Introduction to The Content of the Genome

One key question about any genome is how many genes it contains. However, there’s an even more fundamental question: “What is a gene?” Clearly, genes cannot be defined solely as a sequence of DNA that encodes a polypeptide, because manygenes encode multiple polypeptides and many encode RNAs that serve other functions. Given the variety of RNA functions and the complexities of gene expression, it seems prudent to focus on the gene as a unit of transcription. However, large areas of chromosomes previously thought to be devoid of genes now appear to be extensively transcribed, so at present the definition of a “gene” is a moving target.
We can attempt to characterize both the total number of genes and the number of protein-coding genes at four levels, which correspond 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 might 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 RNA molecules present in a single cell type, a more complex assembly of cells, or a complete organism. Because some genes generate multiple messenger RNAs (mRNAs), the transcriptome is likely to be larger than the actual number of genes in the genome. The transcriptome includes noncoding RNAs such as transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), microRNAs (miRNAs), and others , as well as mRNAs.
The proteome is the complete set of polypeptides encoded by the whole genome or produced in any particular cell or tissue. It should correspond to the mRNAs in the transcriptome, although
there can be differences of detail reflecting changes in the relative abundance or stabilities of mRNAs and proteins. There might also be posttranslational modifications to proteins that allow more than one protein to be produced from a single transcript (this is called protein splicing ).
Proteins can function independently or as part of multiprotein or multimolecular complexes, such as holoenzymes and metabolic pathways where enzymes are clustered together. The RNA polymerase holoenzyme  and the spliceosome  are two examples. If we could identify all protein–protein interactions, we could define the total number of independent complexes of proteins. This is sometimes referred to as the interactome.
The maximum number of polypeptide-encoding genes in the genome can be identified directly by characterizing open reading frames (ORFs). Large-scale analysis of this nature is complicated by the fact that interrupted genes might consist of many separated ORFs, and alternative splicing can result in the use of variously combined portions of these ORFs. We do not necessarily have information about the functions of the polypeptide products—or indeed proof that they are expressed at all—so this approach is restricted to defining the potential of the genome. However, it is presumed that any conserved ORF is likely to be expressed.
Another approach is to define the number of genes directly in terms of the transcriptome (by directly identifying all the RNAs) or proteome (by directly identifying all the polypeptides). 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. In addition, analysis of the transcriptome can reveal how many different mRNAs (e.g., mRNAs containing different combinations of exons) are generated from a particular gene.
Also, we might ask whether a particular gene is essential: What is the phenotypic effect of a null mutation in that gene? If a null mutation is or the organism has a clear defect, we can conclude that the gene is essential or at least beneficial. However, the functions of some genes can be eliminated without apparent effect on the phenotype. Are these genes really dispensable, or does a selective disadvantage result from the absence of the gene, perhaps in other circumstances or over longer periods of time? In some cases, the absence of the functions of these genes could be offset by a redundant mechanism, such as a gene duplication, providing a backup for an essential function.