Increasing the Average Abundance of Low-Abundance cDNAs by Ordered Subdivision of cDNA Populations

It is estimated that 50,000–100,000 genes are expressed across the cell types of higher eukaryotes. As a consequence of differential expression (either regionally, temporally, or environmentally specific), a large proportion of all transcripts (approx 40–45%) represent low-abundance mRNAs, present at 1–20 molecules/cell (1 ). In a given cell type, “low-abundance” mRNAs are likely to represent >95% of the different mRNAs expressed. The lower the abundance of a given transcript, the larger the number of clones in a representative cDNA library which must be screened in order to have a reasonable chance of isolating that message; for example, employing a statistical calculation (2 ), it can be estimated that approx 500,000 clones need be screened to have a 99% probability of finding one representative of a gene expressed at the level of 0.001% (a low-abundance message) of total cellular mRNA. This is of practical significance in all cases, except where high-abundance mRNAs (accumulating to a few percent of total cellular mRNA) are sought. The implications are particularly severe for Human Genome Project expressed sequence tag (EST) studies, which on the basis of automated sequencing, aim to identify all the unknown genes expressed in a particular cell or tissue. Utilizing an unmodified cDNA library, well-resourced laboratories are forced to employ approaches incorporating a 10- to 100-fold redundancy in screening in order to isolate rare mRNAs. However, such approaches are not an option available to the majority of investigators.