Chromosome Structure Changes Quiz

DNA: The Genetic Material

• DNA is the genetic material in eukaryotes
• A single set of human chromosomes stretched end-to-end would be over one meter long
• The cell nucleus is only 2-4 mm in diameter
• DNA must be tightly compacted to fit inside the nucleus
• This DNA-protein complex is called chromatin

Structure of Eukaryotic Chromosomes in Nondividing Cells

• Chromatin is defined as the packaging material of DNA within eukaryotic cells
• Nucleosomes, 30-nm fiber, and radial loop domains are the structures of eukaryotic chromosomes in non-dividing cells
• Noll's results support the beads-on-a-string model of DNA packaging: DNA fragments of 200 base pairs are a consistent result when breaking up chromatin
• Chromosome territory is the area of the nucleus that each chromosome occupies

Euchromatin and Heterochromatin

• Euchromatin are less condensed regions of chromosomes that are transcriptionally active
• Heterochromatin are tightly compacted regions of chromosomes and are transcriptionally inactive (generally)
• Constitutive heterochromatin - highly repetitive sequences that are always heterochromatic in all types of cells
• Facultative heterochromatin - differs among different cells of the body as genes are located and it can convert to euchromatin to regulate gene expression
• Centromeres and telomeres are regions of constitutive heterochromatin

Nucleosomes

• The repeating structural unit within eukaryotic chromatin is the nucleosome
• A nucleosome is composed of double-stranded DNA wrapped around an octamer of histone proteins
• The histone octamer is composed of two copies of each of four different histones: H2A, H2B, H3, and H4
• About 146 or 147 base pairs (bp) of DNA makes 1.65 negative superhelical turns around the octamer
• The linker region between nucleosomes is 20-100 bp
• Nucleosomes are connected to create a 'beads on a string' structure
• Nucleosomes shorten DNA's length about seven-fold

Histone Proteins

• Histone proteins contain positively-charged amino acids (lysine and arginine)
• These positively-charged amino acids bind to the negatively-charged DNA phosphates
• Histone proteins have a globular domain and a flexible, charged amino terminus (tail)

Histone Proteins 2

• There are five types of histones, but H2A, H2B, H3, and H4 are the core histones
• Two of each of the core histones make up the histone octamer
• H1 is the linker histone
• It binds to linker DNA and nucleosomes, but not as tightly as core histones
• Nonhistone proteins also bind the linker region, help in chromosome compaction, and impact gene expression

The Structure of the Nucleosome

• The nucleosome structure model was proposed in 1974 by Roger Kornberg
• DNA double helix is wrapped around an octamer of core histone proteins
• Kornberg's proposal was based on biochemical experiments, x-ray diffraction studies, and electron microscopy images

The Structure of the Nucleosome 2

• Markus Noll tested Kornberg's model
• The hypothesis was that digesting the linker region of chromatin should result in DNA fragments that are only 200 bp long
• The rationale was that linker DNA is more accessible to the enzyme DNase I compared to "core DNA"
• DNase I cuts occur in linker DNA, but not in DNA wrapped around core histones

The Data

• Results of using DNase I to cut DNA fragments support the nucleosome model because it demonstrated 200 bp DNA fragments
• At low DNase concentrations, the linker region was not fully cut and the results were not uniform
• At high DNase concentrations, the linker region is cut and DNA fragments of ~200 bp are seen with consistency

Nucleosomes Join to Form a 30-nm Fiber

• Nucleosomes associate to form a more compact structure: 30-nm fiber
• The 30-nm fiber shortens the total length of DNA seven-fold
• The structure of the 30-nm fiber is difficult to determine, but a zigzag model is proposed

Further Compaction of the Chromosome

• Nucleosomes and 30-nm fibers shorten DNA to about 50-fold
• A third level of compaction involves formation of loops (loop domains)
• CTCF (CCCTC-binding factor) binds to 3 regularly spaced repeats of the sequence CCCTC
• Two different CTCFs bind to the DNA to form a loop
• SMC proteins can also form DNA loops
• SMC proteins are frequently found in the region of CTCFs

Chromosome Territories

• Each chromosome in the nucleus occupies a distinct territory
• These territories are visible by fluorescently labeling chromosomes within interphase cells

Heterochromatin versus Euchromatin

• Euchromatin - less condensed, transcriptionally active
• Heterochromatin - tightly compacted, transcriptionally inactive (generally)

Constitutive versus Facultative Heterochromatin

• Constitutive heterochromatin - chromosomal regions that are heterochromatic in all cells, containing highly repetitive sequences such as centromeres and telomeres
• Facultative heterochromatin - chromosomal regions that differ among different cells of the body and can switch between euchromatin and heterochromatin to regulate gene expression

Structure of Eukaryotic Chromosomes During Cell Division

• Levels of compaction leads to the metaphase chromosome formation

Metaphase Chromosomes

• As cells enter M phase, the level of compaction changes dramatically to become metaphase chromosomes
• Nucleosomes form a zigzag structure to form the 30-nm fiber
• 30-nm fibers form loop domains
• Adjacent nucleosomes and loop domains have closer association
• Metaphase chromosomes are much shorter than interphase chromosomes but much thicker. A metaphase chromosome has a diameter of ~700 nm. Two chromatids have a diameter of ~1400 nm

Metaphase Chromosomes (continued)

• These highly condensed metaphase chromosomes undergo little gene transcription

The Data (cont)

• Results strongly support the nucleosome model for chromosome structure (from DNase I experiments)

Metaphase Chromosomes (again)

• There is controversy over whether or not non-histone proteins form a scaffold to organize the shape of metaphase chromosomes
• When metaphase chromosomes are treated with high salt to remove histones the highly compact configuration is lost
• Bottoms of loops remain attached to a scaffold made from non-histone proteins
• The function of this scaffold is unclear: does it organize metaphase chromosomes or is it just a remnant from high salt treatment

The Chromosome Composition of Humans

• Humans have 46 chromosomes (2n)

Microscopic Examination of Eukaryotic Chromosomes

• Characteristics used to classify and identify chromosomes include size, centromere position, and banding patterns

Genetic Variation

• Genetic variation refers to differences in alleles and chromosomes among members of the same species or among different species
• Allelic variation refers to differences in specific genes.
• Variations in chromosome structure and number affect more than one gene and are important in evolution, causes disease, and used for new crop strains

Variations in Chromosomes Can Be Seen by Light Microscopy

• Cytogeneticists study chromosomes under a light microscope

Chromosome Classification

• Different chromosomes can be classified by size, position of centromere, and banding patterns

Centromere Position

• Metacentric - centromere near the middle
• Submetacentric – slightly off center
• Acrocentric - more off center
• Telocentric - centromere at the end

Karyotype

• A karyotype is a micrograph of metaphase chromosomes from a cell arranged in standard fashion
• Chromosomes are arranged from largest to smallest

Giemsa Staining

• Different chromosomes have similar sizes and centromeric locations
• Staining is used to identify specific chromosomes
• Giemsa stain - G-bands
• The next slide figure shows conventional numbering of G-bands along a set of human chromosomes

Why is the Banding Pattern Useful?

• Distinguish between different chromosomes
• Detect changes in chromosome structure
• Useful to assess evolutionary relationships between species

Changes in Chromosome Structure: An Overview

• Deletions, duplications, inversions, and translocations are four types of changes in chromosome structure

Mutations Can Alter Chromosome Structure

• Deletions occur when a portion of a chromosome is missing
• Duplications occur when a portion of a chromosome is repeated
• Inversions occur when the direction of a part of the genetic material is changed on a single chromosome
• Translocations occur when a segment of one chromosome becomes attached to a non-homologous chromosome

Translocations

• Simple translocations - single piece of chromosome attaches to another
• Reciprocal translocations - two different chromosomes exchange pieces

Deletions

• The phenotypic consequences of deletions depend on
  • Size of the deletion
  • Chromosomal material deleted
  • Are the lost genes vital to the organism?

Deletions (again)

• Terminal deletion - a single break occurs, losing the fragment at the chromosome end
• Interstitial deletion - two breaks occur within a chromosome and the DNA is removed and degraded

Detrimental Effects of Deletions

• Deletions usually cause detrimental phenotypes like cri-du-chat syndrome.

Duplications

• Duplications result in extra genetic material
• They may be caused by abnormal crossing over during meiosis
• Nonallelic homologous recombination can occur when a chromosome contains two or more homologous segments or repetitive sequences
• Copies of a gene can increase from 1 to 2

Duplications (again)

• Duplications tend to have less harmful effects than deletions of a comparable size

Inversions

• A chromosomal inversion is a segment that has been flipped to the opposite orientation
• Total amount of genetic information stays the same
• Pericentric inversion - centromere is within the inverted region
• Paracentric inversion - centromere is outside the inverted region

Consequences of Inversions

• In rare cases, inversions can have a phenotypic effect on an individual
• Breakpoints - the breaks leading to the inversion may occur in a vital gene.
• Position effect - a gene's repositioning in a way that changes its gene expression
• About 2% of the population carries inversions detectable by light microscopes.
• Most inversion heterozygotes are phenotypically normal, but may produce offspring with abnormalities

Inversion Heterozygotes

• Individuals with one copy of a normal chromosome and one copy of an inverted chromosome may be phenotypically normal but have a high probability of producing abnormal gametes due to crossing over in inverted segments.

Inversion Heterozygotes (cont.)

• During meiosis I, homologous chromosomes synapse with each other and an inversion loop must form.
• If a crossover occurs within the inversion loop, highly abnormal chromosomes like dicentric and acentric chromosomes result. The dicentric chromosome contains two centromeres connected by a dicentric bridge, and the acentric fragment has no centromere and is degraded.

Translocations

• Involved with the exchanges between different chromosomes
• Telomeres (ends of eukaryotic chromosomes) prevent translocations from occurring because broken chromosome ends are reactive
• Reciprocal translocations occur when non-homologous chromosomes exchange genetic material

Reciprocal Translocations

• Reciprocal translocations arise through
  • Chromosomal breakage and DNA repair
  • Non-homologous crossovers
• Result in a rearrangement of genetic material without affecting the total amount
• Also called balanced translocations
• Usually without phenotypic consequence
• In rare cases, translocations cause a position effect

Unbalanced Translocation

• Carriers of a balanced translocation have an increased risk of having offspring with an unbalanced translocation
• Unbalanced translocations significantly impact gene material by duplications and/or deletions
• These translocations are associated with phenotypic abnormalities or lethality

Robertsonian Translocation

• Most common chromosomal rearrangement in humans
• The majority of chromosome 21 is attached to chromosome 14
• The translocation occurs so that breaks occur at the extreme ends of non-homologous chromosomes (such as 14 and 21)
• Small acentric fragments are lost
• Larger fragments fuse at centromeric regions to form a single chromosome

Changes in Chromosome Number: An Overview

• Euploidy (variation in the number of complete sets of chromosomes)
• Polyploidy (organisms with three or more sets of chromosomes)
• Aneuploidy (variation in the number of particular chromosomes within a set)

Variation in Chromosome Number

• Euploidy - Variation in the number of complete sets of chromosomes
• Examples: Triploid (3n), Tetraploid (4n)
• Organisms with 3 or more sets of chromosomes are called polyploid (also called euploidy)
• Aneuploidy - Variation in the number of particular chromosomes within a set
• Examples: Trisomy (2n+1), Monosomy (2n-1)

Aneuploidy

• Aneuploidy commonly causes an abnormal phenotype
• An imbalance in the amount of gene products occurs due to three copies of chromosomes which can lead to 150% of hundreds or thousands of gene products from a particular chromosome

Aneuploidy in Humans

• Alterations in chromosome number commonly occur during gamete formation
• About 5-10% of embryos have an abnormal chromosome number, with ~50% of spontaneous abortions due to such abnormalities
• Autosomal aneuploidies that are most compatible with survival are trisomies 13, 18, and 21
• Sex chromosome aneuploidies generally have less severe effects due to X chromosome inactivation

Influence of Age on Aneuploidy

• Some human aneuploidies are influenced by parental age, especially maternal age
• Older parents are more likely to have offspring with abnormal numbers of chromosomes, like Down syndrome (Trisomy 21)

Influence of Age on Aneuploidy (cont.)

• Down Syndrome (Trisomy 21) is an aneuploidy that occurs due to chromosomal nondisjunction (failure of chromosomes to segregate properly during meiosis I or II in the oocyte)
• Age of oocytes affects the frequency of nondisjunction

Euploidy

• Most species of animals are diploid (having 2n pairs of chromosomes)
• Changes in euploidy are often not tolerated
• Polyploidy in mammals is generally lethal

Euploidy (cont.)

• Some euploidy variations naturally occur in certain species, like bees
  • Female bees are diploid
  • Male bees (drones) are monoploid (contain a single set of chromosomes)
• Many examples of vertebrate polyploid animals have been discovered, such as the frog Hyla

Endopolyploidy

• In many animals, certain body tissues display normal variations in the number of sets of chromosomes, producing tissues that are polyploid
• Termed endopolyploidy
• For example, liver cells can be triploid, tetraploid, or even octaploid (8n)
• Polytene chromosomes of insects provide an unusual example of natural variation in ploidy

Polytene Chromosomes

• Occur mainly in the salivary glands of Drosophila and other insects
• Polytene chromosomes facilitate the study of the organization and function of interphase chromosomes
• Easier to see with a microscope due to their banding patterns

Polytene Chromosomes (cont.)

• Chromosomes undergo repeated rounds of chromosome replication without cellular division to produce a bundle of chromosomes in parallel fashion
• The central point where chromosomes aggregate is termed the chromocenter

Polyploidy

• Polyploidy is a condition where cells have more than two paired sets of chromosomes
• It's common in plants:
  • 30-35% of ferns and flowering plants are polyploid
  • Many fruits and grains are polyploids
• Polyploid strains of plants display outstanding characteristics, often being larger in size and more robust than diploid plants

Polyploids

• Polyploids with an odd number of chromosome sets are usually sterile because of unequal separation of homologous chromosomes during anaphase I
• Examples include triploid plants that produce highly aneuploid gametes

Sterility in Agriculture

• Sterility is normally agriculturally undesirable but can be desirable for crops, like seedless watermelons or bananas (triploid varieties) that are propagated by cuttings; and in seedless flowering plants like marigolds which keep blooming.

Mechanisms That Produce Variation in Chromosome Number

• How meiotic or mitotic nondisjunction affect phenotypes
• Autopolyploidy, alloploidy, and allopolyploidy
• The use of colchicine to induce polyploidy in species

Chromosome Number Variation

• Three natural mechanisms for chromosome number variation:
  • Meiotic nondisjunction
  • Mitotic nondisjunction
  • Alloploidy (interspecies crosses)

Meiotic Nondisjunction

• Nondisjunction is the failure of chromosomes to segregate properly during anaphase during either meiosis I or meiosis II
• If a gamete produced during meiosis with nondisjunction participates in fertilization, then the zygote will have an abnormal number of chromosomes

Complete Nondisjunction

• In rare cases, all the chromosomes can undergo nondisjunction and migrate to one daughter cell
• The diploid cell can participate in fertilization with a normal gamete to produce a triploid individual
• The chromosome-less cell is nonviable

Mitotic Nondisjunction

• Occurs after fertilization
• Sister chromatids separate improperly leading to trisomic or monosomic daughter cells
• Chromosome loss - one of the sister chromatids does not migrate to a pole and is degraded or lost if not included in the reformed nucleus
• Leads to normal and monosomic daughter cells

Autopolyploidy

• Complete nondisjunction can produce an individual with one or more extra sets of chromosomes

Allopolyploidy

• Allopolyploidy occurs when a polyploid offspring is derived from two different parental species
• An allotetraploid contains two complete sets of chromosomes from two different species

Experimental Treatments Can Promote Polyploidy

• Drugs, like colchicine, interfere with spindle apparatus and promote nondisjunction