Putative cis-regulatory elements in genes highly expressed in rice sperm cells

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Sharma, Niharika ^a   Russell, Scott D ^b   Bhalla, Prem L ^a   Singh, Mohan B ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

cis regulatory elements; gene expression; male gamete; Oryza sativa; plant reproduction

Indexed keywords

MAGNOLIOPHYTA; ORYZA SATIVA;

EID: 80052605559     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-319     Document Type: Article

References (46)

1. Representative cDNA library from isolated rice sperm cells. Gou XP, Xu Y, Tang L, Yan F, Chen F, Act Bot Sin 2001 43 10 1093 1096
2. Comparative transcriptomics of Arabidopsis sperm cells. Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijá JA, Becker JD, Plant Physiol 2008 148 2 1168 1181 10.1104/pp.108.125229 18667720 (Pubitemid 352847567)
3. Sperm cells of Zea mays have a complex complement of mRNAs. Engel ML, Chaboud A, Dumas C, McCormick S, Plant J 2003 34 5 697 707 10.1046/j.1365-313X. 2003.01761.x 12787250 (Pubitemid 36720203)
4. Expressed sequence tag analysis of Lilium longiflorum generative cells. Okada T, Bhalla PL, Singh MB, Plant Cell Physiol 2006 47 6 698 705 10.1093/pcp/pcj040 16571618 (Pubitemid 43946298)
5. Green sperm. Identification of male gamete promoters in Arabidopsis. Engel ML, Holmes-Davis R, McCormick S, Plant Physiol 2005 138 4 2124 2133 10.1104/pp.104.054213 16055690 (Pubitemid 43733555)
6. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G, Science 2000 290 5499 2105 2110 10.1126/science.290.5499.2105 11118137 (Pubitemid 32001583)
7. Plant cis-acting regulatory DNA elements (PLACE) database. Higo K, Ugawa Y, Iwamoto M, Korenaga T, Nucleic Acids Res 1999 27 1 297 300 10.1093/nar/27.1.297 9847208 (Pubitemid 29209466)
8. SIGNAL SCAN: A computer program that scans DNA sequences for eukaryotic transcriptional elements. Prestridge DS, Comput Appl Biosci 1991 7 2 203 206 2059845
9. MEME: discovering and analyzing DNA and protein sequence motifs. Bailey TL, Williams N, Misleh C, Li WW, Nucleic Acids Res 2006 34 Web server 369 W373
10. Gene expression in the dimorphic sperm cells of Plumbago zeylanica: transcript profiling, diversity, and relationship to cell type. Gou X, Yuan T, Wei X, Russell SD, Plant J 2009 60 1 33 47 10.1111/j.1365-313X.2009.03934.x 19500307
11. GENERATIVE CELL SPECIFIC 1 is essential for angiosperm fertilization. Mori T, Kuroiwa H, Higashiyama T, Kuroiwa T, Nat Cell Biol 2006 8 1 64 71 10.1038/ncb1345 16378100 (Pubitemid 43064798)
12. MicroRNA activity in Arabidopsis male germline. Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD, J Exp Bot 2011 62 5 1611 1620 10.1093/jxb/erq452 21357774
13. cis-Regulatory elements for mesophyll-specific gene expression in the C4 plant Flaveria trinervia the promoter of the C4 phosphoenolpyruvate carboxylase gene. Gowik U, Burscheidt J, Akyildiz M, Schlue U, Koczor M, Streubel M, Westhoff P, Plant Cell 2004 16 5 1077 1090 10.1105/tpc.019729 15100398 (Pubitemid 38641507)
14. Diversity and similarity among recognition sequences of Dof transcription factors. Yanagisawa S, Schmidt RJ, Plant J 1999 17 2 209 214 10.1046/j.1365-313X.1999.00363.x 10074718 (Pubitemid 29079714)
15. Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Yanagisawa S, Plant J 2000 21 3 281 288 10.1046/j.1365-313x.2000.00685.x 10758479 (Pubitemid 30152767)
16. Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Sakai H, Aoyama T, Oka A, Plant J 2000 24 6 703 711 10.1046/j.1365-313x.2000.00909.x 11135105 (Pubitemid 32100469)
17. Activation of the Oryza sativa non-symbiotic haemoglobin-2 promoter by the cytokinin-regulated transcription factor, ARR1. Ross EJ, Stone JM, Elowsky CG, Arredondo-Peter R, Klucas RV, Sarath G, J Exp Bot 2004 55 403 1721 1731 10.1093/jxb/erh211 15258171 (Pubitemid 39059314)
18. Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco. Shirsat A, Wilford N, Croy R, Boulter D, Mol Gen Genet 1989 215 2 326 331 10.1007/BF00339737 2710102
19. The GATA family of transcription factors in Arabidopsis and rice. Reyes JC, Muro-Pastor MI, Florencio FJ, Plant Physiol 2004 134 4 1718 1732 10.1104/pp.103.037788 15084732 (Pubitemid 38527379)
20. Cis-regulatory elements in plant cell signalling. Priest HD, Filichkin SA, Mockler TC, Curr Opin Plant Biol 2009 12 5 643 649 10.1016/j.pbi.2009.07.016 19717332
21. ASF-2: a factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in Cab promoters. Lam E, Chua NH, Plant Cell 1989 1 12 1147 1156 2535536
22. The mechanism of GT element-mediated cell type-specific transcriptional control. Villain P, Mache R, Zhou DX, J Biol Chem 1996 271 51 32593 32598 10.1074/jbc.271.51.32593 8955086 (Pubitemid 27008678)
23. Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex. Le Gourrierec J, Li YF, Zhou DX, Plant J 1999 18 6 663 668 10.1046/j.1365-313x.1999.00482.x 10417717 (Pubitemid 29341883)
24. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Zhou DX, Trends Plant Sci 1999 4 6 210 214 10.1016/S1360-1385(99) 01418-1 10366876 (Pubitemid 29270614)
25. Functional analysis of cis-regulatory elements within the promoter of the tobacco late pollen gene g10. Rogers HJ, Bate N, Combe J, Sullivan J, Sweetman J, Swan C, Lonsdale DM, Twell D, Plant Mol Biol 2001 45 5 577 585 10.1023/A:1010695226241 11414616 (Pubitemid 32515951)
26. Evaluation in tobacco of the organ specificity and strength of the rolD promoter, domain A of the 35S promoter and the 35S2 promoter. Elmayan T, Tepfer M, Transgenic Res 1995 4 6 388 3896 10.1007/BF01973757 7581519
27. A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, Shen QJ, Plant Physiol 2004 134 4 1500 1513 10.1104/pp.103.034967 15047897 (Pubitemid 38527360)
28. Early nuclear events in plant defence signalling: rapid gene activation by WRKY transcription factors. Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE, The EMBO J 1999 18 17 4689 4699 10.1093/emboj/18.17.4689 (Pubitemid 29415523)
29. The WRKY superfamily of plant transcription factors. Eulgem T, Rushton PJ, Robatzek S, Somssich IE, Trends Plant Sci 2000 5 5 199 206 10.1016/S1360-1385(00)01600-9 10785665 (Pubitemid 30300843)
30. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D, Shen QJ, Plant Physiol 2005 137 1 176 189 10.1104/pp.104.054312 15618416 (Pubitemid 43034300)
31. Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds. Stålberg K, Ellerstöm M, Ezcurra I, Ablov S, Rask L, Planta 1996 199 4 515 519 8818291 (Pubitemid 26350738)
32. Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B, Plant Mol Biol 2005 57 2 155 171 10.1007/s11103-004-6910-0 15821875 (Pubitemid 40580343)
33. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signalling. Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K, Plant Cell 2003 15 1 63 78 10.1105/tpc.006130 12509522 (Pubitemid 36137662)
34. ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, Agarwal M, Zhu JK, Genes Dev 2003 17 8 1043 1054 10.1101/gad.1077503 12672693 (Pubitemid 36459456)
35. Coordinate copper- and oxygen-responsive Cyc6 and Cpx1 expression in Chlamydomonas is mediated by the same element. Quinn JM, Barraco P, Eriksson M, Merchant S, J Biol Chem 2000 275 9 6080 6089 10.1074/jbc.275.9.6080 10692397 (Pubitemid 30129891)
36. A novel endo-beta-mannanase gene in tomato LeMAN5 is associated with anther and pollen development. Filichkin SA, Leonard JM, Monteros A, Liu PP, Nonogaki H, Plant Physiol 2004 134 3 1080 1087 10.1104/pp.103.035998 14976239 (Pubitemid 38398256)
37. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K, Plant Cell 1993 5 11 1529 1539 8312738 (Pubitemid 2021767)
38. New light on Myc and Myb. Part II. Myb. Lüscher B, Eisenman RN, Genes Dev 1990 4 12 2235 2241 10.1101/gad.4.12b.2235 2279697
39. Up-regulation of OsBIHD1, a rice gene encoding BELL homeodomain transcriptional factor, in disease resistance responses. Luo H, Song F, Goodman RM, Zheng Z, Plant Biol 2005 7 5 459 468 10.1055/s-2005-865851 16163610 (Pubitemid 41392024)
40. CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, Coupland G, Plant Cell 2006 18 11 2971 2984 10.1105/tpc.106.043299 17138697 (Pubitemid 46013270)
41. Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90-1 gene. Haralampidis K, Milioni D, Rigas S, Hatzopoulos P, Plant Physiol 2002 129 3 1138 1149 10.1104/pp.004044 12114568 (Pubitemid 34801084)
42. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Kagaya Y, Ohmiya K, Hattori T, Nucleic Acids Res 1999 27 2 470 478 10.1093/nar/27.2.470 9862967 (Pubitemid 29210010)
43. The AP2/EREBP family of plant transcription factors. Riechmann JL, Meyerowitz EM, Biol Chem 1998 379 6 633 646 9687012 (Pubitemid 28327562)
44. In silico identification of cis-regulatory elements of phosphate transporter genes in rice (Oryza sativa L.). Hatorangan MR, Sentausa E, Wijaya GY, J Crop Sci Biotechnol 2009 12 1 25 30 10.1007/s12892-008-0054-8
45. Putative cis-regulatory elements associated with heat shock genes activated during excystation of Cryptosporidium parvum. Cohn B, Manque P, Lara AM, Serrano M, Sheth N, Buck G, PLoS One 2010 5 3 9512 10.1371/journal.pone. 0009512 20209102
46. Mclip: motif detection based on cliques of gapped local profile-to-profile alignments. Frickey T, Weiller G, Bioinformatics 2007 23 4 502 503 10.1093/bioinformatics/btl601 17127680 (Pubitemid 46323135)