New experimental and computational approaches to the analysis of gene expression

• Autorzy: Rafalski J. A. , Hanafey M. , Miao G.H. , Ching A. , Lee J.M. , Dolan M. , Tingey S.
• Języki publikacji: EN

Abstrakty

EN

Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained. To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries, from different tissues, developmental stages or induction conditions. This quantitation of message levels is quite accurate for highly expressed messages and, unlike conventional Northern blots, allows comparison of expression levels between different genes. Lists of most highly expresses genes in different libraries can be compiled. Also, if EST data is available for cDNA libraries derived from different developmental stages, gene expression profiles across development can be assembled. We present an example of such a profile for soybean seed development. Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays. The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the tissue of interest. Two-color fluorescent labeling allows accurate mRNA ratio measurements. We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil, carbohydrate and protein in developing seeds. In the future, high density DNA arrays containing the whole gene complement of an organism will become available for the analysis of genome-wide patterns of gene expression.

Słowa kluczowe

EN

elongation factor; gene expression; soybean; Expressed Sequence Tag programme; embryo

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 1998
• Tom: 45
• Numer: 4
• Opis fizyczny: p.929-934,fig.

Twórcy

autor

Rafalski J. A.

autor

Hanafey M.

autor

Miao G.H.

autor

Ching A.

autor

Lee J.M.

autor

Dolan M.

autor

Tingey S.

Bibliografia

• Adams, M.D., et al (1991) Complementary DNA sequencing. Expressed sequence tags and the human genome project. Science 252, 1651-1656.
• Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris. M.S. & Fodor, S.P.A. (1996) Access­ing genetic information with high-density DNA arrays. Science 274, 610-614.
• Derisi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M., Chen, Y.D., Su, Y.A. & Trent, J.M. (1996) Use of a cDNA microarray to analyze gene-expression patterns in human cancer. Nature Genetics 14, 457-460.
• Fodor, S.P.A. (1991) Lightdirected, spatially ad­dressable parallel chemical synthesis. Abstracts of papers of the American Chemical So­ciety 202, 90.
• Gress, T.M., Hoheisel, J.D., Lennon, G.G., Zehetr ner, G. & Lehrach, H. (1992) Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mammalian Genome 3, 609-619.
• Lockhart, D.J., Dong, H., Byrne, M.C. Follettie, M.T., Gallo, M.V., Chee, M.S., Mittman, M., Wang, C., Kobayashi, M., Horton, H. & Brown, E.L. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14, 1675-1680.
• Nguyen, C., Rocha, D., Granjeaud, S., Baldit, M., Bernard, K., Naquet, P. & Jordan, B.R. (1995) Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones. Genomics 29, 207- 216.
• Pietu, G., Alibert, O., Guichard, V., Lamy, B., Bois, F., Leroy, E., Mariage-Samson, R., Houl- gatte, R., Soularue, P. & Auffray, C. (1996) Novel gene transcripts preferentially ex­pressed in human muscles revealed by quanti­tative hybridization of a high density cDNA array. Genome Res. 6, 492-503.
• Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. (1995) Quantitative monitoring of gene- expression patterns with a complementary- DNA microarray. Science 270, 467-470.
• Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O. & Davis, R.W. (1996) Parallel hu­man genome analysis — microarray-based ex­pression monitoring of 1000 genes. Proc. Natl. Acad. ScL U.S.A 93, 10614-10619.
• Shalon, D., Smith, SJ. & Brown. P.O. (1996) A DNA microarray system for analyzing com­plex DNA samples using 2-color fluoroscent- probe hybridization. Genome Res. 6,639-645.
• Yershov, G., Barsky, V., Belgovskiy, A., Kirillov, E., Kreindlin, E., Ivanov, I., Parinov, S., Guschin, D., Drobishev, A., Dubiley, S. & Mirzabekov, A. (1996) DNA analysis and diag­nostics on oligonucleotide microchips. Proc. Nali Acad ScL USA. 93, 4913-1918.