Semin Reprod Med 2001; 19(2): 167-174
DOI: 10.1055/s-2001-15396
Copyright © 2001 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel.: +1(212) 584-4662

Differential Hybridization and Other Strategies to Identify Novel Ovarian Genes

Adriano B. Tavares1 2 , Michael S. Esplin1 , Eli Y. Adashi1
  • 1Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah and
  • 2Department of Obstetrics and Gynecology, School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
Further Information

Publication History

Publication Date:
31 December 2001 (online)

ABSTRACT

Approaches to define patterns of gene expression have applications in a wide range of biological systems. The completion of the human genome project establishes a unique opportunity to understand the molecular control of different biological events through functional analysis. However, the huge database that currently exists will demand the utilization of high-throughput techniques for the assessment of multiple DNA sequences in a rapid and efficient manner. By determining genes with differential expression, it may be possible to decipher the mechanisms that underlie the control of different physiological pathways, which, in turn, may define future strategies to manage them. Although there exist a vast number of tools to screen genes for differential expression, we briefly examine here only some of those with regard to their advantages and disadvantages.

REFERENCES

  • 1 Duguid J R, Dinauer M C. Library subtraction of in vitro cDNA libraries to identify differentially expressed genes in scrapie infection.  Nucleic Acids Res . 1990;  18 2789-2792
  • 2 Hara E, Kato T, Nakada S, Sekiya S, Oda K. Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells.  Nucleic Acids Res . 1991;  19 7097-7104
  • 3 Hedrick S M, Cohen D I, Nielsen E A, Davis M M. Isolation of cDNA clones encoding T cell-specific membrane-associated proteins.  Nature . 1984;  308 149-153
  • 4 Sargent T D, Dawid I B. Differential gene expression in the gastrula of Xenopus laevis.  Science . 1983;  222 135-139
  • 5 Diatchenko L, Lau Y F, Campbell A P. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries.  Proc Natl Acad Sci U S A . 1996;  93 6025-6030
  • 6 Gurskaya N G, Diatchenko L, Chenchik A. Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemagglutinin and phorbol 12-myristate 13-acetate.  Anal Biochem . 1996;  240 90-97
  • 7 Hennebold J D, Tanaka M, Saito J, Hanson B R, Adashi E Y. Ovary-selective genes I: the generation and characterization of an ovary-selective complementary deoxyribonucleic acid library.  Endocrinology . 2000;  141 2725-2734
  • 8 Lee K F, Kwok K L, Yeung W S. Suppression subtractive hybridization identifies genes expressed in oviduct during mouse preimplantation period.  Biochem Biophys Res Commun . 2000;  277 680-685
  • 9 Kumar T R, Wang Y, Lu N, Matzuk M M. Follicle stimulating hormone is required for ovarian follicle maturation but not male fertility.  Nat Genet . 1997;  15 201-204
  • 10 Dube J L, Wang P, Elvin J, Lyons K M, Celeste A J, Matzuk M M. The bone morphogenetic protein 15 gene is X-linked and expressed in oocytes.  Mol Endocrinol . 1998;  12 1809-1817
  • 11 Liang P, Pardee A B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction.  Science . 1992;  257 967-971
  • 12 Sompayrac L, Jane S, Burn T C, Tenen D G, Danna K J. Overcoming limitations of the mRNA differential display technique.  Nucleic Acids Res . 1995;  23 4738-4739
  • 13 Svanberg B, Ling C, Svensson P A, Johnson M, Carlsson B, Billig H. Isolation of differentially expressed aldose reductase in ovaries after estrogen withdrawal from hypophysectomized diethylstilbestrol treated rats: increased expression during apoptosis.  Mol Cell Endocrinol . 2000;  164 183-190
  • 14 Cowan B D, Hines R S, Brackin M N, Case S T. Temporal and cell-specific gene expression by human endometrium after coculture with trophoblast.  Am J Obstet Gynecol . 1999;  180 806-814
  • 15 Mok S C, Wong K K, Chan R K. Molecular cloning of differentially expressed genes in human epithelial ovarian cancer.  Gynecol Oncol . 1994;  52 247-252
  • 16 von Stein D O, Thies W G, Hofmann M. A high throughput screening for rarely transcribed differentially expressed genes.  Nucleic Acids Res . 1997;  25 2598-2602
  • 17 Sun Y, Hegamyer G, Colburn N H. Molecular cloning of five messenger RNAs differentially expressed in preneoplastic or neoplastic JB6 mouse epidermal cells: one is homologous to human tissue inhibitor of metalloproteinases-3.  Cancer Res . 1994;  54 1139-1144
  • 18 Hubank M, Schatz D G. Identifying differences in mRNA expression by representational difference analysis of cDNA.  Nucleic Acids Res . 1994;  22 5640-5648
  • 19 Lisitsyn N, Lisitsyn N, Wigler M. Cloning the differences between two complex genomes.  Science . 1993;  259 946-951
  • 20 Welford S M, Gregg J, Chen E. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization.  Nucleic Acids Res . 1998;  26 3059-3065
  • 21 Chu C C, Paul W E. Fig 1, an interleukin 4-induced mouse B cell gene isolated by cDNA representational difference analysis.  Proc Natl Acad Sci U S A . 1997;  94 2507-2512
  • 22 Bertioli D J, Schlichter U H, Adams M J, Burrows P R, Steinbiss H H, Antoniw J F. An analysis of differential display shows a strong bias towards high copy number mRNAs.  Nucleic Acids Res . 1995;  23 4520-4523
  • 23 O'Neill M J, Sinclair A H. Isolation of rare transcripts by representational difference analysis.  Nucleic Acids Res . 1997;  25 2681-2682
  • 24 Schena M. Genome analysis with gene expression microarrays.  Bioessays . 1996;  18 427-431
  • 25 Schena M, Shalon D, Davis R W, Brown P O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.  Science . 1995;  270 467-470
  • 26 DeRisi J L, Iyer V R, Brown P O. Exploring the metabolic and genetic control of gene expression on a genomic scale.  Science . 1997;  278 680-686
  • 27 Brown M P, Grundy W N, Lin D. Knowledge-based analysis of microarray gene expression data by using support vector machines.  Proc Natl Acad Sci U S A . 2000;  97 262-267
  • 28 Hayward R E, Derisi J L, Alfadhli S, Kaslow D C, Brown P O, Rathod P K. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria.  Mol Microbiol . 2000;  35 6-14
  • 29 Lashkari D A, DeRisi J L, McCusker J H. Yeast microarrays for genome wide parallel genetic and gene expression analysis.  Proc Natl Acad Sci U S A . 1997;  94 13057-13062
  • 30 Wikman F P, Lu M L, Thykjaer T. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples.  Clin Chem . 2000;  46 1555-1561
  • 31 Alon U, Barkai N, Notterman D A. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.  Proc Natl Acad Sci U S A . 1999;  96 6745-6750
  • 32 Schummer M, Ng W V, Bumgarner R E. Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas.  Gene . 1999;  238 375-385
  • 33 DeRisi J, Penland L, Brown P O. Use of a cDNA microarray to analyse gene expression patterns in human cancer.  Nat Genet . 1996;  14 457-460
  • 34 Iyer V R, Eisen M B, Ross D T. The transcriptional program in the response of human fibroblasts to serum.  Science . 1999;  283 83-87
  • 35 Heller R A, Schena M, Chai A. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays.  Proc Natl Acad Sci U S A . 1997;  94 2150-2155
  • 36 Hegde P, Qi R, Abernathy K. A concise guide to cDNA microarray analysis.  Biotechniques . 2000;  29 548, 554-556 558-560
  • 37 Lockhart D J, Winzeler E A. Genomics, gene expression and DNA arrays.  Nature . 2000;  405 827-836
  • 38 Lee M L, Kuo F C, Whitmore G A, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations.  Proc Natl Acad Sci U S A . 2000;  97 9834-9839
  • 39 Eisen M B, Spellman P T, Brown P O, Botstein D. Cluster analysis and display of genome-wide expression patterns.  Proc Natl Acad Sci U S A . 1998;  95 14863-14868
  • 40 Schena M, Shalon D, Heller R, Chai A, Brown P O, Davis R W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.  Proc Natl Acad Sci U S A . 1996;  93 10614-10619