How many genes are expressed?

KEY TERMS:

• The transcriptome is the complete set of RNAs present in a cell, tissue, or organism. Its complexity is due mostly to mRNAs, but it also includes noncoding RNAs.
• Housekeeping genes (Constitutive gene) are those (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types.
• Luxury genes are those coding for specialized functions synthesized (usually) in large amounts in particular cell types.

KEY CONCEPTS:

• mRNAs expressed at low levels overlap extensively when different cell types are compared.
• The abundantly expressed mRNAs are usually specific for the cell type.
• ~10,000 expressed genes may be common to most cell types of a higher eukaryote. 

Many somatic tissues of higher eukaryotes have an expressed gene number in the range of 10,000-20,000. How much overlap is there between the genes expressed in different tissues? For example, the expressed gene number of chick liver is ~11,000-17,000, compared with the value for oviduct of ~13,000-15,000. How many of these two sets of genes are identical? How many are specific for each tissue? These questions are usually addressed by analyzing the transcriptome—the set of sequences represented in RNA.

We see immediately that there are likely to be substantial differences among the genes expressed in the abundant class. Ovalbumin, for example, is synthesized only in the oviduct, not at all in the liver. This means that 50% of the mass of mRNA in the oviduct is specific to that tissue.

But the abundant mRNAs represent only a small proportion of the number of expressed genes. In terms of the total number of genes of the organism, and of the number of changes in transcription that must be made between different cell types, we need to know the extent of overlap between the genes represented in the scarce mRNA classes of different cell phenotypes.

Comparisons between different tissues show that, for example, ~75% of the sequences expressed in liver and oviduct are the same. In other words, ~12,000 genes are expressed in both liver and oviduct, ~5000 additional genes are expressed only in liver, and ~3000 additional genes are expressed only in oviduct.

The scarce mRNAs overlap extensively. Between mouse liver and kidney, ~90% of the scarce mRNAs are identical, leaving a difference between the tissues of only 1000-2000 in terms of the number of expressed genes. The general result obtained in several comparisons of this sort is that only ~10% of the mRNA sequences of a cell are unique to it. The majority of sequences are common to many, perhaps even all, cell types.

This suggests that the common set of expressed gene functions, numbering perhaps ~10,000 in a mammal, comprise functions that are needed in all cell types. Sometimes this type of function is referred to as a housekeeping gene or constitutive gene. It contrasts with the activities represented by specialized functions (such as ovalbumin or globin) needed only for particular cell phenotypes. These are sometimes called luxury genes.