Genetics and Chromosome Structure

DNA: The Genetic Material

• DNA is the genetic material in eukaryotes
• A single set of human chromosomes would be over 1 meter if stretched end-to-end
• A human cell's nucleus is only 2 to 4 mm in diameter
• DNA must be tightly compacted to fit within the cell's nucleus
• The compaction of DNA involves interactions between DNA and proteins
• The complex of DNA and proteins is known as chromatin

Structure of Eukaryotic Chromosomes in Nondividing Cells

• Chromatin is defined as the complex of DNA and proteins in nondividing eukaryotic cells
• Nucleosomes are the repeating structural units within chromatin
• Nucleosomes consist of double-stranded DNA wrapped around an octamer of histone proteins
• The octamer is composed of two copies each of four different core histone proteins (H2A, H2B, H3, and H4)
• Approximately 146 or 147 base pairs (bp) of DNA wrap around the histone octamer
• The linker region between nucleosomes is 20 to 100 bp
• Nucleosomes are sometimes described as "beads on a string"
• Nucleosomes shorten DNA to about seven times its original length
• Histone proteins contain positively charged amino acids (lysine and arginine)
• These positively charged amino acids bind to the negatively charged phosphates along the DNA
• Histone proteins have a globular domain and a flexible, charged amino terminus ('tail')
• There are five types of histones
• H2A, H2B, H3, and H4 are the core histones. Two of each make up the octamer. H1 is the linker histone, which binds to linker DNA and also binds to nucleosomes, but not as tightly as the core histones
• Nonhistone proteins also bind the linker region, which aids in chromosome compaction and affects gene expression
• The model of nucleosome structure was proposed in 1974 by Roger Kornberg
• Kornberg based his proposal on biochemical experiments, x-ray diffraction studies, and electron microscopy images
• Markus Noll tested Kornberg's model and found that digestion of the linker region of chromatin resulted in DNA fragments that were ~200 bp long

Nucleosomes Join to Form a 30-nm Fiber

• Nucleosomes associate with each other to form a more compact structure—the 30-nm fiber
• Shortens the total length of DNA 7-fold
• The structure of the 30-nm fiber has been difficult to determine
• A zigzag model has been proposed

Further Compaction of the Chromosome

• Nucleosomes and the 30-nm fiber shorten the DNA about 50-fold
• A third level of compaction involves the formation of loops (also called loop domains)
• CCCTC binding factor (CTCF) 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 a DNA loop
• SMC proteins are often found in the region of CTCFs

Chromosome Territories

• Each chromosome in the nucleus is located in a distinct chromosome territory
• These territories are visible when chromosomes are fluorescently labeled in interphase cells

Heterochromatin versus Euchromatin

• Euchromatin: Less condensed regions of chromosomes; transcriptionally active
• Heterochromatin: Tightly compacted regions of chromosomes; generally transcriptionally inactive

Constitutive versus Facultative Heterochromatin

• Constitutive heterochromatin: Chromosomal regions that are heterochromatic in all cell types; highly repetitive sequences; includes centromeres and telomeres
• Facultative heterochromatin: Differs among different cells of the body; occurs where genes are located; can convert to euchromatin for gene expression regulation

Structure of Eukaryotic Chromosomes During Cell Division

• As cells enter M phase, the level of compaction changes dramatically to become metaphase chromosomes
• Nucleosomes undergo zigzag structure to form a 30-nm fiber
• 30-nm fibers form loop domains
• Closer association of loop domains with each other and closer association between adjacent nucleosomes
• Chromosomes have a diameter of 700 nm; two chromatids have a diameter of 1400 nm
• Metaphase chromosomes are much shorter in length than interphase chromosomes
• These highly condensed metaphase chromosomes undergo little gene transcription

Metaphase Chromosomes: Scaffold

• Controversy exists about whether nonhistone proteins form a scaffold to organize metaphase chromosomes
• When a metaphase chromosome is treated with high salt to remove histones, the highly compact configuration is lost
• The bottoms of loops remain attached to a scaffold made of nonhistone proteins
• The function of this scaffold remains debated

The Chromosome Composition of Humans

• Humans have a specific number and type of chromosomes
• Chromosomes can be identified and classified by size, centromere position, and banding patterns

Chromosome Classification: Centromere Position

• Metacentric: Centromere near the middle
• Submetacentric: Centromere slightly off center
• Acrocentric: Centromere more off center
• Telocentric: Centromere at the end

Karyotype

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

Giemsa Staining

• Different chromosomes have similar sizes and centromeric locations
• Staining is used to identify specific chromosomes
• Giemsa stain reveals G bands
• Next figure shows a conventional numbering system of G bands on human chromosomes

Changes in Chromosome Structure: Overview

• Four types of chromosome structure changes
• Deletion (also called Deficiency)
• Duplication
• Inversion
• Translocation

Translocations

• Simple translocations: A single piece of chromosome is attached to another chromosome
• Reciprocal translocations: Two different chromosomes exchange pieces

Deletions

• Phenotypic consequences of deletions depend on the size of the deletion and the chromosomal material deleted
• Are the lost genes vital to the organism?
• Deletions can be terminal (at the end of the chromosome) or interstitial (within the chromosome).

Duplications

• Duplications result in extra genetic material
• They can be caused by abnormal crossing over during meiosis
• Duplications are sometimes correlated with size.
• Duplications are more likely to have phenotypic effects if they involve a large piece of the chromosome.

Inversions

• A chromosomal inversion is when a segment of a chromosome is flipped to the opposite orientation
• The total amount of genetic information stays the same, but the segment's genetic sequence is reversed.
• Pericentric inversion: The centromere is within the inverted region
• Paracentric inversion: The centromere is outside the inverted region

Consequences of Inversions

• In some rare cases, inversions can alter the phenotype of an individual
• Position effect: A gene repositioned in a way that alters its gene expression
• About 2% of the human population has detectable inversions but are phenotypically normal
• Less frequently, inversions can produce offspring with genetic abnormalities

Inversion Heterozygotes

• Individuals with one normal chromosome and one inverted chromosome may be phenotypically normal
• However, they have a high probability of producing abnormal gametes due to crossing over in the inverted segment
• During meiosis 1, homologous chromosomes synapse with each other and an inversion loop must form. If a crossover occurs within the inversion loop, highly abnormal chromosomes are produced

Variations in Chromosome Number

• Chromosome numbers can vary in two main ways: euploidy and aneuploidy. Euploidy refers to variations in the number of complete sets of chromosomes, such as triploid (3n) or tetraploid (4n). Aneuploidy refers to variations in the number of particular chromosomes within a set, such as trisomy (2n+1) or monosomy (2n-1). Polyploidy refers to organisms that have more than two chromosome sets. Common in plants but often lethal in mammals.

Aneuploidy

• Aneuploidy commonly causes an abnormal phenotype due to an imbalance in the amount of gene products
• Three copies of a gene can lead to a 150% production of the associated gene products from one chromosome.

Aneuploidy in Humans

• Autosomal aneuploidies (e.g. Trisomy 13, 18, 21) are associated with lower compatibility with survival than sex chromosome aneuploidies
• Sex chromosome aneuploidies often have less severe effects due to X-inactivation

Influence of Age on Aneuploidies

• Some human aneuploidies are influenced by parental age.
• Older parents have a higher chance of producing abnormal offspring, especially mothers.
• This is especially true of Down syndrome (Trisomy 21).

Euploidy

• Most species of animals are diploid. In many cases changes in euploidy are not tolerated
• Polyploidy in mammals is generally a lethal condition, but some euploidy variations are naturally occurring in species, such as bees, which can be haplodiploid

Endopolyploidy

• In many animals, certain body tissues display normal variations in the number of sets of chromosomes
• Diploid animals sometimes produce tissues that are polyploid (called endopolyploidy)
• Examples include liver cells that can be triploid, tetraploid, or even octaploid (8n)
• Polytene chromosomes in insects

Polytene Chromosomes

• Polytene chromosomes are mainly in the salivary glands of Drosophila and some other insects
• Polytene chromosomes have easily seen banding patterns in interphase
• Chromosomes undergo repeated rounds of replication without cellular division, creating a bundle of chromosomes aligned together (the chromocenter)

Polyploidy

• A condition in which the cells of an organism have more than two paired sets of chromosomes is common in plants
• Polyploid strains of plants often display desirable traits, like larger size or robustness

Polyploids and Sterility

• Polyploids with an odd number of chromosome sets are usually sterile because of problems creating normal gametes
• Seedlessness can be a desirable trait for fruits (like watermelons and bananas) or other plants

Explore the critical aspects of metaphase chromosomes, including the effects of high salt treatment and the roles of nonhistone proteins. Understand the distinctions between euchromatin and heterochromatin, along with the implications of genetic variation in biology and agriculture. This quiz is essential for anyone interested in cell biology and genetics.