2. Dr Gihan E-H Gawish, MSc, PhD Ass. Professor Molecular Genetics and Clinical Biochemistry Molecular Genetics and Clinical BiochemistryKSU Chromosome Mutations: introduction, changes in chromosome number, structure, chromosomal rearrangements, the overall incidence of human chromosome mutations and evolution of the genome. 5 th Module Dr Gihan Gawish1

3. Introduction  Gene mutations are one source of genomic change. However, the genome can also be remodeled at a larger scale by alterations to chromosome structure or by changes in the number of copies of chromosomes in a cell. These large-scale variations are termed Dr Gihan Gawish 2 chromosome mutations changes in chromosome numberchanges in chromosome structure

4. Chromosome mutations are important, why? Dr Gihan Gawish 3 They can be sources of insight into gene function on a genomic scale. They reveal several important features of meiosis and chromosome architecture. They constitute useful tools for experimental genomic manipulation. They are sources of insight into evolutionary processes.

5. Dr Gihan Gawish 4 Changes in Chromosome Number changes in whole chromosome sets (resulting in a condition of aberrant euploidy) changes in parts of chromosome sets (resulting in aneuploidy).

6. 5 NameDesignationConstitution Number of chromosomes Monoploid nABC3 Diploid 2n2nAABBCC6 Triploid 3n3nAAABBBCCC9 Tetraploid 4n4nAAAABBBBCCCC12 Monosomic 2n − 12n − 1 ABBCC5 AABCC5 AABBC5 Trisomic 2n + 12n + 1 AAABBCC7 AABBBCC7 AABBCCC7 Chromosome Constitutions in a Normally Diploid Organism with Three Chromosomes (Labeled A, B, and C) in the Basic Set

7. Dr Gihan Gawish 6 Aberrant Euploidy Organisms with multiples of the basic chromosome set euploid Eukaryotes carry one chromosome haploid Eukaryotes carry two chromosome diploid aberrant euploids. Polyploids Organisms that have more or less than the normal number of sets Individual organisms in which there are more than two chromosome sets.

8. Dr Gihan Gawish 7  Aneuploidy is the second major category of chromosome aberrations in which chromosome number is abnormal.  An aneuploid is a individual organism whose chromosome number differs from the wild type by part of a chromosome set.  Generally, the aneuploid chromosome set differs from wild type by only one chromosome or by a small number of chromosomes.  An aneuploid can have a chromosome number either greater or smaller than that of the wild type.  Aneuploid nomenclature is based on the number of copies of the specific chromosome in the aneuploid state.  Aneuploidy is the second major category of chromosome aberrations in which chromosome number is abnormal.  An aneuploid is a individual organism whose chromosome number differs from the wild type by part of a chromosome set.  Generally, the aneuploid chromosome set differs from wild type by only one chromosome or by a small number of chromosomes.  An aneuploid can have a chromosome number either greater or smaller than that of the wild type.  Aneuploid nomenclature is based on the number of copies of the specific chromosome in the aneuploid state. changes in parts of chromosome sets (resulting in aneuploidy)

9. Dr Gihan Gawish 8  The aneuploid condition 2n − 1 is called monosomic (meaning “one chromosome”) because there is only one copy of some specific chromosome present instead of the usual two found in its diploid progenitor.  For autosomes in diploid organisms, the aneuploid 2n+1 is called trisomic,2n − 1 is monosomic, and 2n − 2 (where the − 2 represents homologs) is nullisomic.  In haploids, n+1 is di-somic. Special symbolism has to be used to describe sex-chromosome aneuploids, because we are dealing with two different chromosomes (X and Y) and the homogametic and heterogametic sexes have different sex-chromosome compositions even in euploid individuals. The symbolism merely lists the copies of each sex chromosome, such as XXY, XYY, XXX, or XO (the “O” stands for absence of a chromosome and is included to show that the symbol is not a typographical error). Aneuploidy

10. Dr Gihan Gawish 9  In humans, the most common aneuploidies are trisomies, which represent about 0.3% of all live births. Trisomies are characterized by the presence of one additional chromosome, bringing the total chromosome number to 47. With few exceptions, trisomies do not appear to be compatible with life. In fact, trisomies represent about 35% of spontaneous abortions (Hassold & Hunt, 2001). Most Aneuploidies Are Lethal

11. Dr Gihan Gawish 10  The most common human trisomy involves chromosome 21 and is known as Down syndrome (DS). Today, DS is routinely identified in karyotypes or by using fluorescent probes for chromosome 21 through fluorescence in situ hybridization (FISH) (Antonarakis et al., 2004). Most Aneuploidies Are Lethal Trisomy 21 karyotype. G-banded karyotype of a trisomy 21 female, showing three copies of human chromosome 21. Trisomy 21 karyotype. G-banded karyotype of a trisomy 21 female, showing three copies of human chromosome 21. Diagnosing trisomy 21. Fluorescence in situ hybridization (FISH) of interphase nuclei from a fetus has been used to diagnose trisomy 21. In each cell, there are two green spots (LSI 13 SpectrumGreen probe, Vysis) and three red spots (LSI 21 SpectrumOrange probe, Vysis) marking the 13q14 and 21q22.13-q22.2 chromosomal regions, respectively. Diagnosing trisomy 21. Fluorescence in situ hybridization (FISH) of interphase nuclei from a fetus has been used to diagnose trisomy 21. In each cell, there are two green spots (LSI 13 SpectrumGreen probe, Vysis) and three red spots (LSI 21 SpectrumOrange probe, Vysis) marking the 13q14 and 21q22.13-q22.2 chromosomal regions, respectively.

12. Dr Gihan Gawish 11 Primary Down syndrome is caused by the presence of three copies of chromosome 21. (a) A child who has Down syndrome. (b) Idiogram of a person who has primary Down syndrome. Down syndrome

13. Dr Gihan Gawish 12 Polyploids arise when a rare mitotic or meiotic catastrophe, such as nondisjunction, causes the formation of gametes that have When a diploid gamete fuses with a haploid gamete, a triploid zygote forms, although these triploids are generally unstable and can often be sterile. If a diploid gamete fuses with another diploid gamete, however, this gives rise to a tetraploid zygote, which is potentially stable. Many types of polyploids are found in nature, including tetraploids (four sets of chromosomes), hexaploids (six sets of chromosomes), and other chromosome- pair multiples Polyploidy

14. Dr Gihan Gawish 13 Autopolyploids : polyploids that arise within a species Allopolyploids: that arise due to the hybridization of two distinct species. Autopolyploids are essentially homozygous at every locus in the genome. However, allopolyploids may have varying degrees of heterozygosity depending on the divergence of the parental genomes. Heterozygosity is apparent in the gametes that polyploids produce. Allopolyploids can generally be distinguished from autopolyploids because they produce a more diverse set of gametes Polyploidy

15. Dr Gihan Gawish 14 Polyploid formation and ensuing meiotic and mitotic irregularities

16. 15  Cytologists had been studying chromosome behavior since the late 19th century. Why did it take until 1956 to figure out the correct human chromosome number, thanks to Joe Hin Tjio and Albert Levan? How Cytologists had been Studying Chromosome Number A human metaphase plate, from the original Tjio and Levan paper, showing 46 chromosomes.

17. 16 The origin of aneuploid gametes by nondisjunction at the first or second meiotic division. Nondisjunction at meiosis I is more frequent than that at meiosis II, indicating the necessity of crossovers in the maintenance of the intact tetrad until anaphase I.

18. Dr Gihan Gawish 17 Chromosomal Rearrangements Chromosomal rearrangements encompass several different classes of events: deletions, duplications, inversions; and translocations.

19. Dr Gihan Gawish 18 Inversions Effects of inversions at the DNA level.

20. Dr Gihan Gawish 19 Meiotic products resulting from a single crossover within a paracentric inversion loop. Two nonsister chromatids cross over within the loop.

21. The main diagnostic features of heterozygous inversions are inversion loops, reduced recombinant frequency, and reduced fertility from unbalanced or deleted meiotic products MESSAGE Dr Gihan Gawish 20

22. Dr Gihan Gawish 21 The meiotic products resulting from the two most commonly encountered chromosome segregation patterns in a reciprocal translocation heterozygote Reciprocal Translocations

23. Dr Gihan Gawish 22 When a translocated fragment carries a marker gene, this marker can show linkage to genes on the other chromosome because the recombinant genotypes (in this case, a +. b and a. b + ) tend to be in duplication–deletion gametes and do not survive.

24. Heterozygous reciprocal translocations are diagnosed genetically by semisterility and by the apparent linkage of genes whose normal loci are on separate chromosomes. MESSAGE Dr Gihan Gawish 23

25. Dr Gihan Gawish 24 Applications of Inversions and Translocations1- Gene mapping 2- Synthesizing specific duplications or deletions 3- Position-effect variegation

26. Dr Gihan Gawish 25 Deletions are recognized by deletion loops and pseudodominance. The lethality of large heterozygous deletions can be explained by genome imbalance and expression of deleterious recessives

27. Dr Gihan Gawish 26

28. Dr Gihan Gawish 27 The cause of the cri du chat syndrome of abnormalities in humans is loss of the tip of the short arm of one of the homologs of chromosome 5.  Most human deletions, arise spontaneously in the germ line of a normal parent of an affected person; thus no signs of the deletions are found in the somatic chromosomes of the parents.  In rarer cases, deletion-bearing offspring can arise through adjacent segregation of a reciprocal translocation heterozygote or recombination within a pericentric inversion heterozygote.  Most human deletions, arise spontaneously in the germ line of a normal parent of an affected person; thus no signs of the deletions are found in the somatic chromosomes of the parents.  In rarer cases, deletion-bearing offspring can arise through adjacent segregation of a reciprocal translocation heterozygote or recombination within a pericentric inversion heterozygote.

29. 28  The duplicate regions can be located adjacent to each other, called a tandem duplication, or one duplicated region can be in its normal location and the other in a novel location on a different part of the same chromosome or even on another chromosome, called an insertional duplication.  In a diploid organism, the chromosome set containing the duplication is generally present together with a standard chromosome set.  The cells of such an organism will have three copies of the chromosome region in question, but nevertheless such duplication heterozygotes are generally referred to as duplications because they carry the product of one duplication event. In meiotic prophase, tandem duplication heterozygotes show a loop representing the unpaired extra region.  The duplicate regions can be located adjacent to each other, called a tandem duplication, or one duplicated region can be in its normal location and the other in a novel location on a different part of the same chromosome or even on another chromosome, called an insertional duplication.  In a diploid organism, the chromosome set containing the duplication is generally present together with a standard chromosome set.  The cells of such an organism will have three copies of the chromosome region in question, but nevertheless such duplication heterozygotes are generally referred to as duplications because they carry the product of one duplication event. In meiotic prophase, tandem duplication heterozygotes show a loop representing the unpaired extra region.

30. Dr Gihan Gawish 29 The fate of a million implanted human zygotes. (In Robertsonian translocations centromeres fuse or dissociate.) (From K. Sankaranarayanan, Mutation Research 61, 1979.) Mutation The fate of a million implanted human zygotes. (In Robertsonian translocations centromeres fuse or dissociate.) (From K. Sankaranarayanan, Mutation Research 61, 1979.) Mutation

31. Evolution of the Genome Dr Gihan Gawish 30  Different phylogeneti groups differ considerably in chromosome number and structure.  In some cases, there are differences between closely related groups, and there can even be normal variation within or between populations of one species. OBJECTIVES OF THE COMING SECTION  Some of the ways that chromosome mutations contribute to the evolution of genomes.  Explore and describe the comparative molecular anatomy of genomes.  Different phylogeneti groups differ considerably in chromosome number and structure.  In some cases, there are differences between closely related groups, and there can even be normal variation within or between populations of one species. OBJECTIVES OF THE COMING SECTION  Some of the ways that chromosome mutations contribute to the evolution of genomes.  Explore and describe the comparative molecular anatomy of genomes.

32. Chromosomal Polymorphism 31  Some natural populations show two or more chromosomal forms, a situation called chromosomal polymorphism.  Drosophila, because of its polytene chromosomes, has been a favorite organism for the study of natural chromosomal variation.  In particular, Drosophila shows abundant polymorphism for chromosomal inversions— specifically, paracentric inversions.  Inversion polymorphism is so common that determining the “wild-type gene order” in a species of Drosophila is quite arbitrary.  There are many different gene orders, depending on the inversions present in a given individual fly.  Inversion polymorphism might be prevalent because it allows genes in an inverted region to coevolve, because inversion heterozygosity blocks the production of viable crossover gametes. Other kinds of chromosomal rearrangement polymorphism seem to be rarer, because they tend to be more deleterious than inversions.

33. Chromosomal Changes and Speciation Dr Gihan Gawish 32 (c) D. J. Weatherall and J. B. Clegg, “Recent Developments in Molecular Genetics of Human Hemoglobin,” Cell 16, 1979

34. Duplication and polyploidization supply additional genetic material capable of evolving new functions. MESSAGE Dr Gihan Gawish 33

35. Chromosomal Synteny Dr Gihan Gawish 34 Synteny of human and mouse chromosomes. Since evolutionary divergence, multiple rearrangements have placed homologous blocks of genes in different combinations.

36. The study of synteny shows that chromosomal rearrangements have been instrumental in evolution at the chromosome level. MESSAGE Dr Gihan Gawish 35

37.  Although some congenital defects can be controlled and treated, an estimated 3.2 million of these children are disabled for life.  Moreover, birth defects are the leading cause of infant mortality in the United States. But where do these defects come from? Although some birth defects are inherited, others are a product of harmful environmental factors known as teratogens, and still others are multifactorial, resulting from a complex interaction of genetic and environmental influences.  However, in approximately half of all birth defect cases, the causes are unknown.  Although some congenital defects can be controlled and treated, an estimated 3.2 million of these children are disabled for life.  Moreover, birth defects are the leading cause of infant mortality in the United States. But where do these defects come from? Although some birth defects are inherited, others are a product of harmful environmental factors known as teratogens, and still others are multifactorial, resulting from a complex interaction of genetic and environmental influences.  However, in approximately half of all birth defect cases, the causes are unknown. Every year, about 7.9 million infants (6% of worldwide births) are born with serious birth defects. With the causes of over 50% of birth defects unknown 36 How do we diagnose and prevent them?

38.  Chromosomal abnormalities  Single-gene defects  Multifactorial influences. Prenatal environment can play a major role in the development of defects in all three categories, especially those linked to multifactorial causes.  Chromosomal abnormalities  Single-gene defects  Multifactorial influences. Prenatal environment can play a major role in the development of defects in all three categories, especially those linked to multifactorial causes. Genetic causes of birth defects fall into three general categories: Dr Gihan Gawish 37