Learning outcomes

When you have read Chapter 7, you should be able to:

• Describe the strengths and weaknesses of the computational and experimental methods used to analyze genome sequences
• Describe the basis of open reading frame (ORF) scanning, and explain why this approach is not always successful in locating genes in eukaryotic genomes
• Outline the various experimental methods used to identify parts of a genome sequence that specify RNA molecules
• Define the term ‘homology’ and explain why homology is important in computer-based studies of gene function
• Evaluate the limitations of homology analysis, using the yeast genome project as an example
• Describe the methods used to inactivate individual genes in yeast and mammals, and explain how inactivation can lead to identification of the function of a gene
• Give outline descriptions of techniques that can be used to obtain more detailed information on the activity of a protein coded by an unknown gene
• Describe how the transcriptome and proteome are studied
• Explain how protein interaction maps are constructed and indicate the key features of the yeast map
• Evaluate the potential and achievements of comparative genomics as a means of understanding a genome sequence

a genome sequence is not an end in itself. A major challenge still has to be met in understanding what the genome contains and how the genome functions. The former is addressed by a combination of computer analysis and experimentation, with the primary aim of locating the genes and their control regions. The first part of this chapter is devoted to these methods. The second question – understanding how the genome functions – is, to a certain extent, merely a different way of stating the objectives of molecular biology over the last 30 years. The difference is that in the past attention has been directed at the expression pathways for individual genes, with groups of genes being considered only when the expression of one gene is linked to that of another. Now the question has become more general and relates to the expression of the genome as a whole. The techniques used to address this topic will be covered in the latter parts of this chapter.