Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin.
The name "satellite DNA" refers to how repetitions of a short DNA sequence tend to produce a different frequency of the nucleotides adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient.
Types of satellite DNA
Some types of satellite DNA in humans are:
|Type||Size of repeat unit (bp)||Location|
|α (alphoid DNA)||171||All chromosomes|
|β||68||Centromeres of chromosomes 1, 9, 13, 14, 15, 21, 22 and Y|
|Satellite 1||25-48||Centromeres and other regions in heterochromatin of most chromosomes|
|Satellite 2||5||Most chromosomes|
|Satellite 3||5||Most chromosomes|
A repeated pattern can be between 1 base pair long (a mononucleotide repeat) to several thousand base pairs long, and the total size of a satellite DNA block can be several megabases without interruption. Most satellite DNA is localized to the telomeric or the centromeric region of the chromosome. The nucleotide sequence of the repeats is fairly well conserved across species. However, variation in the length of the repeat is common. For example, minisatellite DNA is a short region (1-5kb) of 20-50 repeats. The difference in how many of the repeats is present in the region (length of the region) is the basis for DNA fingerprinting.
Microsatellites are thought to have originated by polymerase slippage during DNA replication. This comes from the observation that microsatellite alleles usually are length polymorphic; specifically, the length differences observed between microsatellite alleles are generally multiples of the repeat unit length.
Satellite DNA adopts higher-order three-dimensional structures in eukaryotic organisms. This was demonstrated in the land crab Gecarcinus lateralis, who's DNA contains 3% of a GC-rich sequence consisting of tandem repeats of a ~2100 base pair (bp) repeating unit, called RU (7,8,9). The RU is arranged in long tandem arrays with approximately 16,000 copies per genome. Several RU sequences were cloned and sequenced to reveal conserved regions of conventional DNA sequences interspersed with microsatellite repeats, in addition to long runs (20-25 bp) of G and C bases pairs with G on one strand and C on the other (3,4,5). The microsatellite repeats were also biased in strand composition in the microsatellite regions with pyrimidines (C,T) on one strand and purines (A,G) on the other. The most prevalent repeated sequences in the embedded microsatellite regions were CCT/AGG and CCCT/AGGG (3,4,5). The sequence CGCAC/GTGCG was repeated in one microsatellite region in all clones, and that sequence also appeared in a Z-DNA structure within RU (below). The strand biased pyrimidine:purine repeating sequences were shown to adopt triple-stranded structures under superhelical stress or at slightly acidic pH (3). Between the strand-biased microsatellite and GC stretches, all sequence variations retained one or two base pairs with an A residue interrupting the pyrimidine-rich strand and T interrupting the purine-rich strand. This sequence feature was highly distorted as shown by its response to nuclease enzymes (3). Regions consisting of microsatellites with bias in base composition adopted triple-helical structures under superhelical stress and other conditions. Triple-stranded structures imply that the microsatellite domains and GC stretches are loci for intermolecular interactions. Other regions of the RU sequence included variations of a symmetrical DNA sequence of alternating purines and pyrimidines shown to adopt a left-handed Z-DNA helical structure in equilibrium with a stem-loop structure under superhelical stress. The palindromic sequence CGCACGTGCG/CGCACGTGCG, flanked by extended palindromic Z-DNA sequences over a 35 bp domain, adopted a Z-DNA structure with a symmetrical arrangement or alternatively a stem-loop structure centered on a palindrome containing the CGCAC/GTGCG motif (1,2,3). Conserved sequences showed virtually no differences among cloned RU sequences. Variations among cloned RU sequences were characterized by the number of microsatellite repeats, and also by the lengths of C and G stretches where triple stranded structures formed. Other regions of variability among cloned RU sequences were found adjacent to alternating purine and pyrimidine sequences with Z-DNA/stem-loop structures (1,2,3,4,5,7,8,9).
One RU sequence was shown to have multiple copies of an Alu sequence element inserted into a region bordered by inverted repeats where most copies contained just one Alu sequence (8).
Another crab, the hermit crab Pagurus policarus, was shown to have a family of AT-rich satellites with inverted repeat structures that comprised 30% of the entire genome (6). References
1. Fowler, R.F., L.A. Stringfellow, and D.M. Skinner (1988). A domain that assumes a Z-conformation includes a specific deletion in some cloned variants of a complex satellite. Gene 71: 165-176. 2. Fowler, R.F. (1986). Eukaryotic DNA Rich in Alternating Purines and Pyrimidines Adopts an Altered Conformation Similar to Z-DNA. The University of Tennessee, Knoxville, USA. 3. Fowler, R.F. and D.M. Skinner (1986). Eukaryotic DNA diverges at a long and complex pyrimidine-purine tract that can adopt altered conformations. J. Biol. Chem. 261: 8994-9001. 4. Stringfellow, L.A., R.F. Fowler, M.E. LaMarca, and D.M. Skinner (1985). Demonstration of remarkable sequence divergence in variants of a complex satellite by molecular cloning. Gene 38: 145-152. 5. Fowler, R.F., V. Bonnewell, M.S. Spann, and D.M. Skinner (1985). Sequences of three closely related variants of a complex satellite DNA diverge at specific domains. J. Biol. Chem. 260: 8964-8972. 6. Fowler, R.F. and D.M. Skinner (1985). Cryptic satellites rich in inverted repeats comprise 30% of the genome of a hermit crab. J. Biol. Chem. 260: 1296-1303. 7. Skinner, D.M., R.F. Fowler, and V. Bonnewell (1983). "Domains of simple sequences or alternating purines and pyrimidines are sites of sequence divergences in a complex satellite DNA" In: Mechanisms of DNA Replication and Recombination (N.R. Cozzarelli, ed.), A.R. Liss, New York. UCLA Symp. Molec. Cell Biol. 10: 849-861. 8. Bonnewell, V., R.F. Fowler, and D.M. Skinner (1983). An inverted repeat borders a fivefold amplification in satellite DNA. Science 221: 862-865. 9. Skinner, D.M., V. Bonnewell, and R.F. Fowler (1982). Sites of divergence in the sequence of a complex satellite and several cloned variants. Cold Spring Harbor Symp. Quant. Biol. 47: 1151-1157.
- Beridze, Thengiz (1986). Satellite DNA. Springer-Verlag. ISBN 978-0-387-15876-1.
- Hoy, Marjorie A. (2003). Insect molecular genetics: an introduction to principles and applications. Academic Press. p. 53. ISBN 978-0-12-357031-4.