A valid strategy for precise identifications of transcription factor binding sites in combinatorial regulation using bioinformatic and experimental approaches

Plant Methods

Volumn 9, Issue 1, 2013, Pages

  Wang, Hailong ^a,b   Guan, Shan ^a   Zhu, Zhixin ^a,b   Wang, Yan ^a   Lu, Yingqing ^a  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

bHLH; cis element; Dual luciferase transient expression assay; EMSA; MYB

Indexed keywords

EUKARYOTA; IPOMOEA; IPOMOEA PURPUREA; MAGNOLIA; MAGNOLIACEAE; MALUS X DOMESTICA; PETUNIA; ZEA MAYS;

EID: 84882555010     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-9-34     Document Type: Article

References (40)

1. Lelli KM, Slattery M, Mann RS. Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet 2012, 46:43-68. 10.1146/annurev-genet-110711-155437, 22934649.
2. Walhout AJM. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 2006, 16:1445-1454. 10.1101/gr.5321506, 17053092.
3. Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 2006, 16:1455-1464. 10.1101/gr.4140006, 17053094.
4. Hannenhalli S. Eukaryotic transcription factor binding sites - modeling and integrative search methods. Bioinformatics 2008, 24:1325-1331. 10.1093/bioinformatics/btn198, 18426806.
5. Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. Biochimica et biophysica acta 1819, 2012:67-77.
6. Stracke R, Werber M, Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 2001, 4:447-456. 10.1016/S1369-5266(00)00199-0, 11597504.
7. Suzuki A, Wu CY, Washida H, Takaiwa F. Rice MYB protein OSMYB5 specifically binds to the AACA motif conserved among promoters of genes for storage protein glutelin. Plant and Cell Physiology 1998, 39:555-559. 10.1093/oxfordjournals.pcp.a029404, 9664718.
8. Liao Y, Zou HF, Wang HW, Zhang WK, Ma B, Zhang JS, Chen SY. Soybean GmMYB76, GmMYB92, and GmMYB177 genes confer stress tolerance in transgenic Arabidopsis plants. Cell Res 2008, 18:1047-1060. 10.1038/cr.2008.280, 18725908.
9. Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y. Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices. Cell 1994, 79:639-648. 10.1016/0092-8674(94)90549-5, 7954830.
10. Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I, Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH. Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis. Nucleic Acids Res 2011, 39:8992-9008. 10.1093/nar/gkr558, 3203581, 21771861.
11. Blackwell TK, Kretzner L, Blackwood EM, Eisenman RN, Weintraub H. Sequence-specific dna-binding by the c-myc protein. Science 1990, 250:1149-1151. 10.1126/science.2251503, 2251503.
12. Waldmuller S, Link G. Sequence and expression characteristics of three g-Box-binding factor cDNAs from Brassica napus. Plant Mol Biol 1995, 29:507-517. 10.1007/BF00020981, 8534849.
13. Giuliano G, Hoffman NE, Ko K, Scolnik PA, Cashmore AR. A light-entrained circadian clock controls transcription of several plant genes. Embo Journal 1988, 7:3635-3642. 454935, 3208743.
14. Kong Q, Pattanaik S, Feller A, Werkman JR, Chai CL, Wang YQ, Grotewold E, Yuan L. Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R. Proc Natl Acad Sci U S A 2012, 109:E2091-E2097. 10.1073/pnas.1205513109, 3409794, 22778424.
15. Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant Journal 2011, 66:94-116. 10.1111/j.1365-313X.2010.04459.x, 21443626.
16. Payne CT, Zhang F, Lloyd AM. GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1 and TTG1. Genetics 2000, 156:1349-1362. 1461316, 11063707.
17. Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L. TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant Journal 2004, 39:366-380. 10.1111/j.1365-313X.2004.02138.x, 15255866.
18. Koes R, Verweij W, Quattrocchio F. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 2005, 10:236-242. 10.1016/j.tplants.2005.03.002, 15882656.
19. Winkel-Shirley B. It takes a garden. How work on diverse plant species has contributed to an understanding of flavonoid metabolism. Plant Physiol 2001, 127:1399-1404. 10.1104/pp.010675, 1540170, 11743081.
20. Goff SA, Cone KC, Chandler VL. Functional-analysis of the transcriptional activator encoded by the maize-B gene - evidence for a direct functional interaction between 2 classes of regulatory proteins. Genes Dev 1992, 6:864-875. 10.1101/gad.6.5.864, 1577278.
21. Carey CC, Strahle JT, Selinger DA, Chandler VL. Mutations in the pale aleurone color1 regulatory gene of the Zea mays anthocyanin pathway have distinct phenotypes relative to the functionally similar TRANSPARENT TESTA GLABRA1 gene in Arabidopsis thaliana. Plant Cell 2004, 16:450-464. 10.1105/tpc.018796, 341916, 14742877.
22. Quattrocchio F, Wing JF, Leppen HTC, Mol JNM, Koes RE. Regulatory genes-controlling anthocyanin pigmentation are functionally conserved among plant-species and have distinct sets of target genes. Plant Cell 1993, 5:1497-1512. 160381, 12271045.
23. deVetten N, Quattrocchio F, Mol J, Koes R. The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants, and animals. Genes Dev 1997, 11:1422-1434. 10.1101/gad.11.11.1422, 9192870.
24. Chang SM, Lu YQ, Rausher MD. Neutral evolution of the nonbinding region of the anthocyanin regulatory gene Ipmyb1 in Ipomoea. Genetics 2005, 170:1967-1978. 10.1534/genetics.104.034975, 1449781, 15944366.
25. Park KI, Ishikawa N, Morita Y, Choi JD, Hoshino A, Iida S. A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation. Plant Journal 2007, 49:641-654. 10.1111/j.1365-313X.2006.02988.x, 17270013.
26. Morita Y, Saitoh M, Hoshino A, Nitasaka E, Iida S. Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and ca mutations conferring white flowers in the Japanese morning glory. Plant and Cell Physiology 2006, 47:457-470. 10.1093/pcp/pcj012, 16446312.
27. Fried M, Crothers DM. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide-gel electrophoresis. Nucleic Acids Res 1981, 9:6505-6525. 10.1093/nar/9.23.6505, 327619, 6275366.
28. Hellman LM, Fried MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2007, 2:1849-1861. 10.1038/nprot.2007.249, 2757439, 17703195.
29. Ow DW, Wood KV, Deluca M, Dewet JR, Helinski DR, Howell SH. Transient and stable expression of the firefly luciferase gene in plant-cells and transgenic plants. Science 1986, 234:856-859. 10.1126/science.234.4778.856, 17758108.
30. McNabb DS, Reed R, Marciniak RA. Dual luciferase assay system for rapid assessment of gene expression in Saccharomyces cerevisiae. Eukaryot Cell 2005, 4:1539-1549. 10.1128/EC.4.9.1539-1549.2005, 1214206, 16151247.
31. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-W208. 10.1093/nar/gkp335, 2703892, 19458158.
32. Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 2003, 15:1749-1770. 10.1105/tpc.013839, 167167, 12897250.
33. Dare AP, Schaffer RJ, Lin-Wang K, Allan AC, Hellens RP. Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes. Plant Methods 2008, 4:17. 10.1186/1746-4811-4-17, 2491621, 18601751.
34. Roth BA, Goff SA, Klein TM, Fromm ME. C1-dependent and r-dependent expression of the maize bz1 gene requires sequences with homology to mammalian myb and myc binding-sites. Plant Cell 1991, 3:317-325. 160002, 1840914.
35. Sainz MB, Grotewold E, Chandler VL. Evidence for direct activation of an anthocyanin promoter by the maize C1 protein and comparison of DNA binding by related Myb domain proteins. Plant Cell 1997, 9:611-625. 156943, 9144964.
36. Lesnick ML, Chandler VL. Activation of the maize anthocyanin gene a2 is mediated by an element conserved in many anthocyanin promoters. Plant Physiol 1998, 117:437-445. 10.1104/pp.117.2.437, 34963, 9625696.
37. Espley RV, Brendolise C, Chagne D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten HJ, Gardiner SE, Hellens RP, Allan AC. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell 2009, 21:168-183. 10.1105/tpc.108.059329, 2648084, 19151225.
38. Elomaa P, Uimari A, Mehto M, Albert VA, Laitinen RAE, Teeri TH. Activation of anthocyanin biosynthesis in Gerbera hybrida (Asteraceae) suggests conserved protein-protein and protein-promoter interactions between the anciently diverged monocots and eudicots. Plant Physiol 2003, 133:1831-1842. 10.1104/pp.103.026039, 300736, 14605235.
39. Cover T, Hart P. Nearest neighbor pattern classification. IEEE Transactions on Information Theory 1967, 13:21-27.
40. Liu YG, Whittier RF. Thermal asymmetric interlaced PCR - automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 1995, 25:674-681. 10.1016/0888-7543(95)80010-J, 7759102.