Random amplification of genomic ends (RAGE) as an efficient method for isolation and cloning of promoters and uncloned genomic regions

African Journal of Biotechnology

Volumn 8, Issue 19, 2009, Pages 4765-4773

  Kuriakose, Boney ^a,c   Ganesan, V ^a,d   Thomas, George ^b   Viswanathan, Arun ^a,e   Anand, Narayanaswamy ^a  

^a UNIVERSITY OF MADRAS   (India)

^b Interfield Laboratories   (India)

^c UNIVERSITY OF PRETORIA   (South Africa)

^d Acme ProGen Biotech (India) Private Limited   (India)

^e SRI RAMACHANDRA UNIVERSITY   (India)

Author keywords

Anabaena; Asr1; Cylindrospermum; Genome walking; HetR; Oryza malampuzhaensis; Oryza rufipogon; Promoter; RAGE

Indexed keywords

ARTICLE; BACTERIAL GENE; COMPUTER MODEL; CONTROLLED STUDY; CYANOBACTERIUM; CYLINDROSPERMUM STAGNALE; GENE AMPLIFICATION; GENE CONTROL; GENE EXPRESSION; GENE ISOLATION; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; HETR GENE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OSASR1 GENE; PLANT GENE; PLANT STRESS; PROMOTER REGION; RANDOM AMPLIFICATION OF GENOMIC ENDS; REGULATORY SEQUENCE; RICE;

ANABAENA; CYLINDROSPERMUM; CYLINDROSPERMUM STAGNALE; ORYZA MALAMPUZHAENSIS; ORYZA RUFIPOGON;

EID: 70350433950     PISSN: None     EISSN: 16845315     Source Type: Journal    
DOI: None     Document Type: Article

References (30)

1. Amitai-Zeigerson H, Scolnik PA, Bar-Zvi D (1995). Tomato Asr1 mRNA and protein are transiently expressed following salt stress, osmotic stress and treatment with abscisic acid. Plant Sci. 110: 205-213
2. Callis J, Carpenter T, Sun CW, Vierstra RD (1995). Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics, 139: 921-939
3. Chen W, Kuo T (1993) A simple and rapid method for preparation of gram negative bacterial genomic DNA. Nucl. Acids Res. 21: p. 2260
4. Dekeyser RA, Claes B, De Rycke RMU, Habets ME, Van Montagu MC, Caplan AB (1990) Transient gene expression in intact and organized rice tissues. Plant Cell 2: 591-602 (Pubitemid 120029616)
5. Filichkin SA, Leonard JM, Monteros A, Liu P, Nonogaki H (2004). A Novel Endo-β-Mannanase Gene in Tomato LeMAN5 is Associated with Anther and Pollen Development. Plant Physiol. 134: 1080-1087 (Pubitemid 38398256)
6. Fromm M, Taylor LP, Walbot V (1985). Expression of Genes Transferred into Monocot and Dicot Plant Cells by Electroporation. Proc. Nat. Acad. Sci. USA, 82: 5824-5828.
7. Gong H, Hu W, Jiao Y, Pua E (2005). Molecular characterization of a Phi-class mustard (Brassica juncea) glutathione S-transferase gene in Arabidopsis thaliana by 5′-deletion analysis of its promoter. Plant Cell Rep. 24: 439-447.
8. Hall TA (1999). BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41: 95-98.
9. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999). Plant cis-acting regulatory DNA elements (PLACE) database Nucl. Acids Res. 27: 297-300.
10. Hong JK, Hwang BK (2006). Promoter activation of pepper class II basic chitinase gene, CAChi2, and enhanced bacterial disease resistance and osmotic stress tolerance in the CAChi2-overexpressing Arabidopsis. Planta 223: 433-448
11. Horsch RB, Fry JE, Hoffman NL (1985). A simple and general method for transferring genes into plants. Science, 227: 1229-1231.
12. Iucern ND, Bartholomew DM, Hitz WD, Scolnik PA (1993). Tomato (Lycopersicon esculentum) transcript induced by water deficit and ripening. Plant Physiol. 102: 1353-1354
13. Jefferson RA, Kavanagh TA, Bevan MW (1987). GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6: 3901-3907
14. Kalifa Y, Gilad A , Konrad Z, Zaccai M, Scolnik PA, Bar-Zvi D (2004). The water- and salt-stress-regulated Asr1 (abscisic acid stress ripening) gene encodes a zinc-dependent DNA-binding protein. Biochem. J. 381: 373-378.
15. Khush GS (1997). Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35: 25-34.
16. Kuriakose B, Arun V, Gnanamanickam SS, Thomas G (2009). Tissue-specific expression in transgenic rice and Arabidopsis thaliana plants of GUS gene driven by the ' regulatory sequences of an anther specific rice gene YY2. Plant Sci. doi:10.1016/j.plantsci.2009.06.016.
17. Liu YG, Whittier RF (1995). Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics, 25: 674-681
18. Ochman H, Gerber AS, Hartl DL (1988). Genetic applications of an inverse polymerase chain reaction. Genetics, 120: 621-623. (Pubitemid 18260496)
19. Rogers SO, Bendich AJ (1994). Extraction of DNA from plant, fungal and algal tissues. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual. Boston, MA: Kluwer Academic Publishers, D 1: 1-8.
20. Rosenthal A, Jones DSC (1990) Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction. Nucleic Acids Res 18: 3095-3096 (Pubitemid 20178194)
21. Sambrook J, Fritsch EF, Maniatis T (1989). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
22. Shillito RD, Saul MW, Pasrkowski J, Müller M, Potrykus,I (1985). High efficiency direct gene transfer to plants. Nat. Biotech. 3: 1099-1103.
23. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995). An improved PCR method for walking in uncloned genomic DNA. Nucl. Acids Res. 23: 1087-1088.
24. Terauchi R, Kahl G (2000). Rapid isolation of promoter sequences by TAIL-PCR: the 5′-flanking regions of Pal and Pgi genes from yams (Dioscorea). Mol. Gen. Genet. 263: 554-560.
25. Vaidyanathan R, Kuruvilla S, Thomas G (1999). Characterization and expression pattern of an abscisic acid and osmotic stress responsive gene from rice. Plant Sci. 140: 21-30. (Pubitemid 29081225)
26. Wei H, Wang ML, Moore PH, Albert HH (2003). Comparative expression analysis of two sugarcane polyubiquitin promoters and flanking sequences in transgenic plants. J. Plant Physiol. 160: 1241-1251 (Pubitemid 37316977)
27. Werr W, Lorz H (1986). Transient gene expression in a Gramineae cell line. A rapid procedure for studying plant promoters. Mol. Gen. Genet. 202: 471-475
28. Wroblewski T, Tomczak A, Michelmore R (2005). Optimization of Agrobacterium-mediated transient assays of gene expression in lettuce, tomato and Arabidopsis. Plant Biotechnol. J. 3: 259-273 (Pubitemid 41615429)
29. Yang Y, Li R, Qi M (2000). In vivo analysis of plant promoters and transcription factors by agroinfiltration of tobacco leaves. Plant J. 22: 543-551
30. Zhang XH, Chiang VL (1996). Single-stranded DNA ligation by T4 RNA ligase for PCR cloning of 5′-noncoding fragments and coding sequence of a specific gene. Nucl. Acids Res. 24: 990-991.