1. Chapter 14 Chromosomal Rearrangements and Changes in Chromosome Number Reshape Eukaryotic Genomes

2. Outline of Chapter 14
Rearrangements of DNA sequences within and between chromosomes
Deletions
Duplications
Inversions
Translocations
Movements of transposable elements
Changes in chromosome number
Aneuploidy: monosomy and trisomy
Monoploidy
Polyploidy

4. Deletions remove genetic material from genome
Figure 13.2
Fig. 13.2

5. Phenotypic consequences of heterozygosity
Homozygosity for deletion is often but not always lethal
Heterozygosity for deletion is often detrimental
Figure 13.3
Fig. 13.3

6. Deletion heterozygotes affect mapping distances
Recombination between homologues can only occur if both carry copies of the gene
Deletion loop formed if heterozygous for deletion
Identification of deletion location on chromosome
Genes within can not be separated by recombination
Figure 13.4 a
Fig a

7. Deletion loops in polytene chromosomes
Figure 13.4 b
Fig b

8. Deletions in heterozygotes can uncover genes
Pseudodominance shows a deletion has removed a particular gene
Figure 13.5
Fig. 13.5

9. Deletions can be used to locate genes
Deletions to assign genes to bands on Drosophila polytene chromosomes
Complementation tests crossing deletion mutants with mutant genes of interests
Deletion heterozygote reveals chromosomal location of mutant gene
Figure 13.6
Fig. 13.6

10. Deletions to locate genes at the molecular level
Figure 13.7 a
Labeled probe hybridizes to wild-type chromosome but not to deletion chromosome
Fig a

11. Molecular mapping of deletion breakpoints by Southern blotting
Figure 13.7 b,c
Fig b, c

12. Duplications add material to the genome
Figure 13.8 a, b
Fig a,b

13. Duplication loops form when chromosomes pair in duplication heterozygotes
Figure 13.8 c
In prophase I, the duplication loop can assume different configurations that maximize the pairing of related regions
Fig c

14. Duplications can affect phenotype
Novel phenotypes
More gene copies
Genes next to duplication displaced to new environment altering expression
Figure 13.9
Fig. 13.9

15. Unequal crossing over between duplications increases or decreases gene copy number
Figure 13.10
Fig

16. Fig

17. Summary of duplication and deletion effects on phenotpye
Alter number of genes on a chromosome and may affect phenotype of heterozygote
Heterozygosity create one or three gene copies and create imbalance in gene product altering phenotypes (some lethal)
Genes may be placed in new location that modifies its expression
Deletions and duplications drive evolution by generating families of tandemly repeated genes

18. Inversions reorganize the DNA sequence of a chromosome
Produced by half rotation of chromosomal regions after double-stranded break
Also rare crossover between related genes in opposite orientation or transposition
Figure a,b
Fig a,b

19. An inversion can affect phenotype if it disrupts a gene
Figure c
Fig c

20. Inversion heterozygotes reduce the number of recombinant progeny
Inversion loop in heterozygote forms tightest possible alignment of homologous regions
Figure 13.12
Fig

21. Gametes produced from pericentric and paracentric inversions are imbalanced
Figure 13.13
Fig

22. Pericentric inversion Paracentric inversion (cont’d) (cont’d)
Figure (cont’d)
Fig cont’d

23. Inversions suppress recombination
Balancer chromosomes carry both a dominant marker D and inversions (brackets) that prevent recombination with experimental chromosome.
Heterozygous parent will transmit balancer or experimental chromosome.
Dominant mutation has an easily distinguished phenotpye (e.g., curly wing)

24. Translocations attach on part of a chromosome to another
Figure a
Translocation – part of one chromosome becomes attached to nonhomologous chromosome
Reciprocal translocation – two different parts of chromosomes switch places
Fig a

25. Robertsonian translocations can reshape genomes
Figure 13.16
Reciprocal exchange between acrocentric chromosomes generate large metacentric chromosome and small chromosome
Tiny chromosome may be lost from organism
Fig

26. Leukemia patients have too many blood cells
Figure 13.17
Fig

27. Heterozygosity for translocations diminishes fertility and results in pseudolinkage
Figure a, b
Fig a.b

28. Three possible segregation patterns in a translocation heterozygote from the cruciform configuration
Figure c
Fig c
Pseudolinkage – because only alternate segregation patterns produce viable progeny, genes near breakpoints act as if linked

29. Semisterility results from translocation heterozygotes
< 50% of gametes arise from alternate segregation and are viable
Figure d
Fig d

30. Translocation Down syndrome translocation of chromosome 21 is small and thus produces viable gamete, but with phenotypic consequence
Figure 13.19
Fig

31. Transposable elements move from place to place in the genome
1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn
1983 McClintock received Nobel Prize
Found in all organisms
Any segment of DNA that evolves ability to move from one place to another in genome
Selfish DNA carrying only information to self-perpetuate
Most 50 – 10,000 bp
May be present hundreds of time in a genome
LINES, long interspersed element in mammals
~ 20,000 copies in human genome up to 6.4kb in length
SINES, short interspersed elements in mammals
~ 300,000 copies in human genome
~ 7% of genome are LINES and SINES

32. Retroposons generate an RNA that encodes a reverse transciptase like enzyme
Two types
Poly-A tail at 3’ end of RNA-like DNA strand
Long terminal repeat (LTRs) oriented in same direction on either end of element
Figure a
Fig a

33. Figure b
Fig b

34. The process of LTR transposition
Figure 13.23
Fig

35. Transposons encode transposase enzymes that catalyze events of transposition
Figure a
Fig a

36. P elements in Drosophila
After excision of P element transposon, DNA exonucleases first widen gap and then repair it
Repair uses sister chromatid or homologous chromosome as a template
P strains of Drosophila have many copies of P elements
M strains have no copies
Hybrid dysgenesis – defects including sterility, mutation, and chromosomal breakage from cross between P and M strains
Promotes movement of P elements to new positions

37. Figure b

38. Genomes often contain defective copies of transposable elements
Many TEs sustain deletions during transposition or repair
If promoter needed for transcription deleted, TE can not transpose again
Most SINES and LINES in human genome are defective TEs
Nonautonomous elements – need activity of nondeleted copies of same TE for movement
Autonomous elements – move by themselves

39. TEs can generate mutations in adjacent genes spontaneous mutations in white gene of Drosophila
Figure 13.25
Fig

40. TEs can generate chromosomal rearrangements and relocate genes
Figure 13.26
Fig

41. The loss or gain of one or more chromosomes results in aneuploidy

42. Autosomal aneuploidy is harmful to the organism
Monosomy usually lethal
Trisomies – highly deleterious
Trisomy 18 – Edwards syndrome
Trisomy 13 – Patau syndrome
Trisomy 21 – Down syndrome

43. Humans tolerate X chromosome aneuploidy because X inactivation compensates for dosage
Figure 13.27
Fig

44. Mitotic nondisjunction
Failure of two sister chromatids to separate during mitotic anaphase
Generates reciprocal trisomic and monosomic daughter cells
Chromosome loss
Produces one monosomic and one diploid daughter cell
Figure a
Fig a

45. Mosaics – aneuploid and normal tissues that lie side-by-side
Aneuploids give rise to aneuploid clones
Figure b
Fig b

46. Gynandromorph in Drosophila results from female losing one X chromosome during first mitotic division after fertilization
Figure 13.29
Fig

47. Euploid individuals contain only complete sets of chromosomes

48. Monoploid plants have many uses
Monoploid organisms contain a single copy of each chromosome and are usually infertile
Monoploid plants have many uses
Visualize recessive traits directly
Introduction of mutations into individual cells
Select for desirable phenotpyes (herbicide resistance)
Hormone treatment to grow selected cells

49. Figure 13.30
Fig

50. Treatment with colchicine converts back to diploid
plants that express desired phenotypes
Figure c
Fig c

51. Polyploidy has accompanied the evolution of many cultivated plants
1:3 of flowering plants are polyploid
Polyploid often increases size and vigor
Often selected for agricultural cultivation
Tetraploids - alfalfa, coffee, peanuts
Octaploid - strawberries
Figure 13.31
Fig

52. Triploids are almost always sterile
Result from union of monoploid and diploid gametes
Meiosis produces unbalanced gametes
Figure 13.32
Fig

53. Tetraploids are often source of new species
Failure of chromosomes to separate into two daughter cells during mitosis in diploid
Cross between tetraploid and diploid creates triploids – new species, autopolyploids
Figure a
13.33 a

54. Maintenance of tetraploid species depends on the production of gametes with balanced sets of chromosomes
Bivalents- pairs of synapsed homologous chromosomes that ensure balanced gametes
Figure b
Fig b

55. Figure c
Fig c

56. Amphidiploids created by chromosome doubling in germ cells
Some polyploids have agriculturally desirable traits derived from two species
Amphidiploids created by chromosome doubling in germ cells
e.g., wheat – cross between tetraploid wheat and diploid rye produce hybrids with desirable traits
Figure 13.34
Fig