Repetitive Sequences

In eukaryotic DNA, some DNA sequences are reiterated as many as 105 to 106 times in each cell. Whereas practically all of the DNA of E. coli is single-copy (sequences present only once in the genome), only about half of mammalian DNA and about a third of plant DNA fall into this category.

Satellite DNA - Satellite DNA is one type of repeating sequence in eukaryotic DNAs. It involves multiple tandem repetitions, over long stretches of DNA, of very short, simple sequences like (ATAAACT)n. Such DNA can often be separated from the major portion of the DNA by sedimentation to equilibrium in density gradients (Figure 28.3). In higher eukaryotes, satellite DNA usually makes up 10% to 20% of the total genome. The function of highly reiterated sequences is not completely clear. Certain reiterated sequences have been found to be highly concentrated near the centromeres of chromosomes, the regions where sister chromatids are attached. These may thus serve as binding sites for proteins that attach the spindle fibers in mitosis.

Duplication of functional genes - There are other classes of DNA sequences with varying amounts of repetition. Some represent duplications of functional genes, and in many cases the repetitiveness seems to play a useful role, by allowing high levels of production of much-needed transcripts. Examples include the genes for ribosomal RNAs, of which up to several thousand copies may be present, and tRNA genes, with hundreds of copies of each type often found. The same is true for the genes for some much-used proteins, such as the histones that bind to eukaryotic DNA to form the chromatin structure (see here). Even genes that are normally single-copy are sometimes amplified, either in response to environmental stress or in special tissues during embryonic development.

Alu Elements - Other kinds of repeated DNA sequences exist that do not code for proteins, but whose true function remains mysterious. They are often scattered throughout the genome, rather than being clustered like the satellite DNAs. One of the most common such families in mammals is the so-called Alu elements. These sequences, of which there are hundreds of thousands of copies in the human genome, are about 300 bp long. The Alu sequences can be (inefficiently) transcribed into RNA, although they are not translated. The function of the Alu sequences remains uncertain, although some of them may contain origins for DNA replication (see here).

Molecular Parasites - It is also conceivable that many repetitive sequences, such as the Alu elements, serve no useful function. They may simply exist in the genome as "molecular parasites." A way in which such sequences could spread through the genome has been proposed, on the basis of the observation that Alu sequences are flanked by short, repeated oligonucleotides resembling those of transposons (see here). In this view, Alu sequences, like other mobile genetic elements, may be inserted at various places in the genome as reverse transcriptase copies of the RNA that is transcribed from them. Recent studies suggest that the Alu sequences may have been derived from a small RNA (7SL RNA - see here) involved in protein transport across membranes.

See also: Protein Targeting, Size of the Eukaryotic Genome, Gene Amplification (from Chapter 25)

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1. Repetitive DNA

2. Genome Organization