Cấu trúc quy định upstream của các gen lúa: Tóm tắt cơ sở cho phân tích so sánh quy định mạng lưới trên toàn bộ chi và khai thác alen

Rice - Tập 8 - Trang 1-21 - 2015
Benildo G de los Reyes1, Bijayalaxmi Mohanty2, Song Joong Yun3, Myoung-Ryoul Park1, Dong-Yup Lee2
1School of Biology and Ecology, University of Maine, Orono, USA
2Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
3Department of Crop Science and Institute of Agricultural Science and Technology, Chonbuk National University, Chonju, Korea

Tóm tắt

Việc phân tích cấu trúc quy định upstream của các gen lúa và các protein điều tiết tương ứng của chúng là cốt lõi của sinh học mạng lưới và các ứng dụng của nó trong sinh học chức năng so sánh. Với các nguồn tài nguyên sinh học so sánh về gen trong chi Oryza đang phát triển nhanh chóng, việc thiết lập một chú thích genome tham chiếu xác định các yếu tố cis và các yếu tố trans-acting khác nhau, kết nối mỗi locus gen với các tín hiệu bên trong và bên ngoài khác nhau cho sự phát triển, phát triển sinh sản và thích ứng là rất cần thiết để tạo điều kiện cho việc hiểu biết về biến thể phenotypic trong bối cảnh của các mạng lưới điều tiết. Thông tin như vậy cũng rất quan trọng để tạo nền tảng cho việc khai thác sự biến đổi trong chuỗi không mã hóa, xác định các alen và epialleles mới giữa sự đa dạng phenotypic khổng lồ có trong nguồn gen lúa. Bài đánh giá này trình bày một tổng hợp về tình trạng kiến thức và các xu hướng đồng thuận liên quan đến các thành phần cis-acting và trans-acting khác nhau, xác định sự điều chỉnh không gian-thời gian của các gen lúa dựa trên các ví dụ tiêu biểu từ cả các nghiên cứu nền tảng ở những cây mô hình và cây không mô hình khác, cũng như các nghiên cứu gần đây ở lúa. Mục tiêu là tóm tắt cơ sở cho việc chú thích trình tự upstream có hệ thống của các nguồn tài nguyên trình tự genome đang phát triển nhanh chóng trong Oryza nhằm chuẩn bị cho các nghiên cứu sinh học chức năng trên toàn chi. Các quan điểm về các ứng dụng tiềm năng của thông tin này trong việc phát hiện gen, kỹ thuật mạng lưới và giống lúa được hỗ trợ bởi genomics cũng được thảo luận.

Từ khóa

#cấu trúc quy định #gen lúa #sinh học mạng lưới #gen chức năng so sánh #nghiền alen

Tài liệu tham khảo

Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and MYB homologs in drought and abscisic acid regulated gene expression. Plant Cell 9:1859–1868 Abeles FB, Morgan PW, Saltvet ME (1992) Ethylene in Plant Biology, 2nd edn. CA, Academic Press Inc., San Diego, 414 pp Alvarez ME (2000) Salicylic acid in the machinery of hypersensitive cell death and disease resistance. Plant Mol Biol 44:429–442 Bagnaresi P, Biselli C, Orrù L, Urso S, Crispino L, Abbruscato P, Piffanelli P, Lupotto E, Cattivelli L, Valè G (2012) Comparative transcriptome profiling of the early response to Magnaporthe oryzae in durable resistant vs susceptible rice (Oryza sativa L.) genotypes. PLoS ONE 7(12):e51609 Baumann K, De Paolis A, Constantino P, Gualberti G (1999) The DNA binding site of the Dof protein NtBBF1 is essential for tissue-specific and auxin-regulated expression of the rolB oncogene in plants. Plant Cell 11:323–334 Baranowskij N, Frohberg C, Prat S, Willmitzer L (1994) A novel DNA binding protein with homology to Myb oncoproteins containing only one repeat can function as a transcriptional activator. EMBO J 13:5383–5392 Bhattacharyya J, Chowdhury AH, Ray S, Jha JK, Das S, Gayen S, Chakraborty A, Mitra J, Maiti MK, Basu A, Sen SK (2012) Native polyubiquitin promoter of rice provides increased constitutive expression in stable transgenic rice plants. Plant Cell Rep 31:271–279 Bodenhausen N, Reymond P (2007) Signaling pathways controlling induced resistance to insect herbivores in Arabidopsis. Mol Plant-Micr Interact 20:1406–1420 De Bodt S, Thiessen G, Van de Peer Y (2006) Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. Mol Biol Evol 23:1293–1303 Bradnam KR, Korf I (2008) Longer first introns are a general property of eukaryotic gene structure. PLoSOne 3(8):e3093 Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM (2003) A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiol 132:1020–1032 Buchanan-Wolaston V, Earl S, Harrison E, Mathas E, Navabpour S, Page T, Pink D (2003) The molecular analysis of leaf senescence- A genomics approach. Plant Biotech J 1:3–22 Buchanan-Wollaston V (1997) The molecular biology of leaf senescence. J Exptl Bot 48:181–199 Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A 100:5136–5141 Burke TW, Kadonaga JT (1997) The downstream core promoter element DPE is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 11:3020–3031 Butler JEF, Kadonaga JT (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15:2515–2519 Cai M, Wei J, Li X, Caiguo X, Wang S (2007) A rice promoter containing both novel positive and negative cis-elements for regulation of green tissue-specific gene expression in transgenic plants. Plant Biotech J 5:664–674 Chandlee JM (2001) Current molecular understanding of the genetically programmed process of leaf senescence. Physiol Plant 113:1–8 Chapman EJ, Estelle M (2009) Mechanism of auxin-regulated gene expression in plants. Annu Rev Genet 43:265–285 Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Goicoechea JL, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, et al (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Comm 4:1595 Chen PW, Lu CA, Yu TS, Tseng TH, Wang CS, Yu SM (2002) Rice α-amylase transcriptipnal enhancers direct multiple mode regulation of promoters in transgenic rice. J Biol Chem 277:13641–13649 Chen PW, Chiang CM, Tseng TH, Yu SM (2006) Interaction between rice MYBGA and the gibberellin response element controls tissue-specific sugar sensitivity of a-amylase genes. Plant Cell 18:2326–2340 Cheng C, Yun KY, Ressom H, Mohanty B, Bajic VB, Jia Y, Yun SJ, De los Reyes BG (2007) An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics 8:e175 Chinnusamy V, Ohta M, Kanrar S, Lee B, Hong X, Agarwal M, Zhu JK (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17:1043–1054 Choi DW, Rodriguez EM, Close TM (2002) Barley Cbf3 gene identification, expression pattern and map location. Plant Physiol 129:1781–1787 Christensen AH, Quail PH (1996) Ubiquitin promoter-based vectors for high levels of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Res 5:213–218 Ciolkowski I, Wanke D, Birkenbihl RP, Somssich IE (2008) Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function. Plant Mol Biol 68:81–92 Clancy M, Vasil V, Hannah LC, Vasil IK (1994) Maize shrunken-1 intron and exon regions increase gene expression in maize protoplasts. Plant Sci 98:151–161 Clivan P, Svec M (2009) Genome-wide analysis of rice (O. sativa ssp. japonica) TATA box and Y-patch promoter elements. Genome 52:294–297 Creelman RA, Mullet JE (1995) Jasmonic acid distribution and action in plants: Regulation during development and response to biotic and abiotic stress. Proc Natl Acad Sci U S A 92:4114–4119 Croissant-Sych Y, Okita T (1996) Identification of positive and negative regulatory cis-elements of the rice glutelin Gt3 promoter. Plant Sci 116:27–35 Darmasiri N, Darmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445 Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E (2003) AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinfor 4:e25 Dempsey DA, Klessig DF (2012) SOS - too many signals for systemic acquired resistance? Trends Plant Sci 17:538–545 Desveaux D, Subramaniam R, Despres C (2004) A ‘Whirly’ transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis. Dev Cell 6:229–240 Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki Y (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high salt-, and cold-responsive gene expression. Plant J 33:751–763 Farmer EE, Alméras E, Krishnamurthy V (2003) Jasmonates and related oxylipins in plant responses to pathogenesis and herbivory. Curr Opin Plant Biol 6:372–378 Finkelstein R (2006) Studies of abscisic acid perception finally flower. Plant Cell 18:786–791 Fleet CM, Sun T (2005) A DELLAcate balance: The role of gibberellins in plant morphogenesis. Curr Opin Plant Biol 8:77–85 Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690 Freeling M, Subramaniam S (2009) Conserved non-coding sequences (CNSs) in higher plants. Cur Opin Plant Biol 12:126–132 Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12:393–404 Gan S, Amasino RM (1997) Making sense of senescence. Plant Physiol 133:313–319 Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J (2006) DRTF: A database of rice transcription factors. Bioinformatics 22(10):1286–1287 Garcion C, Métraux JP (2006) Salicylic acid. Plant Hormone Signal 24:229–255 Gilmour SJ, Sebolt AM, Salazar MP, Everard JD, Thomashow MF (2000) Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol 124:1854–1865 Giraudat J, Parcy F, Bertandre N, Gosti F, Leung J, Morris PC, Bouvier-Durand M, Vartanian N (1994) Current advances in abscisic acid action and signaling. Plant Mol Biol 26:1557–1577 Gomez-Porras JL, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B (2007) Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 8:260 Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, Kitano H, Matsuoka M (2004) GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. Plant J 37:626–634 Grierson C, Du JS, De Torres ZM, Beggs K, Smith C, Holdsworth M, Bevan M (1994) Separate cis sequences and trans factors direct metabolic and developmental regulation of a potato tuber storage protein gene. Plant J 5:815–826 Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Philips AL, Hedden P, Sun TP, Thomas SG (2006) Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell 18:3399–3414 Gu Y, Yang C, Thara YK, Zhou J, Martin GB (2000) Pti4 is induced by ethylene and salicylic acid, and its product is phosphorylated by the Pto kinase. Plant Cell 12:771–786 Guedes Correa LG, Riano-Pachon DM, Schrago CG, Vincentini dos Santos R, Mueller-Roeber B, Vincents M (2008) The role of bZIP transcription factors in green plants evolution: Adaptive features emerging from four founder genes. PLoSOne 8:e2994 Guiltinan MJ, Marcotte WR Jr, Quatrano RS (1990) A plant leucine zipper protein that recognizes and abscisic acid response element. Science 250:267–271 Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 36:D966–D969 Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J (2005) DATF: A Database of Arabidopsis Transcription Factors. Bioinformatics 21:2568–2569 Guo H, Moose SP (2003) Conserved noncoding sequences among cultivated cereal genomes indentify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15:1143–1158 Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: Genes, promoters and regulatory factors. Plant Mol Biol 49:373–385 Hai P, Guanghai J, Jing Z, Weixiong Z, WenXue Z (2013) DNA methylation polymorphism and stability in Chinese indica hybrid rice. Sci China Life Sci 56:1097–1106 Hamada K, Hongo K, Suwabe K, Shimizu A, Nagayama T, Abe R, Kikuchi S, Yamamoto N, Fujii T, Yokoyama K, Tsuchida H, Sano K, Mochizuki T, Oki N, Horiuchi Y, Fujita M, Watanabe M, Matsuokoa M, Kurata N, Yano K (2011) OryzaExpress: An integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol 52:220–229 Hao D, Ohme-Takagi M, Sarai A (1998) Unique mode of GCC-box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J Biol Chem 273:26857–26861 Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16:369–372 Hart CM, Nagy F, Meins F Jr (1993) A 61-bp enhancer element of the tobacco beta-1,3-glucanase B gene interacts with one or more regulated nuclear proteins. Plant Mol Biol 21:121–131 Hartweck LM (2008) Gibberellin signaling. Planta 229:1–13 Hartweck LM, Olszewski NE (2006) Rice gibberellin insensitive dwarf1 is a gibberellin receptor that illuminates and raises questions about GA signaling. Plant Cell 18:278–282 He C, Lin Z, McElroy D, Wu R (2009) Identification of a rice Actin2 gene regulatory region for high-level expression of transgenes in monocots. Plant Biotech J 7:227–239 Helliwell EE, Yang Y (2013) Molecular strategies to improve rice disease resistance. Methods Molec Biol 956:285–309 Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucl Acids Res 27:297–300 Hobo T, Kowyama Y, Hatori Y (1999) A bZIP factor TRAB1 interacts with VP1 and mediates abscisic acid induced transcription. Proc Natl Acad Sci USA 96:15348–15353 Hong RL, Hamaguchi L, Busch MA, Weigel D (2003) Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing. Plant Cell 15:1296–1309 Hu H, You J, Fang Y, Zhu X, Xiong L (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol Biol 67:169–181 Hwang SH, Lee IA, Yie SW, Hwang DJ (2008) Identification of an OsPR10a promoter region responsive to salicylic acid. Planta 227:1141–1150 Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K, Umemura I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M (2005) Crown rootless1, which is essential for crown root formation in rice, is a target of an auxin response factor in auxin signaling. Plant Cell 17:1387–1396 Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futshuhara Y, Matsuoka M, Yamaguchi J (2001) Slender rice, a constitutive gibberellins response mutant is caused by a null mutation in the SLR1 gene, an orthologue of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13:999–1010 Ishiguro S, Nakamura K (1994) Characterization of a cDNA encoding a novel DNA-binding protein SPF1 that recognizes SP8 sequences in the 5’ upstream regions of genes coding for sporamin and beta-amylase from sweet potato. Mol Gen Genet 244:563–571 Itoh H, Sasaki A, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Hasegwa Y, Minami E, Ashikari M, Matsuoka M (2005) Dissection of the phosphorylation of rice DELLA protein SLENDER RICE1. Plant Cell Physiol 46:1392–1399 Jacquemin J, Bhatia D, Singh K, Wing RA (2012) The International Oryza Map Alignment Project: Development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16:147–156 Jacquemin J, Ammiraju SS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA (2014) Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Molec Plant 7(4):642–656 Jaglo KR, Kleff S, Amundsen KL, Zhang X, Haake V, Zhang JZ, Deits T, Thomashow MF (2001) Components of the Arabidopsis C-repeat/dehydration-responsive element binding factor cold-response pathway are conserved in Brassica napus and other plant species. Plant Physiol 127:910–917 Jaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O, Thomashow MF (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280:104–106 Johansson A, Staal J, Dixelius C (2006) Early responses in the Arabidopsis-Verticillium longisporum pathosystem are dependent on NDR1, JA- and ET-associated signaling via cytosolic NPR1 and RFO1 Mol. Plant Microbe Interact 19:958–969 Jain M, Kaur N, Tyagi AK, Khurana JP (2006a) The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics 6:36–46 Jain M, Tyagi AK, Khurana JP (2006b) Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics 88:360–371 Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006c) Strcuture and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 6:47–59 Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7:106–111 Jang IC, Choi WB, Lee KH, Song SI, Nahm BH, Kim JK (2002) High-level and ubiquitous expression of the rice cytochrome c gene OsCc1 and its promoter activity in transgenic plants provides a useful promoter for transgenesis of monocots. Plant Physiol 129:1473–1481 Jeong YM, Mun JH, Lee I, Woo JC, Hong CB, Kim SG (2006) Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members. Plant Physiol 140:196–209 Juven-Gershon T, Kadonaga JT (2010) Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol 339:225–229 Kaneko M, Itoh H, Euguchi-Tanaka M, Ashikari M, Matsuoka M (2002) The α-amylase induction in endosperm during rice seed germination is caused by gibberellin synthesized in epithelium. Plant Physiol 128:1264–1270 Kasuga M, Kiu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nature Biotech 17:287–291 Kaufmann K, Pajoro A, Angenent GC (2010) Regulation of transcription in plants: Mechanisms controlling developmental switches. Nature Rev Genet 11:830–842 Kieffer M, Neve J, Kepinski S (2010) Defining auxin response contexts in plant development. Cur Opin Plant Biol 13:12020 Kim SY, Wu R (1990) Multiple protein factors bind to a rice glutelin promoter region. Nucl Acids Res 18:6845–6852 Kitomi Y, Ito H, Hobo T, Aya K, Kitano H, Inikai Y (2011) The auxin responsive AP2/ERF transcription actor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J 67:472–484 Koo AJK, Howe GA (2009) The wound hormone jasmonate. Phytochem 70:1571–1580 Lenhard B, Sandelin A, Carninci P (2012) Metazoan promoters: Emerging characteristics and insights into transcriptional regulation. Nature Rev Genet 13:233–245 Lenka SK, Lohia B, Kumar A, Chinnusamy V, Bansal KC (2009) Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. Plant Molec Biol 69:261–271 Lescot M, Déhais P, Thijs G, Marchal M, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327 Lim PO, Kim HJ, Nam HG (2007) Leaf senescence. Ann Rev Plant Biol 58:115–136 Li J, Brader G, Palva ET (2004) The WRKY70 transcription factor: a node of convergence for jasmonate mediated and salicylate-mediated signals in plant defense. Plant Cell 16:319–331 Liu H, Wang S, Yu X, Yu J, He X, Zhang S, Wu P (2005a) ARL1, a LOB domain protein required for adventitious root formation in rice. Plant J 43:47–56 Liu XQ, Bai XQ, Qian Q, Wang XJ, Chen MS, Chu CC (2005b) OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1. Cell Res 15:593–603 Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low temperature-responsive gene expression, respectively in Arabidopsis. Plant Cell 10:1391–1406 Liu L, Zhou Y, Szczerba MW, Li S, Lin Y (2010) Identification and application of a rice senescence-associated promoter. Plant Physiol 153:1239–1249 Liu D, Chen X, Liu J, Ye J, Guo Z (2012) The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. J Exp Bot 63:3899–3911 Lovegrove A, Hooley R (2000) Gibberellin and abscisic acid signaling in aleurone. Trends Plant Sci 5:102–110 Lu J, Ju HP, Zhou GX, Zhu CS, Erb M, Wang XP, Wang P, Lou YG (2011) An EAR-motif-containing ERF transcription factor affects herbivore-induced signaling, defense and resistance in rice. Plant J 68:583–596 Lu CA, Lim EK, Yu SM (1998) Sugar response sequence in the promoter of a rice a-amylase gene serves as a transcriptional enhancer. J Biol Chem 273:10120–10131 Manners JM, Penninckx IAMA, Vermaere K, Kazan K, Brown RL, Morgan A, Maclean DJ, Curtis MD, Cammue BPA, Broekaert WF (1998) The promoter of the plant defensin gene PDF1.2 from Arabidopsis is systemically activated by fungal pathogens and responds to methyl jasmonate but not to salicylic acid. Plant Mol Biol 38:1071–1080 Matys V, Fricke E, Geffers R, GoBling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucl Acids Res 31:374–378 McElroy D, Blowers AD, Jenes B, Wu R (1991) Construction of expression vectors based on the rice actin1 (Act1) 5’ region for use in monocot transformation. Mol Gen Genet 231:150–160 McElroy D, Zhang W, Wu R (1990) Isolation of an efficient actin promoter for in rice transformation. Plant Cell 2:163–171 Mehrotra R, Gupta G, Sethi R, Bhalothia P, Kumar N, Mehrotra S (2011) Designer promoter: An artwork of cis engineering. Plant Mol Biol 75:527–536 Meier S, Gehring C, MacPherson CR, Kaur M, Maqungo M, Reuben S, Mayunga S, Shih MD, Wei FJ, Wanchana S, Mauleon R, Radovanovic A, Bruskiewich R, Tanaka T, Mohanty B, Itoh T, Wing R, Gojobori T, Sasaki T, Swarup S, Hsing Y, Bajic VB (2008) The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network. Rice 1:177–187 Mejia-Guerra MK, Pomeranz M, Morohashi K, Grotewold E (2012) From plant gene regulatory grids to network dynamics. Biochim Biophys Acta 1819:454–465 Miyamoto K, Shimizu T, Lin F, Sainsbury F, Thuenemann E, Lomonossoff G, Nojiri H, Yamane H, Okada K (2012) Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice. J Plant Physiol 169:621–627 Moabbi AM, Agarwal N, Kaderi BE, Ansari A (2011) Role for gene looping in intron-mediated enhancement of transcription. Proc Natl Acad Sci U S A 109:8505–8510 Mohanty B, Hearth V, Wijaya E, Yeo HC, De los Reyes BG, Lee DY (2012) Patterns of cis-element enrichment revealed potential regulatory modules involved in the transcriptional regulation of anoxia response in japonica rice. Gene 511:235–242 Molina C, Grotewold E (2005) Genome-wide analysis of Arabidopsis core promoters. BMC Genomics 6:25e Morris RT, O’Connor TR, Wyrick JJ (2008) Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 24:2915–2917 Nakashima K, Tran LSP, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51:617–630 Nakashima K, Ito Y, Yamaguchi-Shinozaki K (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol 149:88–95 Nam HG (1997) The molecular genetic analysis of leaf senescence. Curr Opin Biotech 8:200–207 Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34:137–144 Nemhauser JL, Mockler TC, Chory J (2004) Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol 2:e258 Nishizawa Y, Kawakami A, Hibi T, He DY, Shibuya N, Minami E (1999) Regulation of the chitinase gene expression in suspension cultured rice cells by N-acetylchitooligosaccharides: differences in the signal transduction pathways leading to the activation of elicitor-responsive genes. Plant Mol Biol 39:907–914 Noh YS, Amasino RM (1999) Identification of a promoter region responsible for the senescence-specific expression of SAG12. Plant Molec Biol 41:181–194 Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, Yamaguchi S (2003) Gibberellin biosynthesis and response during Arabidopsis seed germination. Plant Cell 15:1591–1604 Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7:173–182 Ohme-Takagi M, Suzuki K, Shinshi H (2000) Regulation of ethylene-induced transcription of defence genes. Plant and Cell Physiol 41:1187–1192 Ohta M, Matsui K, Hiratsu K, Shinshi H, Ohme-Takagi M (2001) Repression domains of class II ERF transcriptional repressor share an essential motif for active repression. Plant Cell 13:1959–1968 Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gajobori T, Sasaki T (2006) The rice annotation project (RAP-DB) Hub for Oryza sativa ssp. japonica genome information. Nucl Acids Res 34:D741–D744 Okita TW, Whang YS, Huilo J, Kim WT, Aryan AP, Larsen R, Krishnan HB (1989) Structure and expression of the rice glutelin multigene family. J Biol Chem 264:12573–12581 Parra G, Bradnam K, Rose AB, Korf I (2011) Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucl Acids Res 39:5328–5337 Park SH, Yi N, Kim YS, Jeong MH, Bang SW, Choi YD, Kim JK (2010a) Analysis of five novel putative constitutive gene promoters in transgenic rice plants. J Exptl Bot 61:2459–2467 Park MR, Yun KY, Herath V, Mohanty B, Xu F, Bajic VB, Yun SJ, De los Reyes BG (2010b) Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. Plant Cell Environ 33:2209–2230 Peng H, Zhang J (2009) Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding. Prog Nat Sci 19:1037–1045 Peng X, Hu Y, Tang X, Zhou P, Deng X, Wang H, Guo Z (2012) Constitutive expression of rice WRKY30 gene increases the endogenous jasmonic acid accumulation, PR gene expression and resistance to fungal pathogens in rice. Planta 236:1485–1498 Perez-Rodriguez P, Riano-Pachon DM, Correa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: Updated content and new features of the plant transcription factor database. Nucl Acids Res 38:D822–D827 Pieterse CMJ, Van Wees SCM, Van Pelt JA, Knoester M, Laan R, Gerrits H, Weisbeek PJ, Van Loon LC (1998) A novel signalling pathway controlling induced systemic resistance in Arabidopsis. Plant Cell 10:1571–1580 Qu LQ, Xing YP, Liu W, Xu XP, Song YR (2008) Expression pattern and activity of six glutelin gene promoters in transgenic rice. J Exptl Bot 59:2417–2424 Quint M, Gray WM (2006) Auxin signaling. Cur Opin Plant Biol 9:448–453 Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755–1767 Razem FA, El Kereamy A, Abrams SR, Hill RD (2006) The RNA-binding protein FCA is an abscisic acid receptor. Nature 439:290–294 Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B (2007) PlnTFDB: An integrative plant transcription factor database. BMC Bioinformatics 8:e42 Robatzek S, Somssick IE (2002) Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev 16:1139–1149 Rojo E, Leon J, Sanchez-Serrano JJ (1999) Cross-talk between wound signaling pathways determines local versus systemic gene expression in Arabidopsis thaliana. Plant J 20:135–142 Rose AB, Emami S, Bradnam K, Korf I (2011) Evidence for a DNA-based mechanism of intron-mediated enhancement. Front Plant Sci 2:1–9 Rounsley S, Reddy Marri P, Yu Y, He R, Sisneros N, Goicoechea JL, Lee SJ, Angelova A, Kudrna D, Luo M, Affourtit J, Desany B, Knight J, Niazi F, Egholm M, Wing RA (2009) De novo next generation sequencing of plant genomes. Rice 2:35–43 Ryu HS, Han M, Lee SK, Cho JI, Ryoo N, Heu S, Lee YH, Bhoo SH, Wang GL, Hahn TR, Jeon JS (2006) A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep 25:836–847 Santino A, Taurino M, DeDomenico S, Bonsegna S, Poltronieri P, Pastor V, Flors V (2013) Jasmonate signaling in plant development and defense response to multiple (a)biotic stresses. Plant Cell Rep 32:1085–1098 Sato K, Shimizu T, Kondoh H, Hirguri A, Sasaya T, Choi IR, Omura T, Kikuchi S (2011) Relationship between symptoms and gene expression induced by the infection of three strains of rice dwarf virus. PLoSOne 6:3e18094 Scarpella E, Rueb S, Boot KJM, Hoge JHC, Meijer AH (2000) A role of the rice homeobox gene OsHox1 in provascular fate commitment. Development 127:3655–3669 Scarpella E, Simons EJ, Meijer AH (2005) Multiple regulatory elements contribute to the vascular-specific expression of the rice HD-ZIP gene OsHox1 in Arabidopsis. Plant Cell Physiol 46:1400–1410 Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Caminci P, Hayashizaki Y, Shinozaki K (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13:61–72 Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R. (2009) STIFDB–Arabidopsis Stress-responsive Transcription Factor DataBase. Int J Plant Genomics ID583429: doi:10.1155/2009/583429. Shen QJ, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufficient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119 Shen QJ, Ho TH (1995) Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABA-responsive complexes each containing G-box and a novel cis-acting element. Plant Cell 7:295–307 Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, Toki S, Takatsuji H (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19:2064–2076 Shimono M, Koga H, Akagi A, Hayashi N, Goto S, Sawada M, Kurihara T, Matsushita A, Sugano S, Jiang CJ, Kaku H, Inoue H, Takatsuji H (2012) Rice WRKY45 plays important roles in fungal and bacterial disease resistance. Mol Plant Pathol 13:83–94 Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3:217–223 Shinwari ZK, Nakashima K, Miura S, Masuga M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K (1998) An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low temperature responsive gene expression. Biochem Biophys Res Comm 250:161–170 Shoji T, Kajikawa M, Hashimoto T (2010) Clustered transcription factor genes regulate nicotine biosynthesis in tobacco. Plant Cell 22:3390–3409 Shoji T, Hashimoto T (2012) DNA-binding and transcriptional activation properties of tobacco NIC2-locus ERF189 and related transcription factors. Plant Biotechnol 29:35–42 Singh MP, Lee FN, Counce PA, Gibbons JH (2004) Mediation of partial resistance to rice blast through anaerobic induction of ethylene. Phytopathology 94:819–825 Silverman P, Seskar M, Kanter D, Schweizer P, Metraux JP, Raskin I (1995) Salicylic acid in rice. Biosynthesis, conjugation, and possible role. Plant Physiol 108:633–639 Smale ST (2001) Core promoters: Active contributors to combinatorial gene regulation. Genes Dev 15:2503–2508 Smale ST, Baltimore D (1989) The ‘initiator’ as a transcription control element. Cell 57:103–113 Song Y, You J, Xiong L (2009) Characterization of OsIAA gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Plant Mol Biol 70:297–309 Srivastav AQ, Mehta S, Lindlof A, Bhargava S (2010) Over-represented promoter motifs in abiotic stress-induced DREB genes of rice and sorghum and their probable role in regulation of gene expression. Plant Signal Behav 5:775–784 Stockinger EJ, Yaopan M, Regier MK, Triezenberg SJ, Thomashow MF (2001) Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucl Acids Res 29:1524–1533 Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcription activator element that binds to the C-repeat/DRE, a cis-acting regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A 94:1035–1040 Sutoh K, Yamauchi D (2003) Two cis-acting elements necessary and sufficient for gibberellin-upregulated proteinase expression in rice seeds. Plant J 34:635–645 Suzuki K, Suzuki N, Ohme-Takagi M, Shinshi H (1998) Immediate early induction of mRNAs for ethylene-responsive transcription factors in tobacco leaf strips after cutting. Plant J 15:657–665 Takaiwa F, Kikuchi S, Oono K (1987) Nucleotide sequence of a rice glutelin gene. FEBS Lett 206:33–35 Takaiwa F, Oono K, Wing D, Kato A (1991) Sequence of three members and expression of a new major subfamily of glutelin genes from rice. Plant Molec Biol 17:875–885 Thakur JK, Tyagi AK, Khurana JP (2001) OsIAA1, an Aux/IAA cDNA from rice and changes in its expression as influenced by auxin and light. DNA res 8:193–203 Thomas H, Howart CJ (2000) Five ways to stay green. J Expt Bot 5:329–337 Thomashow MF (1999) Plant cold acclimation: Freezing tolerance genes and regulatory mechanisms. Ann Rev Plant Physiol Plant Molec Biol 50:571–599 Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 43:265–285 Todaka D, Nakashima K, Shinozaki K, Yamaguchi-Shinozaki K (2012) Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice. Rice 5:e6 Ueguchi-Tanaka M, Nakajima M, Katoh E, Ohmiya H, Asano K, Saji S, Hongyu X, Ashikari M, Kitano H, Yamaguchi I, Matsuoka M (2007) Molecular interactions of a soluble gibberellins receptor, GID1 with a rice DELLA protein SLR1 and gibberellins. Plant Cell 19:2140–2155 Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow TY, Hsing YI, Kitano H, Yamaguchi I, Matsuokoa M (2005) GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437:693–698 Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–1868 Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ (1995) Composite structure of auxin response elements. Plant Cell 7:1611–1623 Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K (1993) An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 5:1529–1539 Vlot AC, Dempsey DMA, Klessig DF (2009) Salicylic acid, a multifaceted hormone to combat disease. Annu Rev Phytopathol 47:177–206 Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF (2005) Roles of CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41:195–211 Vogel JM, Roth B, Cigan M, Freeling M (1993) Expression of the two maize TATA binding protein genes and functions of the encoded TBP proteins by complementation in yeast. Plant Cell 5:1627–1638 Wager A, Browse J (2012) Social network: JAZ protein interactions expand our knowledge of jasmonate signaling. Front Plant Sci 3:1–11 Waller F, Furuya M, Nick P (2002) OsARF1, an auxin response factor from rice is an auxin-regulated and classifies as a primary auxin responsive gene. Plant Mol Biol 50:415–425 Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J (2010) SoyDB: A knowledge database of soybean transcription factors. BMC Plant Biol 10:e14 Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, Tang K, Han B, Tao Y (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene 394:13–24 Wang X, Haberer G, Mayer KFX (2009) Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation. BMC Genom 10:284e Wang J, Oard JH (2003) Rice ubiquitin promoters: Deletion analysis and potential usefulness in plant transformation systems. Plant Cell Rep 22:129–134 Washida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K, Takaiwa F (1999) Identification of cis-regualtory elements required for endosperm expression of the rice storage protein glutelin gene GluB-1. Plant Molec Biol 40:1–12 Wasternack C (2007) Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot 100:681–697 Wing RA, Ammiraju SS, Luo M, Kim HR, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar DS, Mackill DJ, Han B, Soderlund C, Stein L, SanMiguel P, Jackson S (2005) The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice species. Plant Molec Biol 59:53–62 Wingender E, Dietze P, Karas H, Knüppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucl Acids Res 24:238–241 Xie X, Lu J, Kullbokas EJ, Golub T, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematics discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338–345 Xu F, Park MR, Mohanty B, Herath V, Kitazumi A, Yun SJ, De los Reyes BG (2012a) Cis-regulatory signatures among orthologous groups of stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. BMC Genomics 13:e497 Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2012b) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotech 30:105–111 Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic and cold stress responsive promoters. Trends Plant Sci 10:88–94 Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopis gene is involved in responsiveness to drought, low temperature or high salt stress. Plant Cell 6:251–264 Yamamoto YY, Ichida H, Matusi M, Obokata J, Sakurai T, Satou M, Seki M, Shinozaki K, Abe T (2007) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8:e67 Yang Y, Qi M, Mei C (2004) Endogenous salicylic acid protects rice plants from oxidative damage caused by aging as well as biotic and abiotic stress. Plant J 40:909–919 Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics 17:87–100 Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149:171–180 Yokotani N, Sato Y, Tanabe S, Chujo T, Shimizu T, Okada K, Yamane H, Shimono M, Sugano S, Takatsuji H, Kaku H, Minami E, Nishizawa Y (2013) WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. J Expt Bot 64:5085–5097 Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, De los Reyes BG (2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol 10:e16 Zarka DG, Vogel JT, Cook D, Thomashow MF (2003) Cold induction of Arabidopsis CBF genes involves multiple ICE (Inducer of CBF Expression) promoter elements and a cold-regulatory circuit that is desensitized by low temperature. Plant Physiol 133:910–918 Zhang Z, Gerstein M (2003) Of mice and men: Phylogenetic footprinting aids the discovery of regulatory elements. BMC J Biol 2:e11 Zhang X, Fowler SG, Cheng H, Lou Y, Rhee SY, Stockinger EJ, Thomashow MF (2004) Freezing-sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing-tolerant Arabidopsis. Plant J 39:905–919 Zhang H, Jin JP, Tang L, Zhao Y, Gu XC, Gao G, Luo JC (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39:D1114–D1117 Zhang J, Peng Y, Guo Z (2008) Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants. Cell Res 18:508–521 Zhang W, McElroy D, Wu R (1991) Analysis of rice Act1 5’ region activity in transgenic rice plants. Plant Cell 3:1155–1165 Zhao Y, Leisy DJ, Okita TW (1994) Tissue-specific expression and temporal regulation of the rice glutelin Gt3 gene are conferred by at least two spatially separated cis-regulatory elements. Plant Molec Biol 25:429–436 Zheng X, Chen L, Li M, Lou Q, Xia H, Wang P, Li T, Liu H, Luo L (2013) Transgenerational variations in DNA methylation induced by drought stress in two rice varieties with distinguished difference to drought resistance. PLoSOne 8:e80253 Zheng Z, Kawagoe Y, Xiao S, Li Z, Okita T, Hau TL, Lin A, Murai N (1993) 5’ distal and proximal cis-acting regulator elements are required for developmental control of a rice seed storage protein glutelin gene. Plant J 4:357–366 Zhu Q, Dabi T, Lamb C (1995) TATA-box and initiator functions in the accurate transcription of a plant minimal promoter in vitro. Plant Cell 7:1681–1689 Zhu Q, Ordiz MI, Dabi T, Beachy RN, Lamb C (2002) Rice TATA binding protein interacts functionally with transcription factor IID and the RF2a bZIP transcriptional activator in an enhanced plant in vitro transcription system. Plant Cell 14:795–803 Zourelidou M, De-Torres Zabala M, Smith C, Bevan MW (2002) Store-keeper defines a new class of plant-specific DNA binding proteins and is a putative regulator of patatin expression. Plant J 30:489–497