Cloning differentially expressed mrnas

Nature Biotechnology

Volumn 14, Issue 13, 1996, Pages 1685-1691

  Wan, Jackson S ^a   Sharp, Stephen J ^a   Poirier, Ghislaine M C ^a   Wagaman, Pamela C ^a   Chambers, James ^a   Pyati, Jayashree ^a   Hom, Yao Ling ^a   Galindo, Jose E ^a   Huvar, Arne ^a   Peterson, Per A ^a   Jackson, Michael R ^a   Erlander, Mark G ^a  

^a R W JOHNSON PHARMACEUTICAL RES I   (United States)

Author keywords

Differential display; Differential gene expression; Electronic subtraction; EST; Subtractive hybridization

Indexed keywords

GAMMA INTERFERON; MESSENGER RNA;

ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION; HELA CELL; HUMAN; HUMAN CELL; MOLECULAR CLONING; PRIORITY JOURNAL; RNA HYBRIDIZATION;

ANTIVIRAL AGENTS; BLOTTING, NORTHERN; CELL COUNT; CLONING, MOLECULAR; DNA, COMPLEMENTARY; GENE EXPRESSION; GENE LIBRARY; HELA CELLS; HUMANS; INTERFERON TYPE II; NUCLEIC ACID HYBRIDIZATION; RIBOSOMAL PROTEINS; RNA, MESSENGER;

EID: 10544244583     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1296-1685     Document Type: Article

References (59)

1. Loros, J.J., Denome, S.A., and Dunlap, J.C. 1989. Molecular cloning of genes under control of the circadian clock in Neurospora. Science 243:385-388.
2. Wilkinson, J.Q., Lanahan, M.B., Conner, T.W., and Klee, H.J. 1995. Identification of mRNAs with enhanced expression in ripening strawberry fruit using polymerase chain reaction differential display. Plant. Mol. Biol. 27:1097-1108.
3. Smith, D.P., Shieh, B.H., and Zuker, C.S. 1990. Isolation and structure of an arrestin gene from Drosophila. Proc. Natl. Acad. Sci. USA 87:1003-1007.
4. Qu, D., et al. 1996. A role for melanin-concentrating hormone in the central regulation of feeding behaviour. Nature 380:243-247.
5. Douglass, J., McKinzie, A.A., and Couceyro, P. 1995. PCR differential display identifies a rat brain mRNA that is transcriptionally regulated by cocaine and amphetamine. J. Neuroscience 15:2471-2481.
6. Wang, X., et al. 1995. Discovery of adrenomedullin in rat ischemic cortex and evidence for its role in exacerbating focal brain ischemic damage. Proc. Natl. Acad. Sci. USA 92:11480-11484.
7. el-Deiry, W.S., et al. 1993. WAFI, a potential mediator of p53 tumor suppression. Cell 75:817-825.
8. Woronicz, J.D., Calnan, B., Ngo, V, and Winoto, A. 1994. Requirement for the orphan steroid receptor Nur77 in apoptosis of T- cell hybridomas. Nature 367:277-281.
9. Travis, G.H., Milner, R.J., and Sutcliffe, J.G. 1989. pp. 49-78 in Neuromethods vol. 16: molecular neurobiological techniques. Boulton, A.A., Baker, G.B., and Campagnoni, A.T. (eds.) The Humana Press, Clifton, NJ.
10. Watson, J.B. and Margulies, J.E. 1993. Differential cDNA screening strategies to identify novel stage-specific proteins in the developing mammalian brain. Developmental Neuroscience 15:77-86.
11. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
12. Adams, M.D., Soares, M.B., Kerlavage, A.R., Fields, C., and Venter, J.C. 1993. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nature Genetics 4:373-380.
13. Franco, G.R., et al. 1995. Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library. Gene 152:141-147.
14. Itoh, K., Matsubara, K., and Okubo, K. 1994. Identification of an active gene by using large-scale cDNA sequencing. Gene 140:295-296.
15. Murakawa, K., Matsubara, K., Fukushima, A., Yoshii, J., and Okubo, K. 1994. Chromosomal assignments of 3′-directed partial cDNA sequences representing novel genes expressed in granulocytoid cells. Genomics 23:379-389.
16. Okubo, K., et al. 1992. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nature Genetics 2:173-179.
17. Velculescu, V.E., Zhang, L, Vogelstein, B., and Kinzler, K.W. 1995. Serial analysis of gene expression. Science 270:484-487.
18. Liang, P. and Pardee, A.B. 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967-971.
19. Welsh, J., et al. 1992. Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 20:4965-4970.
20. Livesey, F.J. and Hunt, S.P. 1996. Identifying changes in gene expression in the nervous system: mRNA differential display. Trends Neurosci. 19:84-88.
21. Axel, R., Feigelson, P., and Schutz, G. 1976. Analysis of the complexity and diversity of mRNA from chicken liver and oviduct. Cell 7:247-254.
22. Bishop, J.O., Morton, J.G., Rosbash, M., and Richardson, M. 1974. Three abundance classes in HeLa cell messenger RNA. Nature 250:199-204.
23. Pestka, S., Langer, J.A., Zoon, K.C., and Samuel, C.E. 1987. Interferons and their actions. Annu. Rev. Biochem. 56:727-777.
24. Sen, G.C. 1991. pp. 349-374 in The hormonal control regulation of gene transcription. Cohen, P. and Foulkes, J.G. (eds.). Elsevier Science Publishers, New York.
25. Revel, M. and Chebath, J. 1986. Interferon-activated genes. TIBS 11:166-170.
26. Adams, M.D., et al. 1992. Sequence identification of 2, 375 human brain genes. Nature 355:632-634.
27. Adams, M.D., Kerlavage, A.R., Fields, C., and Venter, J.C. 1993. 3, 400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genetics 4:256-267.
28. Adams, M.D., et al. 1995. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377:3-174.
29. Sanders, J., Maassen, J.A., Amons, R., and Moller, W. 1991. Nucleotide sequence of human elongation factor-1 beta cDNA. Nucleic Acids Res. 19:4551.
30. Fields, C. and Adams, M.D. 1994. Expressed sequence tags identify a human isolog of the suil translation initiation factor. Biochem. Biophys. Res. Commun. 198:288-291.
31. Yang, Y, Fruh, K., Ahn, K., and Peterson, P.A. 1995. In vivo assembly of the proteasomal complexes, implications for antigen processing. J. Biol. Chem. 270:27687-27694.
32. Strehlow, I., et al. 1993. The gene encoding IFP 53/tryptophanyl-tRNA synthetase is regulated by the gamma-interferon activation factor. J. Biol. Chem. 268:16590-16595.
33. Borjigin, J., Wang, M.M., and Snyder, S.H. 1995. Diurnal variation in mRNA encoding serotonin N-acetyltransferase in pineal gland. Nature 378:783-785.
34. Travis, G.H., Brennan, M.B., Danielson, P.E., Kozak, C.A., and Sutcliffe, J.G. 1989. Identification of a photoreceptor-specific mRNA encoded by the gene responsible for retinal degeneration slow (rds). Nature 338:70-73.
35. Wu, G., Su, S., and Bird, R.C. 1994. Optimization of subtractive hybridization in construction of subtractive cDNA libraries. Genetic Analysis, Techniques & Applications 11:29-33.
36. Rothstein, J.L, et al. 1993. Construction of primary and subtracted cDNA libraries from early embryos. Methods Enzymol. 225:587-610.
37. Rubenstein, J.L., et al. 1990. Subtractive hybridization system using single-stranded phagemids with directional inserts. Nucleic Acids Res. 18:4833-4842.
38. Sive, H.L and St, J.T. 1988. A simple subtractive hybridization technique employing photoactivatable biotin and phenol extraction. Nucleic Acids Res. 16:10937.
39. Usui, H., et al. 1994. Isolation of clones of rat striatum-specific mRNAs by directional tag PCR subtraction. J. Neurosci. 14:4915-4926.
40. Rahmsdorf, H.J., et al. 1986. Interferon-gamma, mitomycin C, and cycloheximide as regulatory agents of MHC class II-associated invariant chain expression. J. Immunol. 136:2293-2299.
41. Rasmussen, U.B., et al. 1993. Identification of a new interferon-alpha-inducible gene (p27) on human chromosome 14q32 and its expression in breast carcinoma. Cancer Res. 53:4096-4101.
42. Gaczynska, M., Rock, K.L., and Goldberg, A.L 1993. Gamma-interferon and expression of MHC genes regulate peptide hydrolysis by proteasomes. Nature 365:264-267.
43. Flodstrom, M., Niemann, A., Bedoya, F.J., Morris, S.M., Jr., and Eizirik, D.L. 1995. Expression of the citrulline-nitric oxide cycle in rodent and human pancreatic beta-cells: Induction of argininosuccinate synthetase by cytokines. Endocrinology 136:3200-3206.
44. Volanakis, J.E. 1995. Transcriptional regulation of complement genes. Ann Rev. Immunol. 13:277-305.
45. Liang, P., Averboukh, L., and Pardee, A.B. 1993. Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. Nucleic Acids Res. 21:3269-3275.
46. Liang, P., et al. 1994. Differential display using one-base anchored oligo-dT primers. Nucleic Acids Res. 22:5763-5764.
47. Liang, P. and Pardee, A.B. 1995. Recent advances in differential display. Current Opinion in Immunology 7:274-280.
48. Zhao, S., Ooi, S.L, and Pardee, A.B. 1995. New primer strategy improves precision of differential display. Biotechniques 18:842-846, 848, 850.
49. Bauer, D., et al. 1993. Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR). Nucleic Acids Res. 21:4272-4280.
50. Aiello, L.P., Robinson, G.S., Lin, Y.W., Nishio, Y, and King, G.L. 1994. Identification of multiple genes in bovine retinal pericytes altered by exposure to elevated levels of glucose by using mRNA differential display. Proc. Natl. Acad. Sci. USA 91:6231-6235.
51. Debouck, C. 1995. Differential display or differential dismay? Current Opinion in Biotechnology 6:597-599.
52. Gasque, P., et al. 1993. Expression of the complement classical pathway by human glioma in culture. A model for complement expression by nerve cells. J. Biol. Chem. 268:25068-25074.
53. Holland, C.A., Mayrand, S., and Pederson, T. 1980. Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138:755-778.
54. Britten, R.J. and Davidson, E.H. 1985. pp. 3-15 in Nucleic acid hybridisation a practical approach. Hames, B.D. and Higgins, S.J. (eds.). Oxford University Press, Oxford, UK.
55. Bertioli, D.J., et al. 1995. An analysis of differential display shows a strong bias towards high copy number mRNAs. Nucleic Acids Res. 23:4520-4523.
56. Van Gelder, R.N., et al. 1990. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87:1663-1667.
57. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
58. Altschul, S.F., Glsh, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
59. Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.