Repetitive DNA is found in all organisms and that in some, including humans, it makes up a substantial fraction of the entire genome. There are various types of repetitive DNA and several classification systems have been devised. The scheme that we will use begins by dividing the repeats into those that are clustered into tandem arrays and those that are dispersed around the genome.
Tandemly repeated DNA: Tandemly repeated DNA is a common feature of eukaryotic genomes but is found much less frequently in prokaryotes. This type of repeat is also called satellite DNA because DNA fragments containing tandemly repeated sequences form ‘satellite’ bands when genomic DNA is fractionated by density gradient centrifugation. The satellite bands contain fragments of repetitive DNA, and hence have GC contents and buoyant densities that are atypical of the genome as a whole. The satellite bands in density gradients of eukaryotic DNA are made up of fragments composed of long series of tandem repeats, possibly hundreds of kb in length. A single genome can contain several different types of satellite DNA, each with a different repeat unit, these units being anything from < 5to > 200 bp. The three satellite bands in human DNA include at least four different repeat types.
One type of human satellite DNA is the alphoid DNA repeats found in the centromere regions of chromosomes. Although some satellite DNA is scattered around the genome, mostis located in the centromeres, where it may play a structural role, possibly as binding sites for one or more of the special centromeric proteins. Alternatively, the repetitive DNA content of the centromere might be a reflection of the fact that this is the last region of the chromosometo be replicated. In order to delay its replication until the very end of the cell cycle, the centromere DNA must lack sequences that can act as origins of replication. The repetitivenature of centromeric DNA may be a means of ensuring that such origins are absent. Although not appearing in satellite bands on density gradients, two other types of tandemlyrepeated DNA are also classed as ‘satellite’ DNA. These are minisatellites and microsatellites. Minisatellites form clusters up to 20 kb in length, with repeat units up to 25bp; microsatellite clusters are shorter, usually < 150 bp, and the repeat unit is usually 13 bp orless. We have already seen one type of minisatellite DNA is Telomeric DNA. In addition totelomeric minisatellites, some eukaryotic genomes contain various other clusters of minisatellite DNA, many, although not all, near the ends of chromosomes. The functions of these other minisatellite sequences have not been identified. The function of microsatellites isequally mysterious. The typical microsatellite consists of a 1-, 2-, 3- or 4-bp unit repeated 1020 times, as illustrated by the microsatellites in the human β T-cell receptor locus. Although each microsatellite is relatively short, there are many of them in the genome. In humans, for example, microsatellites with a CA repeat, that make up 0.25% of the genome, 8 Mb in all. Single base-pair repeats such as: (A)15 make up another 0.15%.
Although their function, if any, is unknown, microsatellites have proved very useful to geneticists. Many microsatellites are variable, meaning that the number of repeat units in the array is different in different members of a species. This is because ‘slippage’ sometimes occurs when a microsatellite is copied during DNA replication, leading to insertion or, less frequently, deletion of one or more of the repeat units. No two individuals have exactly the same combination of microsatellite length variants: if enough microsatellites are examined then a unique genetic profile can be established for every individual. The only exceptions are genetically identical twins. Genetic profiling is well known as a tool in forensic science, but identification of criminals is a fairly trivial application of microsatellite variability. More sophisticated methodology makes use of the fact that a person’s genetic profile is inherited partly from the mother and partly from the father. This means that microsatellites can be used to establish kinship relationships and population affinities, not only for humans but also for other animals, and for plants.
Interspersed genome-wide repeats: Tandemly repeated DNA sequences are thought to have arisen either by replication slippage, as described for microsatellites, or by DNArecombination processes. Both of these events are likely to result in a series of linked repeats, rather than individual repeat units scattered around the genome. Interspersed repeats must therefore have arisen by a different mechanism, one that can result in a copy of a repeat unit appearing in the genome at a position distant from the location of the original sequence. The most frequent way in which this occurs is by transposition, and most interspersed repeats have inherent transpositional activity.
There are two alternative modes of transposition, one that involves an RNAintermediate and one that does not. The version that involves an RNA intermediate is called retro transposition. The basic mechanism involves three steps: • An RNA copy of the transposon is synthesized by the normal process of transcription.
• The RNA transcript is copied into DNA. This conversion of RNA to DNA, the reverse of the normal transcription process, requires a special enzyme called reverse transcriptase. Often the reverse transcriptase is coded by a gene within the transposon and is translated from the RNA copy synthesized in step
• The DNA copy of the transposon integrates into the genome, possibly back into the same chromosome occupied by the original unit, or possibly into a different chromosome. The end result is that there are now two copies of the transposon, at different points in the genome.
RNA transposons or retro elements are features of eukaryotic genomes but have not so far been discovered in prokaryotes.
Endogenous retroviruses (ERVs) are retroviral genomes integrated into vertebrate chromosomes. Some are still active and might, at some stage in a cell’s lifetime, direct synthesis of exogenous viruses, but most are decayed relics that no longer have the capacity to form viruses. These inactive sequences are genome wide repeats but they are not capable of additional proliferation.
Retrotransposons have sequences similar to ERVs but are features of nonvertebrateeukaryotic genomes (i.e. plants, fungi, invertebrates and microbial eukaryotes) rather thanvertebrates. Retrotransposons have very high copy numbers in some genomes, with manydifferent types present. There are two types of retrotransposon: the Ty3 / gypsy family (Ty3 and gypsy are examples of this class in yeast and fruit fly, respectively), whose members possessthe same set of genes as an ERV, and the Ty1/copia family, members of which lack the env gene. Both types are able to transpose but the absence of the env gene means that the Ty1/copia group cannot form infectious virus particles. In fact, despite the presence of env in the Ty3 / gypsy , it has only recently been recognized that some of these elements can form viruses and hence should be looked upon as non-vertebrate retroviruses. Although technically they are interspersed elements, retro transposons are sometimes found in clusters in a genome sequence as a result of the presence of preferred integration sites for transposing elements.
The three types of retro element described so far are LTR elements, as they have long terminal repeats at either end which play a role in the transposition process. Other retro elements do not have LTRs. These are called retro posons and in mammals include the following:
• LINEs (long interspersed nuclear elements) contain a reverse-transcriptase like gene probably involved in the retro transposition process. An example is the human element LINE-1, which is 6.1 kb and has a copy number of 516,000 in the human genome. A LINE contains a pol II promoter and two open reading frames (ORFs), one encoding the endonuclease and the other encoding the reverse transcriptase. LINE activity proceeds as follows: RNA pol II transcribes the LINE DNA into LINE RNA; the LINE RNA is translated into proteins; the proteins and RNA join together and reenter the nucleus; the endonuclease cuts a strand of the target genomic DNA, often in the intron of a gene; the reverse transcriptase copies the LINERNA into LINE DNA which is inserted into the target DNA forming a new LINE element there. Three distant related LINE families are found in the human genome: LINE1, LINE2, and LINE3. Only LINE1 (L1) is still active.
• SINEs (short interspersed nuclear elements) do not have a reverse transcriptase gene but can still transpose, probably by ‘borrowing’ reverse transcriptase enzymes that have been synthesized by other retro elements. SINEs are short sequences (about 100–400 bp) and they contain an internal pol III promoter but do not encode any proteins. All currently known SINEs are derived from tRNA and 7SL RNA genes. Most non-autonomous SINEs 17 share the 3′ end with a resident LINE. The only active SINE in the human genome is the Alu element,which is the major SINE constituting about 11% of the genome (~1 million Alu elements).
• Not all transposons require an RNA intermediate. Many are able to transpose in a more direct DNA to DNA manner. In eukaryotes, DNA transposons are less common than retro transposons, but they have a special place in genetics because a family of plant DNA transposons - the Ac / Ds elements of maize - were the first transposable elements to bed is covered, by Barbara McClintock in the 1950s. DNA transposons are a much more important component of prokaryotic genome anatomies than the RNA transposons. The insertion sequences, IS1 and IS186, are examples of DNA transposons, and a single E. coli genome may contain as many as 20 of these of various types. Other kinds of DNA transposon known in E. coli, and fairly typical of prokaryotes in general, includes: Composite transposons and Tn3-type transposons.
