Abstract
We have obtained an overall gene expression profile of a human fetal liver by sequencing the 5′ ends of random cDNA clones from an unbiased cDNA library. As a result, many novel genes that might be related to liver growth and hemopoiesis have been identified. Poly (A)+ RNA was purified from the liver of a human fetus obtained at the 22nd week of gestation, and a directional library was constructed with oligo d(T)-primed cDNAs synthesized without any normalizing procedures. The 5′ end of each randomly chosen clone was sequenced by the dideoxy-chain termination methods, and each sequence was used for homology search in the public databases such as GenBank, SWISS-PROT, and PIR. Of 1231 random cDNA clones analyzed, 697 clones representing 204 different transcripts (57%), were identical to previously known human genes. The spectrum of the genes in this category reflected well the physiological characteristics of the fetal liver, a combination of hepatic and hemopoietic functions. About 4% of the clones represented novel gene transcripts with significant homologies to known genes of human or other organisms. These included several genes that are known to be involved in cellular differentiation and/or proliferation. About 25% of the clones had no statistically significant match to any known genes. In summary, we have identified 546 different gene transcripts consisting of 204 known human genes, 42 homologous genes, and 300 unknown genes. Thus, this approach appears to be a highly efficient way to identify novel genes of biological interest.
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Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulous, M.H., Xiao, H., Merril, C.R., Wu A., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R., Venter, J.C. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656.
Adams, M.D., Dubnick, M., Kerlavage, A.R., Moreno, R.F., Kelley, J.M., Utterback, T.R., Nagle, J.W., Fields, C., Venter, J.C. (1992). Sequence identification of 2,375 human brain genes. Nature 355, 632–634.
Adams, M.D., Kerlavage, A.R., Fields, C., Venter, J.C. (1993). 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genet. 4, 256–257.
Church, G., Gilbert, W. (1984). Genomic Sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995.
Feinberg, A.P., Vogelstein, B. (1983). A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6.
Hoog, C. (1991). Isolation of a large number of novel mammalian genes by a differential cDNA library screening strategy. Nucleic Acids Res. 19, 6123–6127.
Itoh, K., Okubo, K., Yosii, J., Yokouchi, H., Matsubara, K. (1994). An expression profile of active genes in human lung. DNA Res. 1, 279–287.
Kang, H.M., St-Jacques, B., Schwartz, F., Shin, H-S. (1994) Gene targeting in the Ke4 locus of the mouse in embryonic stem cells. Mol. Cells 4, 27–32.
Khan, A.S., Wilcox, A.S., Polymeropoulous, M.H., Hopkins, J.A., Stevens, T.J., Robinson, M., Orpana, A.K., Sikela, J.M. (1992). Single pass sequencing and physiological and genetic mapping of human brain cDNAs. Nature Genet. 2, 180–185.
Ko, M.S.H. (1990). An equalized cDNA library by reassociation of short double stranded cDNAs. Nucleic Acids Res. 18, 5705–5711.
Okubo, K., Hori, N., Matoba, R., Niiyama, T., Matsubara, K. (1991). A novel system for large-scale sequencing of cDNA by amplification. DNA Seq. 2, 137–144.
Okubo, K., Hori, N., Matoba, R., Niiyama, Fukushima, A., Kojima, Y., Matsubara, K. (1992). Large scale cDNA sequencing for analysis of expression. Nature Genet. 2, 173–179.
Okubo, K., Yoshii, J., Yokouchi, H., Kameyama, M., Matsubara, K. (1994). An expression profile of active genes in human colonic mucosa. DNA Res. 1, 37–45.
Papadopoulous, N., Nicolaides, N.C., Wei, Y.-F., Ruben, S.M., Carter, K.C., Rosen, C.A., Haseltaine, W.A., Fleischmann, R.D., Fraser, C.M., Adams, M.D., Venter, J.C., Hamilton, S.R., Peterson, G.M., Watson, P., Lynch, H.T., Peltomaki, P., Mecklin, J.-P., Chapelle, A., Kinzler, K.W., Vogelstein, B. (1994). Mutation of a mut L homolog in hereditary colon cancer. Science 263, 1625–1628.
Pantanjali, S.R., Primoo, P.S., Weissman, S.M. (1991). Construction of a uniform-abundance (normalized) cDNA library. Proc. Natl. Acad. Sci. USA 88, 1943–1947.
Sambrook, J., Fritsch, E.F., Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press), pp. 25–28.
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Choi, S.S., Yun, J.W., Choi, E.K. et al. Construction of a gene expression profile of a human fetal liver by single-pass cDNA sequencing. Mammalian Genome 6, 653–657 (1995). https://doi.org/10.1007/BF00352374
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DOI: https://doi.org/10.1007/BF00352374