1. Introduction

3.1 Introduction

Key terms defined in this section

Genome is the complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles.
Proteome is the total number of proteins produced by an organism.
Transcriptome is the complete set of mRNAs present in a cell, tissue, or organism.

We can think about the total number of genes at four levels, corresponding to successive stages in gene expression:

• The genome is the complete set of genes of an organism. Ultimately it is defined by the complete DNA sequence, although as a practical matter it may not be possible to identify every gene unequivocally solely on the basis of sequence.
  
• The transcriptome is the complete set of genes expressed under particular conditions. It is defined in terms of the set of mRNA molecules that is present, and can refer to a single cell type or to any more complex assembly of cells up to the complete organism.
  
• The proteome is the complete set of proteins. It should correspond to the transcriptome, although there can be differences of detail reflecting changes in the relartive abundance or stabilities of mRNAs and proteins.
  
• Proteins may function independently or as part of multiprotein assemblies. If we could identify all protein-protein interactions, we could define the total number of independent assemblies of proteins.

We may identify the coding potential of a genome directly, by identifying regions that have open reading frames. Large scale mapping of this nature is complicated by the fact that interrupted genes may consist of many separated open reading frames. Since we do not necessarily have information about the functions of the protein products, or indeed proof that they are expressed at all, this approach is restricted to defining the potential of the genome. (However, a strong presumption exists that any conserved open reading frame is likely to be expressed; see 2 From genes to genomes).

Another approach is to define the number of genes directly in terms of the transcriptome (by directly identifying all the mRNAs) or proteome (by directly identifying all the proteins). This gives an assurance that we are dealing with bona fide genes that are expressed under known circumstances. It allows us to ask how many genes are expressed in a particular tissue or cell type, what variation exists in the relative levels of expression, and how many of the genes expressed in one particular cell are unique to that cell or are also expressed elsewhere.

Concerning the types of genes, we may ask whether a particular gene is essential: what happens to a null mutant? If a null mutation is lethal, or the organism has a visible defect, we may conclude that the gene is essential or at least conveys a selective advantage. But some genes can be deleted without apparent effect on the phenotype. Are these genes are really dispensable, or does a selective disadvantage result from the absence of the gene, perhaps in other circumstances, or over longer periods of time?

This section updated 4-12-2000