Gene expression and proteomics

Research into gene expression and proteomics will enable scientists to decipher the functions of genes and their protein products, and to get a clearer picture of the complex regulatory networks that control fundamental biological processes.

The sequencing of the human genome, and of others used to model human disease – such as the mouse and, most recently, the rat – has provided researchers with information on thousands of different genes, many of which are important to human health. But unfortunately, knowledge of the DNA sequence is not enough on its own to explain how cells work and what goes wrong when disease strikes.

To understand these complex processes, researchers are studying the conditions under which each gene in the DNA sequence is “expressed”, i.e. when, where, and to what extent the gene is stimulated to produce the protein which it encodes. This information gives clues as to the likely biological role – an enzyme or hormone, for example – of the encoded protein.

Messenger molecules

The transformation of the DNA (in a gene) to RNA (an intermediary “messenger” molecule) to protein is considered to be the central dogma of molecular biology. The first step in this process (DNA to RNA) is called transcription and takes place within the cell nucleus. In higher organisms (eukaryotes), the second step in the process (RNA to protein) takes place in the cell cytoplasm.

Transcription and translation are highly regulated processes, changing constantly in response to external and internal stimuli, including normal cellular events like cell division, and during the development of disease. Regulation of a single gene can give rise to messenger RNAs encoding functionally distinct proteins. Between them, the 30 000 genes of the human genome can express hundreds of thousands of proteins, each with a specific role to play.

Current methods for ‘eavesdropping’ on these processes still only capture a small fraction of the information embodied in the molecules. Researchers are developing more powerful tools which will enable much larger-scale analyses and give them the opportunity to study, in parallel, the expression patterns of thousands of genes.

Tools of the trade

The main tool used for these types of analysis is the microarray (also known as a nucleic acid array or DNA chip). A microarray usually consists of thousands of DNA molecules, representing genes taken from cells under specific conditions, such as malignant tumours. The molecules are distributed as “spots” on the surface of a glass or plastic slide. Solutions of fluorescently labelled DNA or RNA are poured over the array and each molecule in the solution searches for a matching partner on the surface, based on the rules of complementary molecular recognition between nucleotide base pairs. The genes that ‘pair-up’ with a complementary molecule are said to be turned on, and their level of expression can be measured by the intensity of the fluorescent marker on each spot. If the gene is turned on, researchers can assume that the gene is important for some aspect of cellular or tissue function under the specific conditions in which it was analysed.

If they are able to measure the levels of gene expression in tens of thousands of genes simultaneously, researchers can obtain a broader view of cellular response under specific conditions without necessarily having identified the most important genes in advance. In this way they hope to find novel, and sometimes unexpected genes involved in biochemical pathways, expression markers to aid disease diagnosis, or new drug targets.

One genome, multiple proteomes

A similar high-throughput approach is being taken in proteomics – the study of the function of all expressed proteins from a single genome. The proteome of an organism is constantly changing, reflecting the dynamic response of cells to their environment. Imagine a caterpillar changing into a butterfly: it has the same genome at both stages in its life cycle, but the differential expression of its genes results in stark differences in its proteome, and thus its physical appearance. Less-visible changes in proteomes, and disruptions to protein interaction networks in the body, are major causes of disease.

To understand the consequences of these changes, researchers are faced with the enormous challenge of developing moment-by-moment analyses of cellular responses. Novel high-throughput technology is being developed to give researchers this possibility. These include proteomic arrays based on protein interaction with reagents like antibodies, mass spectrometry to identify tiny amounts of protein from complex mixtures – in body fluids, for example – and high-performance light and electron microscopy.

Many of these high-throughput technologies, including those for gene expression, will be of strategic importance in biological research and for the biotechnology and pharmaceutical industries, and should eventually become available in clinical medicine to aid diagnosis and therapy.

Projects

Streps
Geninteg
Trans-reg
Plastomics