Differential Display: Theory and Applications

Recent data released by the Human Genome Consortium and Celera Genomics estimates that the human genome might contain about 30,000 protein coding genes (1 , and references therein), of which about 15‰ are believed to be expressed in any given cell type (see Chapter 42). The set of expressed proteins and the corresponding messenger RNAs, termed the transcriptome, defines the phenotype of a given cell, tissue, as well as the whole organism. The identification of genes that are differentially expressed under various physiological conditions is one of the major challenges in molecular biology today, as it provides an overview of the regulatory changes that take place in health and disease and highlights potential targets for drug discovery and therapeutic intervention (2 ). Tremendous efforts are generally required to identify those changes, as the population of altered messengers rarely comprises more than 1‰ of the total transcripts. Over the years, a variety of methods for the identification of differentially regulated genes in cells and tissues have been developed. Northern hybridization (3 ), nuclease protection (4 ), and subtractive (5 ) and differential (6 ) hybridization all have a number of serious drawbacks because they measure only single RNA species at a time and require a relatively large amount of starting material. The latter is particularly significant because rare transcripts, which often represent low-abundant cell cycle regulators, growth factors, and their receptors as well as signal transduction components, might be missed during the analysis.