Repetitive DNA Elements

Transposable elements are classified as either transposons or retrotransposons, depending on their mechanism of amplification. Transposons directly synthesize a DNA copy of themselves, whereas retrotransposons generate an RNA intermediate that is then reverse-transcribed (by the enzyme reverse transcriptase) back into DNA. Transposable elements fall into three major groups: DNA transposons, long terminal repeat (LTR) retrotransposons, and non-LTR retrotransposons. They also are subdivided into autonomous and nonautonomous elements, based on whether they can move independently within the genome or require other elements to perform this process, as shown in Figure 3.

DNA transposons are flanked by inverted repeats and contain two or more open reading frames (ORFs). An ORF is a DNA sequence that can be transcribed to make protein. The ORFs in DNA transposons code for the proteins required for making transposon copies and spreading them through the genome. The nonautonomous elements miniature inverted-repeat transposable elements (MITEs) are derived from a parent DNA transposon that Figure 2. Schematic organization of the structures characteristic of one type of repeated sequences found in eukaryotic genomes. Tandem repeats consist of a different variety of sequence units (shown in parentheses) that are found repeated side by side, with the number of copies being very high. lost ORF sequences, making them unable to amplify on their own. Instead, they must borrow the factors for amplification from external sources.

LTR retrotransposons are very similar to the genomes of retroviruses. They are flanked by 250 to 600 bp direct repeats called long terminal repeats. In general, not only are these elements defective, but they also appear to have deletions typical of nonautonomous families.

Several different groups of non-LTR retrotransposons can be found throughout most, if not all, eukaryotic genomes. One of these groups, the long interspersed repeated elements (LINEs), constitute about 21 percent of the human genome, with L1 and L2 being the dominant elements. Most of the element copies are incomplete and inactive. Two types of non-autonomous elements are thought to use factors made by LINEs: short interspersed repeated elements (SINEs) and retropseudogenes.

SINEs are derived from two types of genes coding for RNA: 7SL (which aids the movement of new proteins into the endoplasmic reticulum) and transfer RNAs. The most abundant human SINE is Alu, constituting about 13 percent of the human genome.

Retropseudogenes are derived from retrotransposition of mRNA derived from different genes. They can be distinguished from the parental gene by their lack of a functional promoter and by their lack of introns. The human genome is estimated to contain 35,000 copies of different retropseudogenes.