MGFD

L 55 & 56
Genomic (genetic or chromosomal) Rearrangements
Dr. Khalid Mohany
Objectives:
• Distinguish between homologous and non-homologous recombination
• Understand the possible consequences of DNA rearrangement
• Describe the basic features of immunoglobulins and gene structure
arrangement
• Understand the role of DNA rearrangement in the generation of
immunoglobulin diversity

Introduction:
 Genomic (Genetic or Chromosomal) rearrangements are structural alteration of
a chromosome that causes a change in the order or position of its loci.
 On a molecular level, genetic recombination is the exchange (or incorporation) of one DNA
sequence with (or into) another.
 These rearrangements are known to play a major role in evolution.
 Their most visible effects are quite straight forward: duplications and deletions account for
numerous gene acquisitions or losses while translocations and inversions have a direct
influence on gene order.
 Genetic recombination during meiosis can lead to a novel set of genetic information that
can be passed on from the parents to the offspring. Most recombination is naturally
occurring.

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 Homologous and non-homologous recombination

1. Homologous recombination
 It is a type of genetic recombination in which nucleotide sequences are exchanged between
two similar or identical molecules (sequences) of DNA.
 It is most widely used by cells to accurately repair harmful breaks
that occur on both strands of DNA, known as double-strand
breaks.
 Homologous recombination also produces new combinations of
DNA sequences during meiosis, the process by
which eukaryotes make gamete cells, like sperm and egg cells in
animals.
 These new combinations of DNA represent genetic variation in
offspring, which in turn enables populations to adapt during the course of evolution.
Homologous recombination is also used in horizontal gene transfer to exchange genetic
material between different strains and species of bacteria and viruses.

2. Non-homologous recombination
 It is a type of genetic recombination in which nucleotide sequences are exchanged between
two different or non-identical molecules (sequences) of DNA.
 Nonhomologous recombination (NHR) is a major pathway for the repair of chromosomal
double-strand breaks in the DNA of somatic cells.
 Other similar NHR mechanism accomplishes other rearrangements of DNA sequences, such
as immunoglobulin and T-cell receptor rearrangements.
 NHR may occur:
A. In vivo:
 Immunoglobulin and T-cell receptor rearrangements
 Repair of double strand breaks

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  Chromosomal rearrangements (most of them are abnormal) e.g.
translocation, deletion, inversion and duplication.
B. In vitro (ex vivo):
 Recombinant DNA technology and transgenic animal

Possible consequences of DNA (genetic) rearrangement

 Homologous recombination (rearrangement) results in the reassortment of genes between
chromosome pairs without altering the arrangement of genes within the genome so, it
usually has no consequences.
 Naturally occurring non homologous recombinations (rearrangements) are important in
controlling gene expression in specific cell types and play an evolutionary role by
contributing to genetic diversity.
 Abnormal non homologous genomic (genetic or chromosomal) rearrangements) occur in
two broad forms—balanced and unbalanced.

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  Balanced rearrangements are those in which there is no net gain or loss of genetic
material, though some rearrangement has occurred—this includes reciprocal
translocations and inversions.
 Unbalanced rearrangements are those in which genetic material is either gained or
lost. Unbalanced rearrangements are caused by deletions or duplications, or the
inheritance of unbalanced translocation products. Both types of rearrangement have
been shown to have impacts on gene expression through a variety of different
mechanisms and usually result in sever abnormal cytogenetic syndromes.

Basic features of immunoglobulins and gene structure arrangement

 Antibodies (immunoglobulins); secreted by B-cells of immune system (B-lymphocytes) in
response to a foreign antigens and are responsible for a type of immunity that is called
humoral immunity (antibody-mediated immunity.).
 B cells of the immune system perform genetic recombination, called immunoglobulin class
switching.
 Immunoglobulin class switching is a biological mechanism that changes an antibody from
one class to another, for example, from an isotype called IgM to an isotype called IgG.

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 Basic features of immunoglobulins
 Immunoglobulins (antibodies) are large, Y-shaped proteins produced mainly by plasma
cells that is used by the immune system to neutralize pathogens such as pathogenic
bacteria and viruses.
 The antibody recognizes a unique molecule of the pathogen, called an antigen
 The immunoglobulin molecule is made up of four polypeptide chains; two identical 'heavy'
chains (H) and two identical 'light' (L) chains. Disulfide bonds between the chains link the
chains together.
 Each heavy chain has two regions, the constant region and the variable region. The constant
region is identical in all antibodies of the same isotype, but differs in antibodies of different
isotypes.
 In mammals there are two types of immunoglobulin light chain, which are called lambda (λ)
and kappa (κ). A light chain has two successive domains: one constant domain and one
variable domain.
 Antibodies have different varieties
known as isotypes or classes.
 There are five antibody isotypes
known as IgA, IgD, IgE, IgG, and IgM.
 They are each named with an "Ig"
prefix that stands for immunoglobulin
 The different suffixes of the antibody isotypes denote the different types of heavy chains
the antibody contains, with each heavy chain class named alphabetically: α (alpha), γ
(gamma), δ (delta), ε (epsilon), and μ (mu). This gives rise to IgA, IgG, IgD, IgE, and IgM,
respectively.

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 Immnuoglobulins gene structure and the role of DNA rearrangement in the
generation of immunoglobulin diversity

Immnuoglobulins gene structure

Immunoglobulin diversity
 Successful recognition and eradication of different types of microbes requires diversity
among antibodies; their amino acid composition varies to allow them to interact with
different antigens.
 It has been estimated that humans generate about 10 billion different antibodies, each
capable of binding a distinct epitope of an antigen.
 Several complex genetic mechanisms have evolved that allow vertebrate B cells to generate
a diverse pool of antibodies from a relatively small number of antibody genes (see the
above figure).

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 Immunoglobulin diversity results from:
1. Domain variability
 e.g. the variable domain, which is present in each heavy and light chain of every antibody
differs in different antibodies generated from distinct B cells.
 Also, antibodies contains area of different hypervariable areas which differ greatly between
different antibodies
2. V (D)J recombination
 Somatic recombination of immunoglobulins, also known as V(D)J recombination, involves
the generation of a unique immunoglobulin variable region.
 The variable region of each immunoglobulin heavy or light chain is encoded in several
pieces—known as gene segments (subgenes).
 These segments are called variable (V), diversity (D) and joining (J) segments. V, D and J
segments are found in Ig heavy chains, but only V and J segments are found in Ig light
chains.

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 Multiple copies of the V, D and J gene segments exist, and are tandemly arranged in
the genomes of mammals. In the bone marrow, each developing B cell will assemble an
immunoglobulin variable region by randomly selecting and combining one V, one D and one
J gene segment (or one V and one J segment in the light chain). As there are multiple copies
of each type of gene segment, and different combinations of gene segments can be used to
generate each immunoglobulin variable region, this process generates a huge number of
antibodies, each with different paratopes, and thus different antigen specificities.
3. Somatic hypermutation and affinity maturation
 Following activation with antigen, B cells begin to proliferate rapidly. In these rapidly
dividing cells, the genes encoding the variable domains of the heavy and light chains
undergo a high rate of point mutation, by a process called somatic hypermutation (SHM).
SHM results in approximately one nucleotide change per variable gene, per cell division. As
a consequence, any daughter B cells will acquire slight amino acid differences in the variable
domains of their antibody chains.
4. Class switching
 Isotype or class switching is a biological process occurring after activation of the B cell,
which allows the cell to produce different classes of antibody (IgA, IgE, or IgG).
 Initially, naive B cells express only cell-surface IgM and IgD with identical antigen binding
regions. Each isotype is adapted for a distinct function; therefore, after activation, an
antibody with an IgG, IgA, or IgE effector function might be required to effectively eliminate
an antigen.
 Class switching allows different daughter cells from the same activated B cell to produce
antibodies of different isotypes. Only the constant region of the antibody heavy chain
changes during class switching; the variable regions, and therefore antigen specificity,
remain unchanged.
 Class switching occurs in the heavy chain gene locus by a mechanism called class switch
recombination (CSR). This mechanism relies on conserved nucleotide motifs, called switch

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 (S) regions, found in DNA upstream of each constant region gene (except in the δ-chain).
The DNA strand is broken by the activity of a series of enzymes at two selected S-regions.
 The variable domain exon is rejoined through a process called non-homologous end
joining (NHEJ) to the desired constant region (γ, α or ε). This process results in an
immunoglobulin gene that encodes an antibody of a different isotype.

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