some of the non-coding DNA is functionally important, eg in the case of regulatory elements and sequences that are important for chromosome function.Indeed, the first comprehensive gene map was based on short sequence tags from cDNA clones. The coding sequence priority prevailed and the first reasonably comprehensive human gene maps were constructed, essentially involving three steps. Initially the cDNA needs to be randomly sequenced. To begin with this meant sequencing short (around 300 bp) sequences at the 3’ ends of cDNA clones from a variety of human cDNA libraries. These short sequences became known as expressed sequence tags (ESTs) because they permitted a simple and rapid PCR assay for a specific expressed sequence gene, (Adams et al., 1991). In this sense therefore, an EST is simply the gene equivalent of an STS (a term used to describe any type of sequence, but often noncoding DNA, which is specific for a particualar locus). Because the 3’ UTR of almost all human genes exceeds 300 bp, the 3’ ESTs typically did not contain coding sequence.It was now necessary to map ESTs to specific chromosomes. 3’ UTR sequences are not as frequently interrupted by introns as coding DNA. This means that it is usually easy to design PCR primers from an EST that will amplify the specific squence in a genomic DNA sample. Because 3’ UTR sequences are not very well conserved during evolution, it is also possible to screen human-rodent somatic cell hybrids for the presence of human EST (the orthologous rodent sequences are usually so diverged that they do not amplify). By using a panel of human monochromosomal somatic cell hybrids (section 10.1.1), an EST can be mapped to a specific human chromosome.Mapping ESTs to subchromosomal locations has been achieved through a huge effort based at some centres to establish integrated STS-based and EST-based maps, such as those produced by the Whitehead institute. This has involved...
