MODULE 5

Cytogenetics is the branch of genetics that studies the structure, function, and behavior of
chromosomes. Chromosomes carry genetic information in the form of DNA and are crucial for the
inheritance of traits.

Chromosomal Changes refer to alterations in chromosome number or structure, which can lead to
genetic disorders, cancer, and developmental abnormalities. These changes are categorized into
structural aberrations and numerical aberrations. Chromosomal aberrations are deviations from the
normal chromosome structure or number. They are often caused by errors during cell division
(meiosis or mitosis) and can have significant effects on an organism’s development and health. There
are two main types of chromosomal aberrations:

Structural Aberrations

Structural aberrations occur due to breaks in the chromosome, which can be caused by factors like
radiation, chemicals, or errors during DNA replication. These breaks can lead to rearrangements,
deletions, duplications, or other alterations in the chromosome structure.Types of Structural
Aberrations:

1. Deletions
- A segment of the chromosome is lost or deleted.
- Can result in the loss of essential genes and cause genetic disorders.
2. Duplications
- A segment of the chromosome is duplicated, resulting in extra copies of certain genes.
- Can lead to gene dosage imbalances and developmental abnormalities.
3. Inversions
- A segment of the chromosome breaks off, flips around, and reattaches in the reverse orientation.
- Inversions can disrupt gene function, especially if they involve regulatory regions or essential
genes.
4. Translocations
- A segment of one chromosome breaks off and attaches to another, non-homologous chromosome.
5. Ring Chromosomes
- A chromosome segment breaks at both ends and forms a ring structure.
- Often associated with genetic disorders due to the loss of genetic material.

Numerical Aberration

Numerical aberrations refer to changes in the number of chromosomes in a cell, leading to abnormal
chromosome counts. This can result in genetic disorders and often occurs due to nondisjunction,
where chromosomes fail to separate properly during cell division.

Types of Numerical Aberrations

1. Aneuploidy
- An abnormal number of chromosomes, either extra or missing chromosomes.
Monosomy: Loss of one chromosome from a pair (2N-1). Example: Turner syndrome (45, X).
Trisomy: Gain of an extra chromosome (2N+1). Example: Down syndrome (Trisomy 21), where there
is an extra chromosome 21.
2. Polyploidy
 - An increase in the entire set of chromosomes (3N, 4N, etc.).
- More common in plants than animals. Polyploidy in humans is usually lethal.
Gene Mutation
Gene mutations are changes in the DNA sequence of a gene, which can alter the gene’s function or
expression. Mutations can occur naturally during DNA replication or be induced by external factors
such as radiation or chemicals. Types of Gene Mutations
1. Point Mutations: Changes in a single nucleotide.
- Silent: No effect on protein function.
- Missense: Alters the amino acid, potentially affecting protein function.
- Nonsense: Introduces a stop codon, leading to a truncated, usually non-functional protein.
2. Frameshift Mutations: Insertions or deletions that shift the reading frame, often resulting in non-
functional proteins.
3. Insertions/Deletions: Addition or loss of nucleotides, which may or may not disrupt the gene
function depending on the size and location.

Complementation Test

A complementation test determines if two mutations associated with a similar phenotype are in the
same gene or in different genes. This test is primarily used in genetic analysis with model organisms.
1. Two mutant strains are crossed, each carrying a different mutation causing a similar defect.
2. Complementation occurs if the mutations are in different genes, producing a normal (wild-type)
phenotype.
3. No complementation occurs if the mutations are in the same gene, leading to the mutant phenotype.

Chromosome Preparation
Chromosome preparation is the process of isolating chromosomes for cytogenetic analysis. It is
essential for studying chromosomal structure, identifying aberrations, and diagnosing genetic
disorders.
Basic Steps
1. Cell Collection: Collect cells (e.g., blood cells).
2. Cell Culture: Cells are cultured and stimulated to divide, typically arrested in metaphase.
3. Hypotonic Treatment: Cells are treated with a hypotonic solution to swell, which spreads the
chromosomes.
4. Fixation: Cells are fixed to stabilize chromosome structure.
5. Slide Preparation: Chromosomes are spread on slides and stained for analysis.

G-Banding

G-banding (Giemsa banding) is a staining technique used to produce a visible karyotype by staining
chromosomes with Giemsa dye.
1. Chromosomes are treated with trypsin to partially digest proteins.
2. Giemsa stain is applied, binding to AT-rich regions and creating a pattern of light and dark bands.
3. Each chromosome has a unique banding pattern, making it easy to identify chromosomal
abnormalities.

Fluorescence In Situ Hybridization (FISH)

FISH is a technique that uses fluorescent probes to bind specific DNA sequences on chromosomes,
allowing visualization under a fluorescence microscope.
1. Chromosomes are prepared on a slide.
2. Fluorescent probes that target specific DNA sequences are applied.
3. Probes hybridize with complementary sequences on the chromosomes.
4. Fluorescent signals are detected, showing the location of specific genes or regions.
Applications
- Identifying specific genes or chromosome regions.
- Detecting chromosomal abnormalities like deletions, duplications, and translocations.
- Used in cancer diagnosis, prenatal testing, and genetic disorder studies.

Disorders Associated with Chromosomal Aberrations

1. **Down Syndrome**: Trisomy 21; an extra copy of chromosome 21 causes developmental delays
and intellectual disabilities.
2. **Turner Syndrome**: Monosomy X (45, X); a missing X chromosome in females, leading to
short stature, infertility, and specific physical features.
3. **Klinefelter Syndrome**: XXY condition; males have an extra X chromosome, leading to
infertility, reduced testosterone, and other developmental issues.
4. **Cri-du-chat Syndrome**: Deletion on chromosome 5; characterized by intellectual disability and
a high-pitched cry resembling a cat.
5. **Williams Syndrome**: Deletion on chromosome 7; leads to developmental delays,
cardiovascular problems, and distinctive facial features.

Philadelphia Chromosome

The Philadelphia chromosome is a specific chromosomal abnormality commonly associated with

chronic myeloid leukemia (CML). It results from a reciprocal translocation between chromosomes 9
and 22, producing a hybrid BCR-ABL gene.
Mechanism
- This translocation creates the BCR-ABL fusion gene, leading to the uncontrolled division of white
blood cells.
- The Philadelphia chromosome is detectable by cytogenetic techniques like FISH or PCR.

Lampbrush Chromosomes
Lampbrush chromosomes are large, extended chromosomes found in the oocytes (immature egg cells)
of some animals, including amphibians and birds, during meiosis.

**Characteristics**:
- Highly extended loops on the chromosome arms give them a "lampbrush" appearance.
- The loops represent active sites of RNA synthesis, where genes are being transcribed intensively to
support rapid cell development.
Module 6

Chromosome Structure

Chromosomes are thread-like structures made of DNA and proteins, found in the nucleus of
eukaryotic cells. They carry genetic information and play a crucial role in inheritance. Each
chromosome has:

Chromatids: Each chromosome is made of two identical chromatids joined at the centromere.
Centromere: The region that joins sister chromatids and attaches to spindle fibers during cell division.
Telomeres: Protective caps at the chromosome ends, preventing deterioration and fusion with
neighboring chromosomes.

Types of Chromosomes

1. Polytene Chromosomes
- Found in the salivary glands of flies (like *Drosophila*).
- Large chromosomes formed by repeated rounds of DNA replication without cell division
(endoreduplication).
- Contain puffs(swollen regions) indicating high gene activity and transcription.
- Used to study gene expression, chromosome structure, and replication.

2. Lampbrush Chromosomes
- Found in the oocytes (immature eggs) of amphibians, birds, and other animals during meiosis.
- Large and extended with visible looped regions
- The loops represent active sites of transcription, where genes are highly expressed to provide RNA
for the growing oocyte.
- Useful for studying transcription and chromatin organization.

Chromatin Organization

Chromatin is the complex of DNA and proteins (mainly histones) that forms chromosomes. It can be
organized into different structures to efficiently pack DNA into the nucleus.

1. Nucleosome Model
- The basic unit of chromatin structure.
 - DNA wraps around histone proteins (H2A, H2B, H3, and H4) to form nucleosomes.
- Each nucleosome consists of about 147 base pairs of DNA wound around a histone octamer.
- Linker DNA connects nucleosomes, and histone H1 binds to it to help compact the structure.

2. Solenoid Model
- Describes the higher-order structure of chromatin.
- Nucleosomes are coiled into a 30 nm fiber, known as the solenoid.
- This coiling further compacts the DNA and helps in regulating gene expression.

3. Leptonemic Model (Leptotene stage in meiosis):

- Represents the earliest visible stage of chromosomes during meiosis.
- Chromosomes appear as thin threads (leptotene), with chromatids not yet distinctly separated.
- Leptonemic organization is significant for synapsis and recombination of homologous
chromosomes.

Oncogenes and Tumor Suppressor Genes

Oncogenes and tumor suppressor genes are critical in regulating cell growth and division. Mutations
in these genes can lead to cancer.

1. Oncogenes
- Mutated or overexpressed versions of normal genes called proto-oncogenes.
- Proto-oncogenes normally promote cell growth and division.
- When mutated, they become oncogenes and cause uncontrolled cell division.
- Examples include RAS, MYC, and HER2 genes.
- Oncogenes act in a dominant manner, meaning only one copy needs to be mutated for cancerous
behavior.

2. Tumor Suppressor Genes

- Genes that normally suppress cell division, promote DNA repair, and induce apoptosis
(programmed cell death).
- Loss of function in these genes can lead to unregulated cell growth and tumor formation.
- Examples include p53, RB1, and BRCA1genes.
- Tumor suppressor genes act in a recessive manner, meaning both copies need to be inactivated for
tumor formation.