KEY TERMS:
- Nonreciprocal recombination (unequal crossing-over) results from an error in pairing and crossing-over in which nonequivalent sites are involved in a recombination event. It produces one recombinant with a deletion of material and one with a duplication.
- Thalassemia is disease of red blood cells resulting from lack of either α or β globin.
- HbH disease results from a condition in which there is a disproportionate amount of the abnormal tetramer β4 relative to the amount of normal hemoglobin (a2β2).
- Hydrops fetalis is a fatal disease resulting from the absence of the hemoglobin α gene.
- Hb Lepore is an unusual globin protein that results from unequal crossing-over between the β and δ genes. The genes become fused together to produce a single β-like chain that consists of the N-terminal sequence of δ joined to the C-terminal sequence of β.
- Hb anti-Lepore is a fusion gene produced by unequal crossing-over that has the N-terminal part of β globin and the C-terminal part of δ globin.
- Hb Kenya is a fusion gene produced by unequal crossing-over between the between Aγ and β globin genes.
- When a genome contains a cluster of genes with related sequences, mispairing between nonallelic genes can cause unequal crossing-over. This produces a deletion in one recombinant chromosome and a corresponding duplication in the other.
- Different thalassemias are caused by various deletions that eliminate α- or β-globin genes. The severity of the disease depends on the individual deletion.
There are frequent opportunities for rearrangement in a
cluster of related or identical genes. We can see the results by comparing the
mammalian β clusters included in Figure 4.5. Although the clusters serve the same function,
and all have the same general organization, each is different in size, there is
variation in the total number and types of β-globin genes, and the numbers and structures of
pseudogenes are different. All of these changes must have occurred since the
mammalian radiation, ~85 million years ago (the last point in evolution common
to all the mammals).
The comparison makes the general point that gene
duplication, rearrangement, and variation is as important a factor in evolution
as the slow accumulation of point mutations in individual genes. What types of
mechanisms are responsible for gene reorganization?
Unequal crossing-over (also
known as nonreciprocal recombination) can occur as
the result of pairing between two sites that are not homologous.
Usually, recombination involves corresponding sequences of DNA held in exact
alignment between the two homologous chromosomes. However, when there are two
copies of a gene on each chromosome, an occasional misalignment allows pairing
between them. (This requires some of the adjacent regions to go unpaired.) This
can happen in a region of short repeats (see Figure 4.1)
or in a gene cluster. Figure 4.11 shows that unequal
crossing-over in a gene cluster can have two consequences, quantitative and
qualitative:
- The number of repeats increases in one chromosome and decreases in the other. In effect, one recombinant chromosome has a deletion and the other has an insertion. This happens irrespective of the exact location of the crossover. In the figure, the first recombinant has an increase in the number of gene copies from 2 to 3, while the second has a decrease from 2 to 1.
- If the recombination event occurs within a gene (as opposed to between genes), the result depends on whether the recombining genes are identical or only related. If the noncorresponding gene copies 1 and 2 are entirely homologous, there is no change in the sequence of either gene. However, unequal crossing-over also can occur when the adjacent genes are well related (although the probability is less than when they are identical). In this case, each of the recombinant genes has a sequence that is different from either parent.
Whether the chromosome has a selective advantage or
disadvantage will depend on the consequence of any change in the sequence of the
gene product as well as on the change in the number of gene copies.
An obstacle to unequal crossing-over is presented by the
interrupted structure of the genes. In a case such as the globins, the
corresponding exons of adjacent gene copies are likely to be well enough related
to support pairing; but the sequences of the introns have diverged appreciably.
The restriction of pairing to the exons considerably reduces the continuous
length of DNA that can be involved. This lowers the chance of unequal
crossing-over. So divergence between introns could enhance the stability of gene
clusters by hindering the occurrence of unequal crossing-over.
Thalassemias result from
mutations that reduce or prevent synthesis of either α or β globin. The
occurrence of unequal crossing-over in the human globin gene clusters is
revealed by the nature of certain thalassemias.
Many of the most severe thalassemias result from deletions
of part of a cluster. In at least some cases, the ends of the deletion lie in
regions that are homologous, which is exactly what would be expected if it had
been generated by unequal crossing-over.
Figure 4.12 summarizes the deletions
that cause the α-thalassemias. α-thal-1 deletions are long, varying in the location of
the left end, with the positions of the right ends located beyond the known
genes. They eliminate both the α genes. The α-thal-2 deletions are short and eliminate only one of
the two α genes. The L deletion removes 4.2 kb of
DNA, including the α2 gene. It probably results
from unequal crossing-over, because the ends of the deletion lie in homologous
regions, just to the right of the ψα and α2 genes,
respectively. The R deletion results from the removal of exactly 3.7 kb of DNA,
the precise distance between the α1 and α2 genes. It appears to have been generated by unequal
crossing-over between the α1 and α2 genes themselves. This is precisely the situation
depicted in Figure 4.11.
Depending on the diploid combination of thalassemic
chromosomes, an affected individual may have any number of α chains from zero to three. There are few differences
from the wild type (four α genes) in individuals
with three or two α genes. But with only one α gene, the excess β
chains form the unusual tetramer β4,
which causes HbH disease. The complete absence of
α genes results in hydrops
fetalis, which is fatal at or before birth.
The same unequal crossing-over that generated the
thalassemic chromosome should also have generated a chromosome with three α genes. Individuals with such chromosomes have been
identified in several populations. In some populations, the frequency of the
triple α locus is about the same as that of the
single α locus; in others, the triple α genes are much less common than single αgenes. This suggests that (unknown) selective factors
operate in different populations to adjust the gene levels.
Variations in the number of α
genes are found relatively frequently, which argues that unequal crossing-over
in the cluster must be fairly common. It occurs more often in the α cluster than in the β
cluster, possibly because the introns in α genes
are much shorter, and therefore present less impediment to mispairing between
nonhomologous genes.
The deletions that cause β-thalassemias are summarized in Figure 4.13. In some (rare) cases, only the β gene is affected. These have a deletion of 600 bp,
extending from the second intron through the 3
The Hb Lepore type provided the
classic evidence that deletion can result from unequal crossing-over between
linked genes. The β and δ genes differ only ~7% in sequence. Unequal
recombination deletes the material between the genes, thus fusing them together
(see Figure 4.11). The fused gene produces a single β-like chain that consists of the N-terminal sequence of
δ joined to the C-terminal sequence of β.
Several types of Hb Lepore now are known, the difference
between them lying in the point of transition from δ to β sequences. So when
the δ and β genes
pair for unequal crossing-over, the exact point of recombination determines the
position at which the switch from δ to β sequence occurs in the amino acid chain.
The reciprocal of this event has been found in the form of
Hb anti-Lepore, which is produced by a gene that
has the N-terminal part of β and the C-terminal
part of δ . The fusion gene lies between normal
δ and β
genes.
Evidence that unequal crossing-over can occur between more
distantly related genes is provided by the identification of Hb Kenya, another fused hemoglobin. This contains the
N-terminal sequence of the Aγ gene and
the C-terminal sequence of the β gene. The fusion
must have resulted from unequal crossing-over between Aγ and β, which differ ~20%
in sequence.
From the differences between the globin gene clusters of
various mammals, we see that duplication followed (sometimes) by variation has
been an important feature in the evolution of each cluster. The human
thalassemic deletions demonstrate that unequal crossing-over continues to occur
in both globin gene clusters. Each such event generates a duplication as well as
the deletion, and we must account for the fate of both recombinant loci in the
population. Deletions can also occur (in principle) by recombination between
homologous sequences lying on the same chromosome. This does not
generate a corresponding duplication.
It is difficult to estimate the natural frequency of these
events, because selective forces rapidly adjust the levels of the variant
clusters in the population. Generally a contraction in gene number is likely to
be deleterious and selected against. However, in some populations, there may be
a balancing advantage that maintains the deleted form at a low
frequency.
The structures of the present human clusters show several
duplications that attest to the importance of such mechanisms. The
functional sequences include two α genes
coding the same protein, fairly well related β and
δ genes, and two almost identical γ genes. These comparatively recent independent
duplications have survived in the population, not to mention the more distant
duplications that originally generated the various types of globin genes. Other
duplications may have given rise to pseudogenes or have been lost. We expect
continual duplication and deletion to be a feature of all gene clusters.