid 34152466)
73. Dickinson, C.D., Evans, R.P. and Nielsen, N.C. (1988) RY repeats are conserved in the 50-flanking regions of legume seed-protein genes. Nucleic Acids Res., 16, 371.
74. Suzuki, M., Ketterling, M.G. and McCarty, D.R. (2005) Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1-and CBF/DREB1-regulated genes of Arabidopsis. Plant Physiol., 139, 437-447. (Pubitemid 43951626)
75. Hwang, J.E., Hong, J.K., Lim, C.J., Chen, H., Je, J., Yang, K.A., Kim, D.Y., Choi, Y.J., Lee, S.Y. and Lim, C.O. (2010) Distinct expression patterns of two Arabidopsis phytocystatin genes, AtCYS1 and AtCYS2, during development and abiotic stresses. Plant Cell Rep., 29, 905-915.
76. Bies-Etheve, N., Gaubier-Comella, P., Debures, A., Lasserre, E., Jobet, E., Raynal, M., Cooke, R. and Delseny, M. (2008) Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana. Plant Mol. Biol., 67, 107-124.
77. Drea, S.C., Lao, N.T., Wolfe, K.H. and Kavanagh, T.A. (2006) Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. Plant J., 46, 723-735. (Pubitemid 43780620)
78. Haslekas, C., Grini, P.E., Nordgard, S.H., Thorstensen, T., Viken, M.K., Nygaard, V. and Aalen, R.B. (2003) ABI3 mediates expression of the peroxiredoxin antioxidant AtPER1 gene and induction by oxidative stress. Plant Mol. Biol., 53, 313-326. (Pubitemid 38097963)
79. Kotak, S., Vierling, E., Baumlein, H. and Koskull-Doring, P. (2007) A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis. Plant Cell, 19, 182-195. (Pubitemid 46852710)
80. Park, J., Lee, N., Kim, W., Lim, S. and Choi, G. (2011) ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds. Plant Cell, 23, 1404-1415.
81. Li, Z. and Thomas, T.L. (1998) PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell, 10, 383-398. (Pubitemid 28553953)
82. Shuai, B., Reynaga-Pena, C.G. and Springer, P.S. (2002) The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol., 129, 747-761. (Pubitemid 34695944)
83. Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R. et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110. (Pubitemid 32001583)
84. To, A., Valon, C., Savino, G., Guilleminot, J., Devic, M., Giraudat, J. and Parcy, F. (2006) A network of local and redundant gene regulation governs Arabidopsis seed maturation. Plant Cell, 18, 1642-1651. (Pubitemid 44025549)
85. Peng, F.Y. and Weselake, R.J. (2011) Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. BMC Genomics, 12, 286.
86. Koudritsky, M. and Domany, E. (2008) Positional distribution of human transcription factor binding sites. Nucleic Acids Res., 36, 6795-6805.
87. Schutze, K., Harter, K. and Chaban, C. (2008) Post-translational regulation of plant bZIP factors. Trends Plant Sci., 13, 247-255.
88. Uno, Y., Furihata, T., Abe, H., Yoshida, R., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2000) Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc. Natl Acad. Sci. USA, 97, 11632-11637.
89. Guerriero, G., Martin, N., Golovko, A., Sundstrom, J.F., Rask, L. and Ezcurra, I. (2009) The RY/Sph element mediates transcriptional repression of maturation genes from late maturation to early seedling growth. New Phytol., 184, 552-565.
90. Ma, Y., Szostkiewicz, I., Korte, A., Moes, D., Yang, Y., Christmann, A. and Grill, E. (2009) Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science, 324, 1064-1068.
91. Park, S.Y., Fung, P., Nishimura, N., Jensen, D.R., Fujii, H., Zhao, Y., Lumba, S., Santiago, J., Rodrigues, A., Chow, T.F. et al. (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science, 324, 1068-1071.
92. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet., 26, 75-83.
93. Bell, O., Tiwari, V.K., Thoma, N.H. and Schubeler, D. (2011) Determinants and dynamics of genome accessibility. Nat. Rev. Genet., 12, 554-564.
94. Roudier, F., Ahmed, I., Berard, C., Sarazin, A., Mary-Huard, T., Cortijo, S., Bouyer, D., Caillieux, E., Duvernois-Berthet, E., Al-Shikhley, L. et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J., 30, 1928-1938.
95. Gagete, A.P., Franco, L. and Isabel, R.M. (2011) The Pisum sativum psp54 gene requires ABI3 and a chromatin remodeller to switch from a poised to a transcriptionally active state. New Phytol., 192, 353-363.
96. Ng, D.W. and Hall, T.C. (2008) PvALF and FUS3 activate expression from phaseolin promoter by different mechanisms. Plant Mol. Biol., 66, 233-244.