Genomics

The genetic analysis of entire genomes is called genomics. Such a broadscale analysis has been made possible by the development of recombinant DNA technology. In humans, knowledge of the entire genome sequence has facilitated searching for genes that produce hereditary diseases. It is also capable of revealing a set of proteins—produced at specific times, in specific tissues, or in specific diseases—that might be targets for therapeutic drugs. Genomics also allows the comparison of one genome with another, leading to insights into possible evolutionary relationships between organisms.

Genomics has two subdivisions: structural genomics and functional genomics. Structural genomics is based on the complete nucleotide sequence of a genome. Each member of a library of clones is physically manipulated by robots and sequenced by automatic sequencing machines, enabling a very high throughput of DNA. The resulting sequences are then assembled by a computer into a complete sequence for every chromosome. The complete DNA sequence is scanned by computer to find the positions of open reading frames (ORFs), or prospective genes. The sequences are then compared to the sequences of known genes from other organisms, and possible functions are assigned. Some ORFs remain unassigned, awaiting further research.

Functional genomics attempts to understand function at the broadest level (the genomic level). In one approach, gene functions of as many ORFs as possible are assigned as above in an attempt to obtain a full set of proteins encoded by the genome (called a proteome). The proteome broadly defines all the cellular functions used by the organism. Function in relation to specific developmental stages also is assessed by trying to identify the “transcriptome,” the set of mRNA transcripts made at specific developmental stages. The practical approach utilizes microarrays—glass plates the size of a microscope slide imprinted with tens of thousands of ordered DNA samples, each representing one gene (either a clone or a synthesized segment). The mRNA preparation under test is labeled with a fluorescent dye, and the microarray is bathed in this mRNA. Fluorescent spots appear on the array indicating which mRNAs were present, thus defining the transcriptome.

Protein manufacture

Recombinant DNA procedures have been used to convert bacteria into “factories” for the synthesis of foreign proteins. This technique is useful not only for preparing large amounts of protein for basic research but also for producing valuable proteins for medical use. For example, the genes for human proteins such as growth hormone, insulin, and blood-clotting factor can be commercially manufactured. Another approach to producing proteins via recombinant DNA technology is to introduce the desired gene into the genome of an animal, engineered in such a way that the protein is secreted in the animal’s milk, facilitating harvesting.

Invention of recombinant DNA technology

Recombinant DNA technology was invented largely through the work of American biochemists Stanley N. Cohen, Herbert W. Boyer, and Paul Berg. In the early 1970s Berg carried out the first successful gene-splicing experiment, in which he combined DNA from two different viruses to form a recombinant DNA molecule. Boyer and Cohen then took the next step of inserting recombinant DNA molecules into bacteria, which replicated, creating many copies of the recombinant molecule. Boyer and Cohen subsequently developed methods for the generation of recombinant plasmids. In 1976, with Robert A. Swanson, Boyer founded the company Genentech, which commercialized Boyer and Cohen’s recombinant DNA technology.

In 1968—prior to the work of Berg, Boyer, and Cohen—Swiss microbiologist Werner Arber discovered restriction enzymes. American microbiologist Hamilton O. Smith subsequently identified type II restriction enzymes. Unlike type I restriction enzymes, which cut DNA at random sites, type II restriction enzymes cleave DNA at specific sites; hence, type II enzymes became important tools in genetic engineering.