1. How Genes Travel on Chromosomes
Chromosomal Rearrangements
and Changes in Chromosome Number
Rearrangements of DNA Sequences
Transposable Genetic Elements
Rearrangements and Evolution: A Speculative Comprehensive Example
Changes in Chromosome Number
Emergent Technologies: Beyond the Karyotype
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 13

2. Figure 13. 1 Comparing the mouse and human genomes
Figure 13.1 Comparing the mouse and human genomes. Mouse chromosome 1 contains large blocks of sequences found on human chromosomes 1, 2, 5, 6, 8, 13, and 18 (portrayed in different colors). Arrows indicate the relative orientations of sequence blocks from the same human chromosome.

3. Two main themes underlying the observations on chromosomal changes
Karyotypes generally remain constant within a species
Most genetic imbalances result in a selective disadvantage
Related species usually have different karyotypes
Closely-related species differ by only a few rearrangements
Distantly-related species differ by many rearrangements
Correlation between karyotypic rearrangements and speciation
First, karyotypes generally remain constant within a species,not because rearrangements and changes in chromosome number occur infrequently(they are, in fact, quite common), but because the genetic instabilities and imbalances produced by such changes usually place individual cells or organisms and their progeny at a selective disadvantage.
These observations suggest there is signifi cant correlation between karyotypic rearrangements and the evolution of new species.

4. Chromosomal rearrangements
Table 13.1

5. Changes in chromosome number
Table 13.1 (cont)

6. REARRANGEMENTS OF DNA SEQUENCES
All chromosomal rearrangements alter DNA sequence.
FOCUS ON!!
on heritable rearrangements that can be transmitted through the germ line from one generation to the next
the genomes of somatic cells can undergo changes in nucleotide number or order.

7. 1) Deletions: origin and detection
deletions remove one or more contiguous base pairs of DNA from a chromosome
errors in replication, from faulty meiotic or mitotic recombination,
exposure to X-rays or other chromosome-damaging agents that break the DNA backbone
Small only one gene, whereas large deletions can generate chromosomes lacking tens or even hundreds of genes

8. 8
Symbols for a deletion are Del or Df (i.e. Del/+ or Df/+ is a deletion heterozygote and Del/Del or Df/Df is a deletion homozygote)
b) One way to detect deletions is by PCR. The two PCR primers shown will amplify a larger PCR product from wild-type DNA than from DNA with a deletion.
Fig. 13.2

9. Most point mutations would not cause such changes as in the PCR detected mutations
Larger deletions are sometimes identifiable because they affect the expression of two or more adjacent genes.
Very large deletions are visible at the relatively low resolution of a karyotype

10. Heterozygosity for deletions may have phenotypic consequences
With some genes, an abnormal phenotype can be caused by an imbalance in gene dosage (i.e. 2 copies vs. 1 copy of an autosomal gene)
In humans, deletion heterozygotes with loss of >3% of genome are not viable
Why should heterozygosity for a deletion have harmful consequences when the Del/ individual has at least
one wild-type copy of all of its genes?
The answer is that changes in gene dosage —the number of times a given gene is present in the cell nucleus—can create a genetic imbalance.
This imbalance in gene dosage alters the amount of a particular protein relative to all other proteins, and this alteration can have a variety of phenotypic effects.
Fig. 13.3

11. This imbalance in gene dosage changes the phenotypic effects.
Del/ + individual is known as a deletion heterozygote
Even small deletions can be harmful in heterozygotes.
a relatively small deletion from the short arm of chromosome 5 have cri du chat syndrome
Why should heterozygosity for a deletion have harmful consequences when the Del/+ individual has at least one wild-type copy of all of its genes?
abnormal cry reminiscent of a mewing kitten. The syndrome also leads to mental retardation.
This imbalance in gene dosage alters the amount of a particular protein relative to all other proteins,
and this alteration can have a variety of This imbalance in gene dosage alters the
amount of a particular protein relative to all other proteins, and this alteration can have a variety of phenotypic
effects.
gene dosage —the number of times a given gene is present in the cell nucleus—can create a genetic imbalance.
This imbalance in gene dosage changes the phenotypic effects.

12. Some rare genes, the normal diploid level of gene expression is essential to individual survival; fewer than two copies of such a gene results in lethality.
Decrease in gene dosage are noticeable but not catastrophic for some genes
Drosophila containing only one copy of the wild-type Notch gene have visible wing abnormalities but otherwise seem to function normally

13. ANOTHER REASON why heterozygosity for a deletion can be harmful
If the gene encodes a protein that helps control cell division, a cell without any wild-type protein may divide out of control and generate a tumor.
Thus, individuals born heterozygous for certain deletions have a greatly increased risk of losing both copies of certain genes and developing cancer.
Retinoblastoma (RB), the most malignant form of eye cancer
Reveal heterozygosity for deletions on chromosome 13
Cells from the retinal tumors of these same patients have a
mutation in the remaining copy of the RB gene on the nondeleted
chromosome 13.

14. Deletion loops form in the chromosomes of deletion heterozygotes
Recombination between homologs can occur only at regions of similarity
No recombination can occur within a deletion loop
Consequently, genetic map distances in deletion heterozygotes will not be accurate
Figure 13.4: During prophase of meiosis I, the undeleted region of the normal chromosome has nothing with which
to pair and forms a deletion loop. No recombination can occur within the deletion loop. In this simplified fi gure, each line represents two chromatids.
s a result, these genes cannot be separated by recombination, and the map distances between them, as determined by the phenotypic classes in the progeny of a Del/ individual, will be zero.
Fig. 13.4

15. In deletion heterozygotes, pseudodominance can "uncover" a recessive mutation
Similar to a complementation test
Examine phenotype of a heterozygote for recessive allele and deletion:
If the phenotype is mutant, the mutant gene must lie inside the deleted region
If the phenotype is wild-type, the mutant gene must lie outside the deleted region
Figure 13.5: A fly of genotype st/Del displays the recessive scarlet eye color. The deletion has thus “uncovered” the scarlet (st) mutation.
The uncovering of a mutant recessive phenotype demonstrates a lack of complementation because neither chromosome
can supply wild-type gene function.
A fly of genotype st/Del displays the recessive scarlet eye color.
The deletion has thus “uncovered” the scarlet (st) mutation.
Fig. 13.5

16. Diagnosing DiGeorge syndrome by fluorescence in situ hybridization (FISH)
DiGeorge syndrome in humans:
Accounts for 5% of all congenital heart defects
Affected people are heterozygous for a 22q11 deletion
FISH on human metaphase chromosomes
Green dots; control probe for chromosome 22
Red dot; probe from 22q11 region
The green signal is a control probe that identifi es both chromosome 22’s.
The red signal is a fluorescent probe from region 22q11, which is deleted in one of the chromosome 22’s in DiGeorge syndrome patients.
These homologous metaphase chromosomes do not pair with each other and thus do not form a
deletion loop
Fig

17. Summary of phenotypic and genetic effects of deletions
Homozygosity or heterozygosity for deletions can be lethal or harmful
Depends on size of deletions and affected genes
In deletion heterozygotes, deletions reveal the effects of recessive mutations
Deletions can be used to map and identify genes
Homozygosity or even heterozygosity for deletions can be lethal or harmful; the effects depend on the size of the deletion
and the identity of the deleted genes. In deletion heterozygotes, deletions reveal or “uncover” recessive mutations
on the intact homolog because the phenotype is no longer masked by the presence of a dominant wild-type
allele. Geneticists can use these properties of deletions to map and identify genes.

18. 2) Types of duplications (Dp)
Duplications increase the number of copies of a particular chromosomal region.
In tandem duplications, repeats
of a region lie adjacent to each other, either in the same order or in reverse order
In nontandem (or dispersed ) duplications, the two or more copies of a
region are not adjacent to each other and may lie far apart on the same chromosome or on different chromosomes.

19. Chromosome breakage can produce duplications
Duplications arise by chromosomal breakage and faulty repair, unequal crossing-over, or errors in DNA replication
According to one scenario, nontandem duplications could be produced by insertion of a fragment elsewhere on the homologous chromosome
Duplications arise by chromosomal breakage and faulty repair, unequal crossing-over, or errors in DNA replication
( Fig b ). (b) In one scenario for duplication formation, X-rays break one chromosome
twice and its homolog once. A fragment of the fi rst chromosome inserts elsewhere on its homolog to produce a nontandem duplication
Fig b

20. Most duplications have no obvious phenotypic consequences
can be detected only by cytological or molecular means
During the prophase of meiosis I in heterozygotes for such duplications ( Dp/ +), the repeated bands form a duplication loop —a bulge in the Dp -bearing chromosome that has no similar region with which to pair in the unduplicated normal homologous
chromosome.

21. Different kinds of duplication loops in duplication heterozygotes (Dp/+)
Different configurations can occur in prophase I of meiosis
During the prophase of meiosis I in heterozygotes for such duplications ( Dp/ ), the repeated bands form a duplication loop —a bulge in the Dp -bearing chromosome that has no similar region with which to pair in the unduplicated normal homologous
chromosome.
Duplication loops form when chromosomes pair in duplication heterozygotes (Dp/). During prophase I, the duplication loop can
assume different confi gurations. A single line represents two chromatids in this simplifi ed diagram
Fig c

22. Duplication heterozygosity can cause visible phenotypes
Increased gene dosage can result in a mutant phenotype
Most duplications have no obvious phenotypic consequences and can be detected only by cytological or molecular means.
Fig a

23. For rare genes, survival requires exactly two copies
In a very large
duplication have additive deleterious effects that risk
survival.
In humans, heterozygosity for duplications
covering more than 5% of the haploid genome is most often lethal.
Fig b

24. Unequal crossing-over can increase or decrease copy number
Genotype of X chromosome
Phenotype
Out-of-register pairing during meiosis can occur in a Bar-eyed female
Fig

25. Summary of phenotypic and genetic effects of duplications
Novel phenotypes may occur because of increased gene copy number or because of altered expression in new chromosomal environment
Homozygosity or heterozygosity for a duplication can be lethal or harmful
Depends on size of duplication and affected genes
Unequal crossing-over between duplicated regions on homologous chromosomes can result in increased and decreased copy number

26. 3) Chromosome breakage can produce inversions (In)
The half-circle rotation of a chromosomal region known as an inversion ( In )
Pericentric inversion – centromere is within the inverted segment
Paracentric inversion – centromere is not within the inverted segment
radiation produces
two double-strand breaks in a chromosome’s DNA
Fig a

27. Intrachromosomal recombination can also produce inversions
Recombination occurs between related sequences that are in opposite orientations on the same chromosome
Fig b

28. Phenotypic effects of inversions
Most inversions do not result in an abnormal phenotype
Abnormal phenotypes can occur if:
Inversion disrupts a gene (Fig c)
Inversion places a gene in chromosomal environment that alters its expression
i.e. Gene is placed near regulatory sequences for other genes or near heterochromatin (PEV, chapter 12)
Inversions can act as crossover suppressors
In inversion heterozygotes, no viable offspring are produced that carry chromosomes resulting from recombination in inverted region

29. Inversions can disrupt a gene
Fig c

30. Inversion loops form in inversion heterozygotes
Formation of inversion loop allows tightest possible alignment of homologous regions
Crossing over within the inversion loop produces aberrant recombinant chromatids
Fig

31. Why pericentric inversion heterozygotes produce few if any recombinant progeny
Each recombinant chromatid has a centromere, but each will be genetically unbalanced
Zygotes formed from union of normal gametes with gametes carrying these recombinant chromatids will be nonviable
Fig a

32. Why paracentric inversion heterozygotes produce few if any recombinant progeny
One recombinant chromatid lacks a centromere and the other recombinant chromatid has two centromeres Zygotes formed from union of normal gametes with gametes carrying the broken dicentric recombinant chromatids will be nonviable
Fig b

33. whether an inversion is pericentric or paracentric, crossing-over within the inversion loop of an inversion heterozygote has the same effect:
formation of recombinant gametes that after fertilization prevent the zygote from developing.
only gametes containing chromosomes that did not recombine within the inversion loop can yield viable progeny, inversions act as crossover suppressors.
This does not mean that crossovers do not
occur within inversion loops, but simply that there are no
recombinants among the viable progeny of an inversion
heterozygote.

34. Balancer chromosomes are useful tools for genetic analysis
Balancer chromosomes have a dominant visible marker and multiple, overlapping inversions
In progeny of crosses of heterozygotes with a marked balancer and a non-inversion chromosome
No viable progeny with recombinants on this chromosome will be produced because of crossover suppression
Progeny that don't carry the marked chromosome must carry the nonrecombined, unmarked chromosome
Balancer chromosome
Normal chromosome with mutations of interest
Fig

35. Summary of phenotypic and genetic effects of inversions
Inversions don't add or remove DNA, but can disrupt a gene or alter expression of a gene
In inversion heterozygotes, recombination within inverted segment results in genetically unbalanced gametes (nonviable zygotes)
Geneticists can take advantage of this:
Balancer chromosomes with inversions are useful genetic tools
The production of genetic lines of known composition.

36. 4) Translocations attach part of one chromosome to another chromosome
Reciprocal translocation (Fig )
Two different chromosomes each have a chromosome break
Reciprocal exchange of fragments – each fragment replaces the fragment on the other chromosome
Two chromosome breaks can produce a reciprocal translocation

37. Chromosome painting reveals a reciprocal translocation
Translocated chromosomes are stained red and green
Non-translocated chromosomes are stained entirely red or entirely green
(b) Karyotype of a human genome containing a translocation. The two translocated chromosomes are stained both
red and green (arrows). Two normal, non-translocated chromosomes are stained entirely red or entirely green (arrowheads), indicating that this person is heterozygous for the translocation.
Fig b

38. Robertsonian translocations can reshape genomes
Robertsonian translocation (Fig )
Chromosomal breaks occur at or near centromeres of two acrocentric chromosomes (13, 14, 15, 21, 22 and the Y chromosome)
Generates one large metacentric chromosome and one small chromosome, which is usually lost
Fig

39. Phenotypic effects of reciprocal translocations
Most reciprocal translocations don't affect the phenotype because they don't add or remove DNA
Abnormal phenotypes can be caused if translocation breakpoint disrupts a gene or results in altered expression of a gene
Translocations in somatic cells can result in oncogene activation (Fig )
Defects that are observed in translocation heterozygotes
Unbalanced gametes are produced, which results in reduced fertility (Fig )
Genetic map distance are altered because of pseudolinkage
Several kinds of cancer are associated with translocations in somatic cells. In normal cells, genes known as
protooncogenes help control cell division.
Translocations that relocate these genes can turn them into tumor producing oncogenes whose protein products have an
altered structure or level of expression that leads to runaway cell division.

40. How a reciprocal translocation helps cause one kind of leukemia
a) Uncontrolled divisions of large, dark-staining white blood cells in a leukemia patient (right) produce a higher ratio of white to red blood cells than that in a normal individual (left).
Translocations in somatic cells can result in oncogene activation

41. A reciprocal translocation is the basis for chronic myelogenous leukemia
Fig b

42. DIAGNOSIS AND TREATMENT OF CML
To confirm a diagnosis of myelogenous leukemia
a blood sample from the patient
a pair of PCR primers derived from opposite sides of the breakpoint
The PCR will amplify the region between the primers only if the DNA sample contains the translocation
To monitor the effects of chemotherapy

43. To treat CML
The protein encoded by c-abl is a protein tyrosine kinase, an enzyme that adds phosphate groups to tyrosine amino acids on other proteins.
cell growth and division (active with a growth signal)
the fused protein encoded by bcr/c-abl in cells carrying the translocation is not amenable to regulation.
It is always active, even in the absence of growth factor, and this leads to runaway cell division
Gleevec ®
inhibits the enzymatic activity of the protein tyrosine kinase encoded by bcr/c-abl.
98% of participants experienced a complete disappearance of leukemic blood cells

44. In a translocation homozygote, chromosomes segregate normally during meiosis I
If the breakpoints of a reciprocal translocation do not affect gene function, there are no genetic consequences in homozygotes
Fig a

45. Chromosome pairing in a translocation heterozygote
In a translocation heterozygote, the two haploid sets of chromosomes carry different arrangements of DNA
Chromosome pairing during prophase I of meiosis is maximized by formation of a cruciform (crosslike) structure
Three segregation patterns are possible (Fig c)
Fig b

46. during prophase of the first meiotic division, the translocated chromosomes and their normal homologs assume a crosslike configuration in which four chromosomes, rather than the normal two, pair to achieve a maximum of synapsis between similar regions

47. Three chromosome segregation patterns are possible in a translocation heterozygote
Balanced gametes are produced only by alternate segregation, and not by adjacent-1 or adjacent-2 segregation
Fig c

48. Semisterility in a corn plant that is heterozygous for a reciprocal translocation
Slightly less than 50% of gametes arise from alternate segregation and are viable
Unbalanced ovules resulting from adjacent-1 or adjacent-2 segregation are aborted
Fig d

49. Pseudolinkage is observed in heterozygotes with reciprocal translocations
In non-translocation heterozygotes, there are only two possible segregation patterns
With all offspring viable, Mendel's law of independent assortment would be observed with unlinked genes
In a reciprocal translocation heterozygote, only the alternate segregation pattern results in viable progeny
In outcrosses, genes located on the nonhomologous chromosomes would behave as if they are linked

50. Down syndrome arising from a Robertsonian translocation between chromosomes 21 and 14
Three chromosome segregation patterns
14q21q translocation heterozygote
Fig
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th edition, Chapter 13

51. END OF THE WEEK!