Summary
Identification and characterization of differentially expressed genes may be an important first step toward the understanding of both normal physiology and disease. A multitude of techniques belonging to two main categories have been developed to identify the differences in gene expression between samples from different biological origin: selection techniques and global techniques. Whereas the selection techniques strive to identify specific differentially expressed genes, the global techniques analyze the total transcriptome or a major part of the RNA population in a defined biological material. By exploiting the known sequences of the adaptors used in suppressive subtraction hybridization technique, a strategy named novel rescue—suppression-subtractive hybridization was developed. It should facilitate the discovery of differentially expressed genes.
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Saiki, R. K., Scharf, S., Faloona, F., et al. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.
Kacharmina, J. E., Crino, P. B., and Eberwine, J. (1999) Preparation of cDNA from single cells and subcellular regions. Methods Enzymol. 303, 3–18.
Liu, M., Subramanyam, Y. V., and Baskaran, N. (1999) Preparation and analysis of cDNA from a small number of hematopoietic cells. Methods Enzymol. 303, 45–55.
Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring, NY.
Sargent, T. D. and Dawid, I. B. (1983) Differential gene expression in the gastrula of Xenopus laevis. Science 222, 135–139.
Timberlake, W. E. (1980) Developmental gene regulation in Aspergillus nidulans. Dev. Biol. 78, 497–510.
Hedrick, S. M., Cohen, D. I., Nielsen, E. A., and Davis, M. M. (1984) Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature 308, 149–153.
Sagerstrom, C. G., Sun, B. I., and Sive, H. L. (1997) Subtractive cloning: past, present, and future. Annu. Rev. Biochem. 66, 751–783.
Rubenstein, J. L., Brice, A. E., Ciaranello, R. D., Denney, D., Porteus, M. H., and Usdin, T. B. (1990) Subtractive hybridization system using single-stranded phagemids with directional inserts. Nucleic Acids Res. 18, 4833–4842.
Rothstein, J. L., Johnson, D., Jessee, J., et al. (1993) Construction of primary and subtracted cDNA libraries from early embryos. Methods Enzymol. 225, 587–610.
Houge, G. (1993) Simplified construction of a subtracted cDNA library using asymmetric PCR. PCR Methods Appl. 2, 204–209.
Wang, Z. and Brown, D. D. (1991) A gene expression screen. Proc. Natl. Acad. Sci. USA 88, 11,505–11,509.
Yokota, H. and Oishi, M. (1990) Differential cloning of genomic DNA: cloning of DNA with an altered primary structure by in-gel competitive reassociation. Proc. Natl. Acad. Sci. USA 87, 6398–63402.
Hubank, M. and Schatz, D. G. (1999) cDNA representational difference analysis: a sensitive and flexible method for identification of differentially expressed genes. Methods Enzymol. 303, 325–349.
Lisitsyn, N., Lisitsyn, N., and Wigler, M. (1993) Cloning the differences between two complex genomes. Science 259, 946–951.
Hubank, M. and Schatz, D. G. (1994) Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res. 22, 5640–5648.
Diatchenko, L., Lau, Y. F., Campbell, A. P., et al. (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025–6030.
Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A., and Lukyanov, S. A. (1995) An improved PCR method for walking in uncloned genomic DANN. Nucleic Acids Res. 23, 1087, 1088.
Gurskaya, N. G., Diatchenko, L., Chenchik, A., et al. (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal. Biochem. 240, 90–97.
Lukyanov, K., Diatchenko, L., Chenchik, A., et al. (1997) Construction of cDNA libraries from small amounts of total RNA using the suppression PCR effect. Biochem. Biophys. Res. Commun. 230, 285–288.
Leirdal, M., Shadidy, M., Rosok, O., and Sioud, M. (2004) Identification of genes differentially expressed in breast cancer cell line SKBR3: potential identification of new prognostic biomarcers. Int. J. Mol. Med. 14, 217–222.
Liang, P. and Pardee, A. B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 957–971.
Liang, P., Zhu, W., Zhang, X., et al. (1994) Differential display using one-base anchored oligo-dT primers. Nucleic Acids Res. 22, 5763, 5764.
Martin, K. J. and Pardee, A. B. (1999) Principles of differential display. Methods Enzymol. 303, 234–258.
Welsh, J., Chada, K., Dalal, S. S., Cheng, R., Ralph, D., and McClelland, M. (1992) Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 20, 4965–4970.
Wang, X. and Feuerstein, G. Z. (1995) Direct sequencing of DNA isolated from mRNA differential display. BioTechniques 18, 448–453.
Liang, P. and Pardee, A. B. (1995) Recent advances in differential display. Curr. Opin. Immunol. 7, 274–280.
Liang, P. (1998) Factors ensuring successful use of differential display. Methods 16, 361–364.
Cho, Y.-J., Prezioso, V. R., and Liang, P. (2002) Systematic analysis of intrinsic factors affecting differential display. BioTechniques 32, 762–766.
Rosok, O., Odeberg, J., Rode, M., et al. (1996) Solid-phase method for differential display of genes expressed in hematopoietic stem cells. BioTechniques 21, 114–121.
Sompayrac, L., Jane, S., Burn, T. C., Tenen, D. G., and Danna, K. J. (1995) Overcomming limitations of the mRNA differential display technique. Nucleic Acids Res. 23, 4738–4739.
Luce, M. J. and Burrows, P. D. (1998) Minimizing false positives in differential display. BioTechniques 24, 766–768.
Bosch, I., Melichar, H., and Pardee, A. B. (2000) Identification of differentially expressed genes from limited amounts of RNA. Nucleic Acids Res. 28, E27.
Adams, M. D., Kelley, J. M., Gocayne, J. D., et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656.
Wilcox, A. S., Khan, A. S., Hopkins, J. A., and Sikela, J. M. (1991) Use of 3′ untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome. Nucleic Acids Res. 19, 1837–1843.
Adams, M. D., Kerlavage, A. R., Fleischmann, R. D., et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377 (Suppl.), 3–174.
Hastie, N. D. and Bishop, J. O. (1976) The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9, 761–764.
Zhang, L., Zhou, W., Velculescu, et al. (1997) Gene expression profiles in normal and cancer cells. Science 276, 1268–1272.
Bonaldo, M. F., Lennon, G., and Soares, M. B. (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6, 791–806.
Soares, M. B., Bonaldo, M. F., Jelene, P., Su, L., Lawton, L., and Efstratiadis, A. (1994) Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. USA 91, 9228–9232.
Berry, R., Stevens, T. J., Walter, N. A., et al. (1995) Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. Nat. Genet. 10, 415–423.
Houlgatte, R., Mariage-Samson, R., Duprat, S., et al. (1995) The Genexpress index: a resource for gene discovery and the genic map of the human genome. Genome Res. 5, 272–304.
Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487.
Yamamoto, M., Wakatsuki, T., Hada, A., and Ryo, A. (2001) Use of serial analysis of gene expression (SAGE) technology. J. Immunol. Methods 250, 45–66.
Silva, A. P., De Souza, J. E., Galante, P. A., Riggins, G. J., De Souza, S. J., and Camargo, A. A. (2004) The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucleic Acids Res. 32, 6104–6110.
Saha, S., Sparks, A. B., Rago, C., et al. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–512.
Unneberg, P., Wennborg, A., and Larsson, M. (2003) Transcript identification by analysis of short sequence tags—influence on tag length, restriction site and transcript database. Nucleic Acid Res. 31, 2217–2226.
Datson, N. A., van der Perk-de Jong, J., van den Berg, M. P., de Kloet, E. R., and Vreugdenhil, E. (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res. 27, 1300–1307.
Peters, D. G., Kassam, A. B., Yonas, H., O’Hare, E. H., Ferrell, R. E., and Brufsky, A. M. (1999) Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. Nucleic Acids Res. 27, e39.
Ye, S. Q., Zhang, L. Q., Zheng, F., Virgil, D., and Kwiterovich, P. O. (2000) miniSAGE: gene expression profiling using serial analysis of gene expression from 1 microg total RNA. Anal. Biochem 287, 1444–1452.
Brenner, S., Johnson, M., Bridgham, J., et al. (2000) Gene expression analysis by massively parallell signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630–634.
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.
Chee, M., Yang, R., Hubbell, E., et al. (1996) Accessing genetic information with high-density DNA arrays. Science 274, 610–614.
Duggan, D. J., Brittner, M., Chen, Y., Meltzer, P., and Trent, J. H. (1999) Expression profiling using cDNA microarrays. Nat. Genet. 21(Suppl. 1), 10–14.
Schulze, A. and Downward, J. (2001) Navigating gene expression using microarrays—a technical review. Nat. Cell Biol. 3, E190–E195.
Chung, C. H., Bernard, P. S., and Peron, C. M. (2002) Molecular portraits and the family tree of cancer. Nat. Genet. 32(Suppl. 2), 533–540.
Weeraratna, A. T., Nagel, J. E., de Mello-Coelho, V., and Taub, D. D. (2004) Gene expression profiling: from microarrays to medicine. J. Clin. Immunol. 24, 213–224.
Penn, S. G., Rank, D. R., Hanzel, D. K., and Barker, D. L. (2000) Mining the human genome using microarrays of open reading frames. Nat. Genet. 26, 315–318.
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Røsok, Ø., Sioud, M. (2007). Discovery of Differentially Expressed Genes. In: Sioud, M. (eds) Target Discovery and Validation Reviews and Protocols. Methods in Molecular Biology™, vol 360. Humana Press. https://doi.org/10.1385/1-59745-165-7:115
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DOI: https://doi.org/10.1385/1-59745-165-7:115
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