Transposable elements, also known as jumping genes, are DNA sequences that can move within genomes. They are found in both prokaryotes and eukaryotes and make up over 50% of some genomes. There are three main types: DNA transposons which move DNA directly; retrotransposons which move via an RNA intermediate; and poly-A retrotransposons which encode reverse transcriptase. Transposition occurs through excision of the element from one site and insertion into another, sometimes disrupting genes and causing mutations. While causing mutations, transposons also contribute to genetic diversity.

1. TRANSPOSONS

2. CONTENTS:
- Introduction
- Transposable elements in prokaryotes and eukaryotes
- Types of transposable elements
- Mechanisms of various types of transposable elements
- Examples of transposable elements

3. What are Transposons?
- Mobile genetic elements that moves from one DNA site
to another
- Normal ubiquitous components of the genomes
- Found in both prokaryotes and eukaryotes
- Also known as “jumping genes”
- Movement occurs through recombination between the
DNA sequences at the very ends of the transposable
element and a sequence in the DNA of the host cell

4. Fig: Transposition of a mobile genetic element to a new site in the host DNA.
Recombination, in some cases, involves excision of the transposon from the old
DNA location (left).In other cases, one copy of the transposon stays at the old
location, and another copy is inserted into the new DNA site (right).

5. - When transposable elements move, they often show little sequence
selectivity in their choice of insertion sites. As a result, transposons can
insert within genes, often completely disrupting gene function.
- Causes mutation leading to various genetic diseases
- Transposable elements are also useful in some cases
- More than 50% of human and maize genomes are composed of
transposons-related sequences
- That is why transposons are the most common source of new mutation
in many organisms
- Compared to human and maize,the fly and yeast have very less
amount of transposable elements,suggesting that transposon content
in different genomes is highly variable

6. GREEN: Transposable elements(repeated elements)
PURPLE: Cellular genes

7. Transposable elements in Prokaryotes:
- TEs can move to new positions on the same chromosome(because only one
chromosome)
- Move onto plasmids or phage chromosomes
- Examples are: 1)Insertion sequence (IS)
2)Transposons (Tn)
1) IS elements are the simplest transposable elements found in prokaryotes
- Contains only genes required to mobilize the elements and insert it into a
chromosome at a new location. Consist of fewer than 2500 nucleotide
pairs and contain only genes whose products are involved in promoting or
regulating transposition
- Identified first in E.coli as a result of their effect on the expression of three
genes that control the metabolism of sugar galactose
- Not similar with point mutation or deletion but rather insertion of an approx.
800bp DNA segment into a gene. This particular DNA segment is called IS1

8. Fig:Structure of an inserted IS50
element showing its terminal
inverted repeats and target site
duplication. The terminal
inverted repeats are imperfect
because the fourth nucleotide pair
(highlighted) from each
end is different.
Fig:Production of target site duplications
by the insertion of an IS element

9. 2) Transposons:
- Tn contains gene for the insertion of the DNA segment into the chromosome
and mobilization of the element to other location on the chromosome
- Two types of prokaryotic transposons-
a) Composite transposons
b) Non composite transposons
a) Composite transposons are complex
transposons with a central region containing
genes(e.g- genes that confer resistance
to antibiotics),flanked on both sides by IS
elements (also called IS modules)
e.g- Tn10

10. b) Non composite transposons also have a central region containing genes
but do not terminate with IS elements. Transposition occurs by encoding
enzymes by genes present in the central region
e.g- Tn3

11. Transposable elements in Eukaryotes:
- In 1940s Barbara McClintock did a series of genetic experiments with
corn that led her to hypothesize the existence of what she called the
“controlling genes” which modify or supress gene activity and are
mobile in the genome
- TE have been studied mostly in yeast, Drosophila, corn and human
- Functional eukaryotic TE have genes that encodes enzymes required
for transposition and they integrate into chromosomes at a number of
sites
- Chromosome mutation such as duplication, deletion, inversions,
translocation or breakage occurs

12. Barbara McClintock and Robin Holliday, 1984 Symposium on Recombination at the
DNA Level: McClintock proposed the existence of transposons to account forthe results of
her genetic studies with maize, carried out in the 1940s the Nobel Prize in Physiology or
Medicine in recognition of this work came more than 30 years later, in 1983. Holliday
proposed the fundamental model of homologous recombination that bears his name.
Discovery of Transposons

13. Classification of Transposable Elements
Transposons can be divided into the following three families on the basis of their
overall organization and mechanism of transposition:
1)DNA transposons: Encodes protiens that moves the DNA element directly to a
new position or replicate the DNA to produce a new element that integrates
elsewhere in the genome (both prokaryotes and eukaryotes)
2)Virus-like retrotransposons: This class includes the retroviruses. These
elements are also called long terminal repeat(LTR) retrotransposons.Encodes a
reverse transcriptase for making DNA copies of their RNA transcripts which
subsequently integrates at new sites in the genome (only prokaryotes)
3)Poly-A retrotransposons: These elements are also called non-viral
retrotransposons. The element terminates in the 5’ and 3’ untranslated region
(UTR) sequences and encodes two enzymes: an RNA-binding enzyme (ORF1)
and an enzyme having both reverse transcriptase and endonuclease activities
(ORF2).

14. (a) DNA transposons: The element includes the terminal inverted-repeat sequences (green with white
arrows), which are the recombination sites, and a gene encoding transposase.
(b) Virus-like retrotransposons and retroviruses: The element includes two LTR sequences that flank a
region encoding two enzymes: integrase and reverse transcriptase (RT).
(c) Poly-A retrotransposons: The element terminates in the 5’ and 3’ untranslated region (UTR)
sequences and encodes two enzymes: an RNA-binding enzyme (ORF1) and an enzyme having both
reverse transcriptase and endonuclease activities (ORF2).

15. 1)DNA Transposons:
- DNA transposons carry both DNA sequences that function as recombination
sites and genes encoding proteins that participate in recombination
- The recombination sites are at the two ends of the element and
are organized as inverted-repeat sequences
- These terminal inverted repeats vary in length from 25 bp to a few hundred
base pairs
- DNA transposons may carry a few additional genes, sometimes encoding
proteins that regulate transposition or provide a function useful to the element
or its host cell
- For example, many bacterial DNA transposons carry genes encoding proteins
that promote resistance to one or more antibiotic(s). The presence of the
transposon therefore causes the host cell to be resistant to that antibiotic

16. DNA Transposition by a Cut-and-Paste Mechanism:
- This recombination pathway involves the excision of the transposon from its
initial location in the host DNA, followed by integration of this excised
transposon into a new DNA site
Initiation
- To initiate recombination, the transposase binds to the terminal inverted repeats
at the end of the transposon
- Once the transposase recognizes these sequences, it brings the two ends of
the transposon DNA together to generate a stable protein–DNA complex. This
complex is called the synaptic complex or transpososome
- This complex functions to ensure that the DNA cleavage and joining reactions
needed to move the transposon occur simultaneously on the two ends of the
element’s DNA
- It also protects the DNA ends from cellular enzymes during recombination

17. Excision
- The next step is the excision of the transposon DNA from its original location
in the genome where the transposase subunits within the transpososome first
cleave one DNA strand at each end of the transposon, exactly at the junction
between the transposon DNA and the host sequence in which it is inserted
- The transposase cleaves the DNA such that the transposon sequence terminates
with free 3′-OH groups at each end of the element’s DNA
- To finish the excision reaction,the other DNA strand at each end of the element
must also be cleaved
- After excision of the transposon, the 3′-OH ends of the transposon DNA, attack
the DNA phosphodiester bonds at the site of the new insertion
- As a result of this attack, the transposon DNA is covalently joined to the DNA at
the target site

18. Figure:The cut-and-paste
mechanism of
transposition.Movement of a
transposon from a target site in
the (gray) host DNA to a new
site in the (blue) DNA

19. 2)Virus like retrotransposons and retroviruses:
- Like DNA transposition, Virus-like retrotransposons and retroviruses also carry
inverted terminal repeat sequences that are the sites of recombinase binding
and action
- The terminal inverted repeats are embedded within longer repeated sequences;
these sequences are organized on the two ends of the element as direct
repeats and are called long terminal repeats (LTRs)
- Virus-like retrotransposons encode two proteins needed for their mobility:
integrase (the transposase) and reverse transcriptase
- Reverse transcriptase(RT) is a special type of DNA polymerase that can use an
RNA template to synthesize DNA. This enzyme is needed for transposition
because an RNA intermediate is required for the transposition reaction.
Because these elements convert RNA into DNA, the reverse of the normal
pathway of biological information flow (DNA to RNA), they are known as “retro”
elements

20. - The distinction between virus-like retrotransposons and retroviruses is that the
genome of a retrovirus is packaged into a viral particle, escapes its host cell,
and infects a new cell. In contrast, the retrotransposons can move only to new
DNA sites within a cell but can never leave that cell
Mechanism of Virus-like retrotransposition and retroviruses:
- Virus-like retrotransposons and retroviruses insert into new sites in the
genome of the host cell, using the same steps of DNA cleavage and DNA
strand transfer(like DNA transposition)
- A cycle of transposition starts with transcription of the retrotransposon (or
retroviral) DNA sequence into RNA by a cellular RNA polymerase
- Transcription initiates at a promoter sequence within one of the LTRs and
continues across the element to generate a nearly full-length RNA copy of the
element’s DNA
- The RNA is then reverse-transcribed to generate a double-stranded DNA
molecule. This DNA molecule is called the cDNA

21. - The cDNA that is recognized by the integrase protein for recombination with a
new target DNA site
- Integrase assembles on the ends of this cDNA and then cleaves a few
nucleotides off the 3′ end of each strand
- Integrase then catalyzes the insertion of these cleaved 3′ ends into a DNA
target site in the host-cell genome using the DNA strand transfer reaction

22. Figure:Mechanism of
retroviral integration and
transposition of virus-like
retrotransposons

23. 3)Poly-A Retrotransposons:
- The poly-A retrotransposons do not have the terminal inverted repeats present
in the other transposon classes. Instead, the two ends of the element have
distinct sequences
- One end is called the 5′-UTR, whereas the other end has a region called the 3′-
UTR followed by a stretch of A:T base pairs called the poly-A sequence
- Retrotransposons carry two genes, known as ORF1 and ORF2. ORF1 encodes
an RNA-binding protein. ORF2 encodes a protein with both reverse
transcriptase activity and an endonuclease activity

24. Poly-A Retrotransposons Move by a “Reverse Splicing” Mechanism:
- The poly-A retrotransposons move using an RNA intermediate using a
mechanism called target-site-primed reverse transcription
- The first step is transcription of the DNA of an integrated element by a cellular
RNA polymerase
- Although the promoter is embedded in the 5′-UTR, it can in this case direct
RNA synthesis to begin at the first nucleotide of the element’s sequence
- This newly synthesized RNA is exported to the cytoplasm and translated to
generate the ORF1 and ORF2 proteins. These proteins remain associated with
the RNA that encoded them
- The protein–RNA complex then re-enters the nucleus and associates with the
cellular DNA
- Since the ORF2 protein has both a DNA endonuclease activity and a reverse
transcriptase activity, the endonuclease initiates the integration reaction by
introducing a nick in the chromosomal DNA

25. - T-rich sequences are preferred cleavage sites. The presence of these Ts at the
cleavage site permits the DNA to basepair with the poly-A tail sequence of the
element RNA
- The 3′-OH DNA end generated by the nicking reaction then serves as the primer
for reverse transcription of the element RNA. The ORF2 protein also catalyzes
this DNA synthesis
- The remaining steps of transposition, although not yet well-understood, include
synthesis of the second cDNA strand, repair of DNA gaps at the insertion site,
and ligation to seal the DNA strands

26. Figure: Transposition of a
poly-A retrotransposon by
target-site primed reverse
transcription

27. Examples of Transposable elements in Prokarotes and Eukaryotes:
1)IS element in E.coli:
- IS elements- IS1, IS2 and IS10R
- Each of IS elements are present upto 30 copies in the genome
- Each having characteristic length and unique nucleotide sequence
- IS1 is 768bp long present in 4 to 19 copies on E.coli chromosome
- IS element size may vary from 768 bp to more than 5000bp
- IS elements end with inverted repeats (IRs) of 9 to 41bp i.e. same sequence
is found at each end , but in opposite orientations
- When they integrate at random points along the chromosome, they often
cause mutation by disrupting either the coding sequence of a gene or a
gene’s regulatory region

28. 2) Ty elements in yeast:
- Ty element is about 5.9 kb long and includes two directly repeated terminal
sequences called long terminal repeats (LTR) or deltas (δ)
- Each delta contains a promoter and sequences recognized by transposing
enzymes
- The Ty elements encodes a single, 5700 bp nucleotide mRNA that begins at
the promoter in the delta at the 5′ end of the element
- The mRNA transcript contains two open reading frames, designated by TyA
and TyB, that encodes two different proteins required for transposition

29. 3) Human Retrotransposons:
- Repetative classes of DNA sequence- LINE(long interspersed sequences) and
SINE(short interspersed sequences)
- LINEs are repeated sequences more than 5000bp long, interspersed among
unique-sequence DNA upto approx. 35000 bp long
- SINEs are 100-400 bp repeated sequences interspersed between unique-
sequence DNA 1000-2000 bp long
- LINEs and SINEs both are retrotransposons but only LINEs encodes for
enzymes needed for transposition. SINEs depends upon the enzymes encoded
by LINEs for transposition

30. 4) HIV-1:
- HIV-1 — the cause of AIDS — and other human retroviruses (e.g., HTLV-1, the
human T-cell leukemia/lymphoma virus) behave like retrotransposons.
- The RNA genome of HIV-1 contains a gene for reverse transcriptase and one
for integrase.
- The integrase serves the same function as the transposases of DNA
transposons. The DNA copies can be inserted anywhere in the
genome.Molecules of both enzymes are incorporated in the virus particle.