Rice Biotechnology Lab - The Monocot Group: Gene Expression and Gene Silencing

Research funded Texas ATP grant 010366-0092-1999, NSF grant MCB 0110477, and Dow AgroSciences


Current Staff
Xiangyu Shi - Graduate Assistant, Genetics
Yiming Jiang - Graduate Assistant, Genetics
Dr. Chandra Emani - Visiting Research Scientist
Dr. Timothy C. Hall - Director

Recent Staff Members
Dr. Tao Wang - Graduate Assistant, Biology
Dr. Yeon-Hee Lee - Visiting Research Scientist
Dr. Magda Cervera - Visiting Scholar
Dr. Jinjiang Dong - Associate Scientist
Dr. Sophie Fernandez - Postdoctoral Research Associate
Dr. Rakesh Pancholy - Postdoctoral Research Associate
Ying Rong - Research Assistant
Dr. Prapapan "Lee" Teerawanichpan - Visiting Scholar
Dr. Guojun Yang - Postdoctoral Research Associate

Research Outline
As one of the most important food crops worldwide, rice is a very attractive candidate for improvement through biotechnological approaches. Its small genome (400-430 Mb) also makes rice an excellent model cereal for many studies. We have transformed rice with numerous genes and are especially interested in conferring resistance to the rice water weevil, the major insect pest of rice in Texas. Although direct DNA transformation techniques (electroporation, biolistics) yield transgenic plants (Battraw and Hall, 1990; Battraw and Hall, 1992), they are highly susceptible to gene silencing and other forms of unreliable expression. We now make extensive use of Agrobacterium-mediated transformation techniques (Dong et al., 1996) and have developed and patented a panicle method for rice transformation (Dong et al., 2001). We have collaborative interactions with industry in which we have transformed rice with gene constructs that are predicted to give resistance to microbial pathogens.

A major interest of the lab is currently gene silencing in rice. A detailed study of rice transformed biolistically with herbicide (bialaphos) resistance and putative insect resistance (Btt CryIIIA) genes showed that the transgene insert was present in many, rearranged copies that were frequently highly methylated and silenced (Kumpatla et al., 1997; Kumpatla and Hall, 1999). Germination of seedlings in the presence of 5-azacytidine resulted in reactivation of expression, but most plants were re-silenced within 50 days (Kumpatla and Hall, 1998a). Studies on inheritance of this transgene locus revealed that onset of silencing could recur through at least the R3 generation (Kumpatla and Hall, 1998b).

As we have reviewed (Kumpatla et al., 1998; Iyer et al., 2000), it has become evident that silencing serves many functions in plants and other organisms. These include protection against invasive DNA and RNA and vital roles in developmental processes. We have characterized silencing events in rice lines transformed with RCg2, a root-preferential promoter and lines bearing a three-gene construct (Hall et al., 2001). These appear to be very useful targets for reactivation of expression using knock-out techniques to debilitate the transgene silencing mechanisms. Genes encoding methyltransferases and chromatin-remodeling functions are key candidates for these studies.

Additional research foci include the production of transgenic rice expressing antimicrobial genes and an investigation of position effect on gene expression that includes the use of fluorescent in situ hybridization (FISH) techniques (Kharb et al., 2001).


Recent Publications
(Click here for a complete listing of our lab publications)

Dong, J., Kharb, P., Teng, W. and Hall, T.C. 2001. Characterization of rice transformed via an Agrobacterium-mediated inflorescence transformation. Mol. Breeding 7: 187-194.

Dong, J.J., Teng, W.M., Buchholz, W.G. and Hall, T.C. 1996. Agrobacterium-mediated transformation of javanica rice. Mol. Breeding 2: 267-276.

Hall, T. C., Kumpatla, S. P., Kharb, P., Iyer, L., Cervera, M., Jiang, Y., Wang, T., Yang, G., Teerawanichpan, P. Narangajavana, J. and Dong, J. 2001. Gene silencing and its reactivation in transgenic rice. p. 465-481. In: Rice Genetics IV (G. S. Khush, D. S. Brar and B. Hardy eds) Science Publishers, Inc., New Delhi (India) and International Rice Research Institute, Los Baņos (Philippines).

Iyer, L.M., Kumpatla, S.P., Chandrasekharan, M.B. and Hall, T.C. 2000. Transgene Silencing in Monocots. Plant Mol. Biol. 43: 323-346.

Kharb, P., Dong, J., Islam-Faridi, M.N., Stelly, D.M. and Hall, T.C. 2001. Fluorescence in situ hybridization of single copy transgenes in rice chromosomes. In Vitro Cell. Dev. Biol. - Plant 37: 1-5.

Kumpatla, S.P., Chandrasekharan, M.B., Iyer, L.M., Li, G. and Hall, T.C. 1998. Genome intruder scanning and modulation systems and transgene silencing. Trends Plant Sci. 3: 97-104.

Kumpatla, S.P. and Hall, T.C. 1998a. Longevity of 5-azacytidine-mediated gene expression and re- establishment of silencing in transgenic rice. Plant Mol. Biol. 38: 1113-1122.

Kumpatla, S.P. and Hall, T.C. 1998b. Recurrent onset of epigenetic silencing in rice harboring a multi-copy transgene. Plant J. 14: 129-135.

Kumpatla, S.P. and Hall, T.C. 1999. Organizational complexity of a rice transgene locus susceptible to methylation-based silencing. IUBMB Life 48: 459-467.

Kumpatla, S.P., Teng, W., Buchholz, W.G. and Hall, T.C. 1997. Epigenetic transcriptional silencing and 5-azacytidine-mediated reactivation of a complex transgene in rice. Plant Physiol. 115: 361-373.

Yang, G., Dong, J., Chandrasekharan, M.B. and Hall, T.C. 2001. Kiddo, a new transposable element family closely associated with rice genes. Mol. Genet. Genomics. 266: 417-424.

Yang, G. and Hall, T.C. 2003 (March). MDM-1 and MDM-2: Two Mutator-derived MITE families in rice. J. Mol. Evol. 56: 255-264.

Yang, G. and Hall, T.C. 2003. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res. 31: 3659-3665

Teerawanichpan, P., Chandrasekharan, M.B., Jiang, Y., Narangajavana, J. and Hall, T.C. 2003. Characterization of two rice DNA methyltransferase genes and RNAi-mediated restoration of promoter activity in silenced rice callus. Planta Sep 25 [Epub ahead of print]