Table

A Sampler of Some Sequence Repeat Elements.

Tandemly repeated DNA

Minisatellites such as di-((TA)n) tri- ((CAA)n) or tetranucleotide ((GAGA)n) repeats Microsatellites (10-40bp) and Macrosatellites (3-20kb)

Telomeres

Long arrays of TTAGGG repeats

Centromeres

A complex of highly variable duplicate repeats of variable length, nature, and origin, often A-T rich, elements often having inverted repeat ends

Interspersed repeats

Short interspersed Nuclear Elements (SINES), generally evolved from small RNA

species, usually tRNA, but also 7SL cytoplasmic RNA Alu repeat family (primate specific); ~1,500,000 copies in the human genome each about

280 bp long, usually flanked by 6-18 bp direct repeats B1, B2 (mouse); ~150,000 copies in the mouse genome 140-190bp long Mariner (Mariner-like) elements, about 80 bp long, two inverted 37bp regions, flanked by TA dinucleotide

Long Interspersed Nuclear Elements (LINES) (mammal specific); called

"retroelements" because they are related to retroviruses and retrotransposons L1 element (Kpn repeat), generally 6-8 kb long, but as small as 500 bp

Transposable elements (TEs)

Transposable elements with Long Terminal Repeats 1.5-10kb Retroposons derived from RNA and transposed to DNA via cDNA DNA transposons, transposed directly from DNA to DNA

Transposable repeat elements

Miniature Inverted-Repeat Transposable Elements (MITE) (eukaryotes) 80-500 bp, terminal inverted repeats (TIRs) Maize transposable elements; Ds/Ac; Ac is 4563bp long, and contains 11-bp terminal inverted repeats; Ds are truncated versions of Ac. Ds requires Ac to move, and is called "nonautonomous;" Ac can move without Ds, and is called "autonomous" P elements (Drosophila), 2907bp, terminal 31 bp inverted repeat

Whole Gene or Cluster Duplication

Tandem gene duplications (e.g., Hox, globin, olfactory receptors, immunoglobulin, and R-genes)

Gene cluster duplications (e.g., 4 clusters of Hox and associated genes) Whole genome duplications, for which there is some evidence in vertebrates cell. These repeat sequences can have functions; for example, they may be used to help the packaging or replication of the genome (e.g., see papers in Caporale 1999). Regardless of their origin, some appear subsequently to have experienced mutation that, in their new context, affects protein coding and expression. This is interesting because the Japanese puffer fish (Fugu rubripes) has basically the same genes as other fish but a substantial scarcity of repeat (and other noncoding) elements. Like wise, despite the highly structured nature of centromeric DNA, cell division can apparently take place without it (Amor and Choo 2002).

Genes have arisen historically through duplication events. Functional pieces of genes, or whole genes, are occasionally duplicated or transposed during meiosis. Gene duplication produces a family of related genes. They may remain in tandem on the same chromosome or may be inserted in other chromosomes. Gene families constitute another type of repeat element in the genome; the number of members of a gene family can range from only a few to hundreds. As with other duplicates like Alu, the individual copies can accumulate subsequent mutational variation. Gene duplication is a fundamental characteristic of evolution (Ohno 1970).

Figure 4-4 exemplifies the origin and evolution of gene families with a famous example, the Hox genes, that are involved in many aspects of embryological pat-

Ancestral gene 5

Hypothetical "Proto-Hox" 5' stage

Brachiopod

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