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Chapter 4: Clusters and repeats. 4.1 Introduction Duplication of DNA is a major force in evolution. Figure 4.1 After a gene has been duplicated, differences may accumulate between the copies. The genes may acquire different functions or one of the copies may become inactive.
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Chapter 4: Clusters and repeats
4.1 Introduction • Duplication of DNA is a major force in evolution
Figure 4.1After a gene has been duplicated, differences may accumulate between the copies. The genes may acquire different functions or one of the copies may become inactive.
gene family:A set of genes descended by duplication and variation from some ancestral gene. • Gene clusters :a duplication has generated two adjacent related genes, hundreds of identical genes lie in a tandem array. • Recombination is a key event in evolution of the genome.
Figure 4.2 Chiasma formation is responsible for generating recombinants.
Figure 4.3 Recombination involves pairing between complementary strands of the two parental duplex DNAs.
How does the genome change its content of genes? Figure 4.4 Unequal crossing-over results from pairing between non-equivalent repeats in regions of DNA consisting of repeating units. Here the repeating unit is the sequence ABC, and the third repeat of the red allele has aligned with the first repeat of the blue allele. Throughout the region of pairing, ABC units of one allele are aligned with ABC units of the other allele. Crossing-over generates chromosomes with 10 and 6 repeats each, instead of the 8 repeats of each parent.
Figure 4.5 All functional globin genes have an interrupted structure with three exons. The lengths indicated in the figure apply to the mammalian b-globin genes.
Figure 4.6 Each of the a-like and b-like globin gene families is organized into a single cluster that includes functional genes and pseudogenes (y). Pseudogenes: inactive but stable components of the genome derived by mutation of an ancestral active gene.
Figure 4.7 Clusters of b-globin genes and pseudogenes are found in vertebrates. Seven mouse genes include 2 early embryonic, 1 late embryonic, 2 adult genes, and 2 pseudogenes. Rabbit and chick each have four genes.
Figure 4.8 All globin genes have evolved by a series of duplications, transpositions, and mutations from a single ancestral gene.
4.3 Sequence divergence is the basis for the evolutionary clock
Figure 4.9 Divergence of DNA sequences depends on evolutionary separation. Each point on the graph represents a pairwise comparison.
Figure 4.10 All globin genes have evolved by a series of duplications, transpositions, and mutations from a single ancestral gene.
Figure 4.11 Replacement site divergences between pairs of b-globin genes allow the history of the human cluster to be reconstructed. This tree accounts for the separation of classes of globin genes.
4.4 Pseudogenes are dead ends of evolution Pseudogenes (Ψ) : Some DNA sequences that are related to those of the functional genes, but that cannot be translated into a functional protein.
Figure 4.12 Many changes have occurred in a β globin gene since it became a pseudogene.
Figure 4.13 Pseudogenes could arise by reverse transcription of RNA to give duplex DNAs that become integrated into the genome.
If pseudogenes are evolutionary dead ends, simply an unwanted accompaniment to the rearrangement of functional genes, why are they still present in the genome? • survived in present populations, in past times, any number of other pseudogenes may have been eliminated.
Figure 4.14 Clusters of β-globin genes and pseudogenes are found in vertebrates. Seven mouse genes include 2 early embryonic, 1 late embryonic, 2 adult genes, and 2 pseudogenes. Rabbit and chick each have four genes.
Figure 4.15 Gene number can be changed by unequal crossing-over. If gene 1 of one chromosome pairs with gene 2 of the other chromosome, the other gene copies are excluded from pairing, as indicatedby the extruded loops. Recombination between the mispaired genes produces one chromosome with a single (recombinant) copy of the gene and one chromosome with three copies of the gene (one from each parent and one recombinant).
Figure 4.16 Thalassemias result from various deletions in the a-globin gene cluster.
Figure 4.17 Deletions in the b-globin gene cluster cause several types of thalassemia.
4.6 Genes for rRNA form tandem repeats two cases of large gene clusters that contain many identical copies of the same gene or genes: histone proteins: Number: rRNA genes varies from 7 in E. coli, 100~200 in lower eukaryotes, to several hundred in higher eukaryotes. A point of major interest is what mechanism(s) are used to prevent variations from accruing in the individual sequences.???
Figure 4.18 A tandem gene cluster has an alternation of transcription unit and nontranscribed spacer and generates a circular restriction map.
Figure 4.19 The nucleolar core identifies rDNA under transcription, and the surrounding granular cortex consists of assembling ribosomal subunits. This thin section shows the nucleolus of the newt Notopthalmus viridescens.
Figure 4.20 Transcription of rDNA clusters generates a series of matrices, each corresponding to one transcription unit and separated from the next by the nontranscribed spacer.
Figure 4.21 The nontranscribed spacer of X. laevis rDNA has an internally repetitious structure that is responsible for its variation in length.
crossover fixation model: an entire cluster is subject to continual rearrangement by the mechanism of unequal crossing-over
Figure 4.23 Unequal recombination allows one particular repeating unit to occupy the entire cluster. The numbers indicate the length of the repeating unit at each stage.
Figure 4.24 Mouse DNA is separated into a main band and a satellite by centrifugation through a density gradient of CsCl.
Figure 4.25 Individual bands containing particular genes can be identified by in situ hybridization
Figure 4.26 Cytological hybridization shows that mouse satellite DNA is located at the centromeres.
Figure 4.27 Satellite DNAs of D. virilis are related. More than 95% of each satellite consists of a tandem repetition of the predominant sequence
Figure 4.29 The repeating unit of mouse satellite DNA contains two half-repeats, which are aligned to show the identities (in color).
Figure 4.30 The alignment of quarter-repeats identifies homologies between the first and second half of each half-repeat. Positions that are the same in all 4 quarter-repeats are shown in red; identities that extend only through 3 quarter-repeats are indicated by grey letters in the pink area.
Figure 4.31 The alignment of eighth-repeats shows that each quarter-repeat consists of an a and a b half. The consensus sequence gives the most common base at each position. The "ancestral" sequence shows a sequence very closely related to the consensus sequence, which could have been the predecessor to the a and b units. (The satellite sequence is continuous, so that for the purposes of deducing the consensus sequence, we can treat it as a circular permutation, as indicated by joining the last GAA triplet to the first 6 bp.)
Figure 4.32 The existence of an overall consensus sequence is shown by writing the satellite sequence in terms of a 9 bp repeat. G A A A A A C G T G A A A A A T G A G A A A A A A C T G A A A A A A C T AG TC
Figure 4.33 Digestion of mouse satellite DNA with the restriction enzyme EcoRII identifies a series of repeating units (1, 2, 3) that are multimers of 234 bp and also a minor series (½, 1½, 2½) that includes half-repeats (see text later). The band at the far left is a fraction resistant to digestion.
4.11 Minisatellites are useful for genetic mapping minisatellite or VNTR (variable number tandem repeat)
For example, one minisatellite has a repeat length of 64 bp, and is found in the population with the following distribution: 7% 18 repeats 11% 16 repeats 43% 14 repeats 36% 13 repeats 4% 10 repeats
