Repeated Sequences
The mammalian genome can roughly be divided into two classes of DNA: unique and repeated. Unique sequence DNA occurs only once per haploid genome and codes for structural genes. Repeated sequence DNA refers to multiple copies of particular sequences that are found more than once, ranging from a few (ten or less) to many (greater than a thousand) times in the genome. Depending on the organism, repeated sequences can account for 20-80% of the total DNA. This diverse group can be further subdivided into moderate and highly repetitive elements. The moderately repetitive category is comprised primarily of the tRNA (transfer RNA) and rRNA (ribosomal RNA) genes. In humans, the rRNA genes are clustered on the short arm of only 10 chromosomes, but the tRNA genes are more widely distributed in at least 50 different sites in the genome. These RNA genes are transcribed and the products are used in translation. The highly repetitive sequences are quite different in that they are usually non-coding, and due to this, were once thought to be nonfunctional and termed "junk" DNA. However, although highly repeated sequences do not produce a product, it has been shown that many have important roles in the cell.
The majority of the highly repeated sequences are arranged in tandem repeats. Of the remaining repeated sequences in the genome, one group is the pseudogenes, inactive regions that have a sequence similar to an active structural gene. Some gene families include several different pseudogenes that are thought to be evolutionary variants of the functional gene.
Interspersed repeats are another type of repeated sequence that are widely distributed throughout the genome, but tend to occur singly rather than in clusters. The two primary classes are : 1) SINES, short interspersed nuclear elements, and 2) LINES, long interspersed nuclear elements such as LINE-1 or L1. SINES show some homology to RNA genes. The Alu repeats are the best studied of this group and are the most common sequence in the human genome. They are approximately 280 bp long and are generally found in regions adjacent to genes. The LINES are much larger, up to 7 kb in length. LINES may be transcribed but are not translated. Together, SINES and LINES are estimated to comprise approximately 10% of mammalian genomes. The function of these regions is unknown.
Transposable elements, LTRs (long terminal repeats), and retroviral-like elements (RTLV) make up another small group of repeated sequences. Analysis has shown a similarity between these elements and repeated sequences that occur in bacteria and viruses. In addition, some bacterial plasmids have repeated sequences known as iterons that are important in regulating the binding of a protein important in plasmid replication.
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