Figure 1. Representative C_ot curves adapted from Britten and Kohne (1968). (a) The authors generated C_ot curves for individual DNA samples. The number of unique base pairs in each DNA sample is noted above the graph. The dotted line indicates the point at which half of the DNA is reannealed (C_ot_1/2). The higher the C_ot value, the more complex the DNA. (b) Different C_ot_1/2 fractions present in mammalian DNA. Arrows indicate the types of DNA present in each fraction. Dashed lines indicate the C_ot_1/2 for each fraction.

Figure 2. Mechanisms for generating simple repetitive DNA arrays of different sizes. (a) Saltatory replication: a repeat array is excised from its native chromosomal amplification and is replicated. Integration at the original chromosomal position results in an increase in array size. Integration at an ectopic chromosomal position results in dispersal of the array. (b) Unequal crossing-over: homologous repeats are denoted by the different shaded boxes. Unequal crossing-over (denoted by the X) results in the gain of an array in one homologue and the loss of an array in the other. (c) DNA slippage: staggered mispairing in the leading DNA strand during replication results in a duplication of arrays. Staggered mispairing in the template strand results in a deletion of arrays.

Figure 3. Transposition and retrotransposition mechanisms. (a) Transposition: the transposon is excised from donor DNA (blue box) and integrates into target DNA (yellow box). Nonreplicative and conservative transposition often results in the loss of the transposon from donor DNA. Replicative transposition occurs via a cointegrate intermediate and generates two molecules. The first is indistinguishable from the original donor molecule. The second contains a simple insertion of the transposon into target DNA. The inverted repeats at the termini of the transposon, the transposon open reading frame (green rectangle), and the short target-site duplications, which typically flank transposons, are indicated with red arrows (see Kleckner (1990) for further details). (b) LTR-retrotransposition: the element-encoded RNA and proteins are copackaged into cytoplasmic VLPs, where cDNA synthesis takes place. The double-stranded cDNA is subsequently integrated into chromosomal DNA by an element-encoded integrase. The structure of a typical LTR retrotransposon is shown. The Env gene is usually absent or mutated. The short target-site duplications, which typically flank LTR retrotransposons, are indicated with red arrows (for a review, see Craig et al. (2001) Mobile DNA II). (c) L1 retrotransposition: the L1-encoded proteins and L1 RNA coassemble into a ribonucleoprotein particle (RNP), which is a proposed intermediate in retrotransposition. The RNP enters the nucleus and an L1-encoded endonuclease nicks chromosomal DNA to expose a 3’ hydroxyl residue, which is used as a primer for cDNA synthesis. This mode of priming is termed target-site primed reverse transcription (TPRT). The variable length target-site duplications, which typically flank L1s, are indicated with red arrows. Notably, both processed pseudogenes and Alu elements may be mobilized by TPRT (see Moran and Gilbert, 2001). (d) An alternative model for Alu retrotransposition: Alu RNA can form a foldback molecule, which can self-prime reverse transcription. The foldback occurs between T-rich sequences in the RNA polymerase III terminator (T T T T T T) and the poly (A) tail (A_n) of the Alu RNA, and results in the formation of a hairpin that may be used as a primer for cDNA synthesis. The A and B boxes of a typical RNA polymerase III promoter are indicated. The red arrows flanking the Alu element indicate the variable length target-site duplications (see Maraia and Sarrowa, 1995).