This document provides an overview of transposable elements (TEs). It discusses that TEs are DNA sequences that can move within genomes. There are two major classes of TEs - retrotransposons which move via an RNA intermediate, and DNA transposons which move directly through a cut-and-paste or copy-and-paste mechanism. The document outlines different types of TEs found in bacteria, eukaryotes, and the human genome. It also discusses the impact of TEs in causing mutations and their applications in genetic engineering and mutagenesis experiments.

2. Overview
 Introduction
 History
 Nomenclature
 General characteristics
 Mechanism of transposition
 Bacterial transposons
 Eukaryotic transposons
 Applications
 Conclusion

3. Introduction
 Transposable or mobile genetic elements/Jumping
genes/ Molecular parasite
 “Piece of DNA that can move from one location to
another in a cell's genome”
 Recombination b/w transposon and another DNA –
target site
 Bacteria – target site within chromosome or from
plasmid to chromosome or b/w plasmid (vice versa)
 Jump from one location to another (cut-and-paste
translocation)

4.  Identified in eukaryotes, prokaryotes etc.
 More abundant in eukaryotic genomes than prokaryotes
 High proportion of species genome
10% of several fish species
12 % of the Caenorhabditis. elegans genome
37% of the mouse genome
45% human genome
up to >80% - some plants like maize

5. History
 1940s-cytogenic studies in maize
kernels
 1960s - James Shapiro and
others found transposable
elements (TE) in bacteria and
other species
 1st TE found in bacteria is called
insertion sequences (IS)
 Recombinant technology – TE in
all organisms
Barbara McClintock (1983)- Nobel
Prize in Physiology or Medicine

6. Nomenclature
 Campbell et al., 1977 – nomenclature in prokaryotes
 Named as insertion sequences – IS1, IS2, IS3 etc.
 Antibiotic resistance genes named as Tn (Tn1-ampr,
Tn2, Tn3 etc).
 Eukaryotes – nonstandard way
Drosophila- copia, p-elements
Yeast- Ty,
maize- Ac&Ds,
Human- Alu

7. General characteristics of TE
 DNA sequences – code for enzymes – insertion of
identical copy – new DNA site
 Recombination and replication process – lead to two
daughter copies (Parent site and target site)
 TE cannot replicate apart from the host chromosome
 Most have inverted repeats (IR) – EM
 Transposition-not require extensive areas of homology
b/w the transposon & target site

8.  Transposons – IIIr lysogenic prophages – except –
originate in one chromosomal location – move -
different location in the same chromosome
 TEs differ from phages (lack virus life cycle) &
plasmids (unable to reproduce autonomously and exist
apart from the chromosome)
 Multiple copies - antibiotic resistance - single R plasmid
by moving genes - different plasmids

9. • Movement of TE from
one location to another
Mechanism of transposition

10. Class I: retrotransposons
Retrotransposition:
The element makes an
RNA copy of itself which
is reversed-transcribed
into a DNA
copy which is then
inserted
IIIr to viral retroelement
except RNA from
exogenous
Eukaryotic genomes

11. Class II: DNA Transposons
 No RNA intermediate
 Move directly from one position to another within
the genome using a transposase to "cut and paste"
them within the genome

12. Conservative transposition:
The element itself moves from the
donor site into the target site
"cut and paste"
Replicative transposition:
The element moves a copy of itself
to a new site via a DNA intermediate
"copy and paste"

14. Class III: Miniature-inverted-repeats-transposable
elements ( MITEs)
 Too small to code for any protein
 Transposition- unknown
 Human, plants and animals

15. Bacteria
 Vary in structure
1. Insertion sequences
2. Composite transposons
3. Tn3-type transposon
4. Transposable phage Mu

16. Insertion sequence (IS)
 Simplest TE
 750 -1600 bp (0.3 kb)
1. Transposase genes – enzymes required for transposition
2. Both ends – identical or very similar sequences of nt in
reversed orientation – inverted repeats (9 to 41 bp – vary)
 Replicatively or conservatively
 IS-cause mutations - within the coding sequence of a gene
or within a DNA region that regulates gene expression
 Single E.coli may contain 20 types-IS1, IS2, IS3 etc.

17. • Transposase – staggered cuts in DNA – IIIr to
restriction enzymes
• ITRs – recognition sites for binding to
enzymes

18. Composite transposons
 1st characterized in E.coli
 contains genes other than those required for transposition
– IS with ARG (2.5-10kb)
 Often reside on plasmids and conservative
 may help bacteria adapt to new environments

20. Tn 5 & Tn903
kanamycin
Some prokaryotic
transposons

21. schematic map of a plasmid carrying many resistance genes

22. Transposition reaction from plasmid entry into the recipient cell to integration of the
transposon into the genome

23. Non composite transposons
 Lack flanking insertion sequences (IS)
 Inverted repeats + Transposase gene + antibiotic
resistance gene (s) + Resolvase (site specific
recombination)
 Tn3 & Tn7 (5kb)

25. Bacteriophage Mu
• Bacterial viruses transpose replicatively as part
of their normal infection cycle
• DNA-based transposition
• Temperate (lysogenic) bacteriophage
• Longest transposon so far
• Carries genes for viral head & tail formation
• Giant mutator transposon - 100 target sites

26. Simplified cartoon of the Mu genetic map

27. Life cycle of phage mu
(A) Mu infects a sensitive host, -
linear DNA enters the cell –
inserted "cut and paste"
mechanism
(B) Lysogens of wild-type Mu –
stable - not induced by UV or
DNA damaging agents.
but temperature sensitive
repressor - Mu c(Ts) - induced -
42°C
(C) Repressor – inactivated - A &
B proteins are expressed and
Mu transposes – Replicative 50
- 100 new sites on the
chromosome.
Late phage gene products - phage
heads, tails, lysis proteins, etc

28. Human genome
• LINEs- long interspersed
nuclear elements
• SINEs-short interspersed
nuclear elements
• Approx. 350, 000 DNA
transposons – all with
transposase and inverted
repeats – majority
inactive

29. Plants
 Active transposons
Eg. Ac/Ds transposon – 1st
McClintock
Spm element – maize
 Work as family
Ac have transposase
not Ds
Variegated pigmentation in maize kernals caused
by transposition in somatic cells

30. Effects
 Gene inactivation
 Mutation
 Gene alterations (Insertions, excisions, Duplication or
translocation)
 Moderate gene expression or induce recombination
 Mutations results in diseases
Hemophilia A & B,
X-linked severe combined immunodeficiency
Porphyria, cancer etc.,

31. Applications
 Induce mutations (Insertional mutagenesis)
 TE – insert - specific site - genome of an organism give
it a high potential to be used for genetic modification
 Gene therapy (Non-viral alternative)
 Act – probe for cloning genes that are mutated by
insertion of a particular element. Initially genetic
screening is used to identify the mutation caused by
transposon
 Genes are isolated from given species due to transposon
tagging (preferred choice if one specific gene is desired)

32.  DNA transposons, PiggyBac, Tol2 and Sleeping Beauty
have been evaluated for gene therapy in animal
experiments, primary cell gene delivery and a few pre-clinical
trials
 Several DNA transposons, such as P element,
PiggyBac, Tol2, Hsmar1 and Sleeping Beauty, have
been utilized for mutagenesis in invertebrate and
vertebrate cells

33. Characteristics of DNA Tranposons used
in Genomics
Cargo capacity
Transposition efficiency
Gene Silencing and Stability of Gene Insertion
Insertion Site Targeting

36. • All the organisms – present – huge fraction of
total DNA sequences
• Major cause of mutations and genome
rearrangement
• Used in genetic studies
• Mutation – used to produce different colors of
grapes, corn and other fruits

37. Thank you