13. cis-acting sites and trans-acting molecules

1.13 cis-acting sites and trans-acting molecules

Key terms defined in this section

cis /I> configuration describes two sites on the same molecule of DNA.
trans /I> configuration of two sites refers to their presence on two different molecules of DNA (chromosomes).

A crucial step in the definition of the gene was the realization that all its parts must be present on one contiguous stretch of DNA. In genetic terminology, sites that are located on the same DNA are said to be in cis. Sites that are located on two different molecules of DNA are described as being in trans. So two mutations may be in cis (on the same DNA) or in trans (on different DNAs).

Figure 1.20 The cistron is defined by the complementation test. Genes are represented by bars; red stars identify sites of mutation.

There is a crucial difference in the effects of two mutations in the same gene that depends on whether they are in cis or trans configuration. This gave rise to the development of the cis/trans complementation test, which defines a gene as a unit that must be present on one chromosome. In a diploid that carries two different mutations at a particular gene locus, the distribution of the mutations determines whether a functional allele is present. If both mutations are in cis on one allele, the other allele has no mutations, and is wild type. But if the mutations are in trans, so that each allele has one mutation, both alleles are mutant (see Figure 1.20). We may now extend the concept of the difference between cis and trans effects from defining the coding region of a gene to describing the interaction between regulatory elements and a gene.

Figure 1.33 Control sites in DNA provide binding sites for proteins; coding regions are expressed via the synthesis of RNA.

Suppose that the ability of a gene to be expressed is controlled by a protein that binds to the DNA close to the coding region. In the example depicted in Figure 1.33, messenger RNA can be synthesized only when the protein is bound to the DNA. Now suppose that a mutation occurs in the DNA sequence to which this protein binds, so that the protein can no longer recognize the DNA. As a result, the DNA can no longer be expressed.

So a gene can be inactivated either by a mutation in a control site or by a mutation in a coding region. The mutations cannot be distinguished genetically, because both have the property of acting only on the DNA sequence of the single allele in which they occur. They have identical properties in the cis/trans test, and a mutation in a control region is therefore defined as comprising part of the gene in the same way as a mutation in the coding region.

Figure 1.34 A cis-acting site controls the adjacent DNA but does not influence the other allele.

Figure 1.34 shows that a deficiency in the control site affects only the coding region to which it is connected; it does not affect the ability of the other allele to be expressed. A mutation that acts solely by affecting the properties of the contiguous sequence of DNA is called cis-acting.

Figure 1.35 A trans-acting mutation in a protein affects both alleles of a gene that it controls.

We may contrast the behavior of the cis-acting mutation shown in Figure 1.34 with the result of a mutation in the gene coding for the regulator protein. Figure 1.35 shows that the absence of regulator protein would prevent both alleles from being expressed. A mutation of this sort is said to be trans-acting.

Reversing the argument, if a mutation is trans-acting, we know that its effects must be exerted through some diffusible product (typically a protein) that acts on multiple targets within a cell. But if a mutation is cis-acting, it must function via affecting directly the properties of the contiguous DNA, which means that it is not expressed in the form of RNA or protein.