The subset of genes expressed in a given cell or tissue type such as the prostate may be defined as the transcriptome, the dynamic link between the genome, the proteome, and the cellular phenotype associated with physical characteristics(1). Studies in the 1970's using reassociation kinetics to estimate the number of different cellular transcripts indicate that between 10,000 and 30,000 distinct mRNAs are present in mammalian cells or organs (2,3). Recent data produced using the method of Serial Analysis of Gene Expression (SAGE) support these estimates of transcript diversity in mammalian epithelial cells with estimates of 14,000-20,000 different mRNAs per cell (4). Although the identification of alternatively spliced transcripts and highly homologous gene family members may increase or decrease these estimates slightly, they nevertheless provide a rough estimate of the complexity of cellular gene activity. Based upon these data, the 25,000 prostate EST clusters that we have assembled should roughly comprise the prostate transcriptome. It is likely that this assembled dataset comprises all of the abundant and most of the moderately abundant prostate transcripts (5). Ongoing work involves the acquisition of the remaining low abundance transcripts. Approaches to achieving this goal involve the construction of cDNA libraries from highly selected purified cell populations such as luminal epithelial and neuroendocrine cells, and from prostate tissues at different stages of development (e.g. fetal prostate) or under different hormonal influences (e.g. androgen stimulation). Another useful strategy involves the iterative removal of abundant and previously identified cDNAs in order to select for rare species. A high-throughput method using cDNA array-based technology has been developed to facilitate this process (6).
Link to current human prostate transcriptome.
Functional annotation of LNCAP01 library (adapted from Tigr)
1. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., and Kinzler, K. W.
2. Hastie, N. D. and Bishop, J. O. The expression of three abundance classes of messenger RNA in mouse tissue, Cell. 9: 761-774, 1976.
3. Bishop, J. O., Morton, J. G., Rosbash, M., and Richardson, M. Three Abundance Classes in Hela Cell Messenger RNA, Nature. 250: 199-204, 1974.
4. Zhang, L., Zhou, W., Velculescu, V. E., Kern, S. E., Hruban, R. H., Hamilton, S. R., Vogelstein, B., and Kinzler, K. W. Gene Expression Profiles in Normal and Cancer Cells, Science. 276: 1268-1272, 1997.
5. Nelson, P. S., Ng, W. L., Schummer, M., True, L. D., Liu, A. Y., Bumgarner, R. E., Ferguson, C., Dimak, A., and Hood, L. An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones, Genomics. 47: 12-25, 1998.
6. Nelson, P. S., Hawkins, V., Schummer, M., Bumgarner, R., Ng, W. L., Ideker, T., Ferguson, C., and Hood, L. Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays, Genet Anal. 15: 209-15, 1999.