6.3: Ectopic recombination

As we saw in the previous section, aneuploidies arise from nondisjunctions in meiosis, resulting in gamets that are not correctly haploid. However, many structural variants are smaller than an entire chromosome, often "just" tens or hundreds of thousands of bases -- how do they arise? The answer is ectopic recombination, where crossing-over in meiosis takes place between two homologous DNA sequences at non-allelic loci -- so-called non-allelic homologous recombination, or NAHR. To understand how this might take place, first we need an introduction to a very common class of repeated sequences called transposable elements.

Transposable Elements

Transposable elements (TEs) are also known as mobile genetic elements, or more informally as jumping genes. They are present throughout the chromosomes of almost all organisms. These DNA sequences have a unique ability to be cut or copied from their original location and inserted into new locations in the genome. This is called transposition. These insert locations are not entirely random, but TEs can, in principle, be inserted into almost any region of the genome. TEs can therefore insert into genes, disrupting its function and causing a mutation. Researchers have developed methods of artificially increasing the rate of transposition, which makes some TEs a useful type of mutagen. However, the biological importance of TEs extends far beyond their use in mutant screening. TEs are also important causes of disease and phenotypic instability, and they are a major mutational force in evolution.

There are two major classes of TEs in eukaryotes (Figure \(\PageIndex{3}\)).

• Class I elements include retrotransposons; these transpose by means of an RNA intermediate. The TE transcript is reverse transcribed into DNA before being inserted elsewhere in the genome through the action of enzymes such as integrase.
• Class II elements are known also as transposons. They do not use reverse transcriptase or an RNA intermediate for transposition. Instead, they use an enzyme called transposase to cut DNA from the original location and then this excised dsDNA fragment is inserted into a new location. Note that the name transposon is sometimes used incorrectly to refer to any type of TEs, but in this book we use transposon to refer specifically to Class II elements.

Figure \(\PageIndex{3}\): Diagrams of the two main types of transposable elements. (TEs) Class I elements transpose via an ssRNA intermediate, which is reverse transcribed to dsDNA prior to insertion of this copy in a new site in the genome. Class II elements do not involve an RNA intermediate; most Class II elements are cut from their original location as dsDNA, prior to being inserted into a new site in the genome. Although the diagram shows TEs being inserted on the same chromosome as they originated from, TEs can also move to other chromosomes within the same cell.

TEs are relatively short DNA sequences (100-10,000 bp), and encode no more than a few proteins (if any). Normally, the protein-coding genes within a TE are all related to the TE’s own transposition functions. These proteins may include reverse transcriptase, transposase, and integrase. However, some TEs (of either Class I or II) do not encode any proteins at all. These non-autonomous TEs can only transpose if they are supplied with enzymes produced by other, autonomous TEs located elsewhere in the genome. In all cases, enzymes for transposition recognize conserved nucleotide sequences within the TE, which dictate where the enzymes begin cutting or copying.

The human genome consists of nearly 45% TEs, the vast majority of which are families of Class I elements called LINEs and SINEs. The short, Alu type of SINE occurs in more than one million copies in the human genome (compare this to the approximately 21,000, non-TE, protein-coding genes in humans). Indeed, TEs make up a significant portion of the genomes of almost all eukaryotes. Class I elements, which usually transpose via an RNA copy-and-paste mechanism, tend to be more abundant than Class II elements, which mostly use a cut-and-paste mechanism. But even the cut-paste mechanism can lead to an increase in TE copy number. For example, if the site vacated by an excised transposon is repaired with a DNA template from a homologous chromosome that itself contains a copy of a transposon, then the total number of transposons in the genome will increase.

Besides greatly expanding the overall DNA content of genomes, TEs contribute to genome evolution in many other ways. As already mentioned, they may disrupt gene function by insertion into a gene’s coding region or regulatory region. More interestingly adjacent regions of chromosomal DNA are sometimes mistakenly transposed along with the TE; this can lead to gene duplication. The duplicated genes are then free to evolve independently, leading in some cases to the development of new functions. The breakage of strands by TE excision and integration can disrupt genes, and can lead to chromosome rearrangement or deletion if errors are made during strand rejoining. Furthermore, having so many similar TE sequences distributed throughout a chromosome sometimes allows mispairing of regions of homologous chromosomes at meiosis, which can cause unequal crossing-over, resulting in deletion or duplication of large segments of chromosomes. Thus, TEs are a potentially important evolutionary force, and may not be included as merely “junk DNA”, as they once were.

 

Repeated sequences lead to NAHR

As we have seen, transposable elements lead to a huge amount of repetitive sequences in complex eukaryotic genomes. The result is relatively frequent ectopic recombination. When homologous chromosomes form synapses prior to crossing-over, regions consisting of repeated homologous sequences line up -- even if they are not alleles. If crossing-over happens at such a location -- non-allelic homologous recombination -- it results in a pair of reciprocal gametes, one of which has a duplication and one of which has a deletion. This is shown in the image below (credit: the Eichler lab)

 

 

Over time, these repeated regions themselves can cause NAHR, leading to further expansion of the repeated region:

By Lee M. Silver - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/inde...curid=15030041

 

Subsequent mutations to the repeated loci can lead to subfunctionalization or neofunctionalization, which is a primary mechanism of genomic evolution.