Batzer and Deininger 2002 Nature Reviews Genetics

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Unformatted text preview: CACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGT Sg ................................................................--..... Y ................................................................--..... Ya5 ................................................................--..... Ya8 ................................................................--..... Yb8 ........................................................T......T--..... Sx CAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA-TTAGCCGG Sg ....................................................................... Y ......A.........T......T....C.................................A........ Ya5 ......A.........T..C...T..A.C.................................A........ Ya8 ......A.........T..C...T..A.C........................C........A-....... Yb8 ......A.........T......T....A.................................A........ Sx GGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGA Sg ....................................................................... Y ............G.........G.................................G..G........... Ya5 .....A......G.........G...........T.....................G..G........... Ya8 .....A......G.........G...T.......T.....................G..G........... Yb8 ....C.......G.........G.................................G..G........... Sx GGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC Sg ....................................................................... Y ....C.................................................................. Ya5 ....C.....................C............................................ Ya8 ....C.....................C............................................ Yb8 A...C....................T...........G................................. GCAGTCCG Figure 1 | Alignment of Alu-subfamily consensus sequences. The consensus sequence for the Alu Sx subfamily is shown at the top, with the sequences of progressively younger Alu subfamilies underneath. The dots represent the same nucleotides as the consensus sequence. Deletions are shown as dashes, and mutations are shown in coloured boxes; all are colour-coded according to the family in which the ancestral mutation arose. Each of the newer subfamilies, such as Ya5 or Yb8, has all the mutations of the ancestral Alu elements, as well as five or eight extra mutations, respectively, that are diagnostic for the particular Alu subfamily. This figure primarily illustrates the newer subfamilies and does not attempt to show many of the older Alu subfamilies. Alu element as a retrotransposition-competent source gene are not fully understood, several factors have been suggested to influence the amplification process. These include transcriptional capacity of individual elements, ability of the specific transcript to associate with the retrotransposition mechanism, and possibly the length and homogeneity of the A-tail to allow effective priming3,23,30,42,43. Mutations that accumulate in the source genes are subsequently inherited by their copies. Therefore, the human Alu family is composed of several distinct subfamilies of different genetic ages that are characterized by a hierarchical series of mutations. Several laboratories have identified a number of human Alu elements that share common diagnostic sequence features and comprise subfamilies or clades that have expanded in different evolutionary time frames, as reviewed in REF. 1. FIGURE 1 compares the consensus sequences of several Alu subfamilies. Older Alu subfamilies are characterized by the smallest number of diagnostic subfamily-specific mutations. These older elements have also accumulated the largest number of random mutations (up to 20% PAIRWISE DIVERGENCE), which confirms their ancient origin8. By contrast, the younger families of Alu elements are characterized by an increasing number of subfamily-specific mutations, together with a smaller number of random mutations (as little as 0.1% pairwise divergence) that accumulate after the individual Alu elements integrate into the genome35,44–46. Alu amplification rate Alu source genes and subfamily structure MINISATELLITE A class of repetitive sequences, 7–100 nucleotides each, that span 500–20,000 bp, and are especially located throughout the genome, towards chromosome ends. PSEUDOGENE A DNA sequence that was derived originally from a functional protein-coding gene that has lost its function owing to the presence of one or more inactivating mutations. RENATURATION CURVE A plot of DNA annealing as a function of DNA concentration and time. The amount of DNA (as a percentage) that has renatured (reassociated/ reannealed) plotted against ‘C0t ’, where ‘C0’ refers to the initial DNA concentration and ‘t ’ is the time of renaturation. PAIRWISE DIVERGENCE The number of nucleotide differences between two aligned DNA sequences. Only a few human Alu elements, the so-called ‘master’ or source genes, seem to be retrotransposition competent30. Individual Alu copies contain an internal RNApolymerase-III promoter, but this promoter is not sufficient for active transcrip...
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