Transposable elements are segments of DNA that can change their position within the genome. They are divided into two classes based on their mechanism of movement. Class 1 elements encode reverse transcriptase and form DNA copies from RNA transcripts. Class 2 elements encode proteins that directly move the DNA. Transposable elements in prokaryotes include insertion sequences (IS elements) and transposons, while eukaryotes also contain retrotransposons similar to retroviruses. Transposition can disrupt genes or regulatory sequences and cause mutations. McClintock's work with maize introduced the concept of mobile genetic elements controlling gene expression.

1. Transposable Elements

3. General Features of Transposable Elements
1. Transposable elements are divided into two classes on the basis of their
mechanism for movement:
a. Some encode proteins that move the DNA directly to a new position or
replicate the DNA to produce a new element that integrates elsewhere.
This type is found in both prokaryotes and eukaryotes.
b. Others are related to retroviruses, and encode reverse transcriptase
for making DNA copies of their RNA transcripts, which then integrate at
new sites. This type is found only in eukaryotes.
2. Transposition is non- homologous recombination

4. Transposable Elements in Prokaryotes
3. Transposable elements can cause genetic changes by :
a. Inserting into genes.
b. Increase or decrease gene expression by insertion into
regulatory sequences.
c. Produce chromosomal mutations through the
mechanics of transposition.
Prokaryotic examples include:
a. Insertion sequence (IS) elements.
b. Transposons (Tn).
c. Bacteriophage Mu (replicated by transposition)

5. Insertion Sequences
1. IS elements are the simplest transposable elements found in prokaryotes
2. Encode only genes for mobilization and insertion of its DNA.
3. IS elements are commonly found in bacterial chromosomes and plasmids.
4. Prokaryotic IS elements range in size from 768 bp to over 5 kb.
5. The ends of all sequenced IS elements show inverted terminal repeats
(IRs) of 9–41 bp.

6. The insertion sequence (IS) transposable element, IS1

7. 6. Integration of IS elements may:
a. Disrupt coding sequences or regulatory regions.
b. Alter expression of nearby genes by the action of IS element
promoters.
c. Cause deletions and inversions in adjacent DNA.
7. When an IS element transposes:
a. The original copy stays in place, and a new copy inserts randomly into
the chromosome.
b. The IS element uses the host cell replication enzymes for precise
replication.
c. Transposition requires transposase, an enzyme encoded by the IS
element.
d. Transposase recognizes the IR sequences to initiate transposition.

8. Schematic of the integration of an IS element into chromosomal DNA

9. Transposons
1. Transposons are similar to IS elements, but carry additional genes, and
have a more complex structure. There are two types of prokaryotic
transposons:
a. Composite transposons carry genes (e.g., antibiotic resistance)
flanked on both sides by IS elements (IS modules).
i. The IS elements are of the same type, and called ISL (left) and
ISR (right).

10. Structure of the composite transposon Tn10
ii. Tn10 is an example of a composite transposon . It is 9.3 kb, and
contains:
(1) 6.5 kb of central DNA with genes that include tetracycline
resistance (a selectable marker).
(2) 1.4 kb IS elements (IS10L and IS10R) at each end, in an
inverted orientation.

11. b. Noncomposite transposons also carry genes (e.g., drug resistance)
but do not terminate with IS elements.
i. Transposition proteins are encoded in the central region.
ii. The ends are repeated sequences
iii. An example is Tn3 : 1. length is about 5 kb, with 38-bp inverted terminal
repeats 2. It has three genes in its central region:
(a) bla encodes β-lactamase, which breaks down ampiciliin.
(b) tnpA --- transposase, needed for insertion into a new site.
(c) tnpB ---- resolvase, involved in recombinational events needed for transposition
(not found in all transposons).

12. Bacteriophage Mu
1. Bacteriophage Mu (mutator) can cause mutations when it transposes. Its
structure includes:
a. A 37 kb linear DNA in the phage particle; central phage DNA and
unequal lengths of host DNA at the ends .
b. The DNA’s G segment can invert, and is found in both orientations in
viral DNA.
2. Mu integrates into the host chromosome: The Mu prophage now replicates
only when the E. coli chromosome replicates.

13. Transposable Elements in Eukaryotes
1. Rhoades (1930s) working with sweet corn, observed interactions between
two genes.
2. McClintock (1940s-50s), working with corn (Zea mays) proposed the
existence of “controlling elements” that regulate other genes and are
mobile in the genome.
a. Most studied are transposons of yeast, Drosophila, corn and humans.
b. Structure is very similar to that of prokaryotic transposable elements.

14. Transposons in Plants
1. Plant transposons also have IR sequences, and generate short direct target
site repeats.
2. Can insert into a gene and produce a mutant allele.
i. Autonomous elements, which can transpose by themselves.
Alleles produced by an autonomous element are mutable alleles,
creating mutations that revert when the transposon is excised from
the gene.
ii. Nonautonomous elements, which lack a transposition gene and
rely on the presence of another transposon to supply the missing
function.
Mutation by these elements is stable.

15. McClintock ---- “mobile controlling element” in wheat kernel
(1) The element is Ds (dissociation).
(2) Its transposition is controlled by Ac (activator) .

16. Ty Elements in Yeast
Ty elements share characteristics with bacterial transposons :
a. Terminal repeated sequences.
b. Integration at non-homologous sites.
Ty element is -----
a. 5.9 kb including 2 terminal direct repeats of 334 bp, the long terminal
repeats (LTR) or deltas (δ).
b. Each delta contains a promoter and transposase recognition sequences.

17. Drosophila transposons
It is estimated that 15% of the Drosophila genome is mobile!
a. The copia retro transposons : 5-100 widely scattered copies per
genome
i. All copia elements in Drosophila can transpose, and there are
differences in number and distribution between fly strains.
ii. Structurally, copia elements are similar to yeast Ty elements:
LTRs of 276 bp flank a 5 kb DNA segment.

18. b. P elements : cause hybrid dysgenesis, a series of defects
(mutations, chromosomal aberrations and sterility) that result from
crossing certain Drosophila strains
i. A mutant lab strain female (M) crossed with a wild-type male (P)
will result in hybrid dysgenesis.
ii. A mutant lab strain male (M) crossed with a wild-type (P)
female (reciprocal cross) will have normal offspring.
iii. Thus, hybrid dysgenesis results when chromosomes of the P male
parent enter cytoplasm of an M type oocyte, but cytoplasm from P
oocytes does not induce hybrid dysgenesis.

19. The model is based on the observation that the M strain has no P
elements, while the haploid genome of the P male has about 40 copies.
(1) The F1 of an M female crossed with a P male have P
elements inserted at new sites .
(2) P elements encode a repressor protein that prevents
transposase gene expression, preventing transposition.
(3) Cytoplasm in an M oocyte lacks the repressor, and so
when fertilized with P-bearing chromosomes, transposition
occurs into the maternal chromosomes, leading to hybrid
dysgenesis

20. Structure of the autonomous P transposable element found in Drosophila
melanogaster

21. SINEs (Short interspersed elements)
 human SINE repeat (short interspersed sequence) or the AluI restriction site in its
sequence.
 short (about 100-400 bp)
 A single family of SINEs (ALU)
 This family is the only active SINE in the human genome

22. SINEs (Short interspersed
elements)
 A human case of a genetic disease, neurofibromatosis,
provides some evidence.
i. Neurofibromatosis (tumor like growths on the
body) result from an autosomal dominant mutation.
ii. In a patient’s DNA, an unusual sequence was
detected in one of the introns of the neurofibromatosis
gene.
iii. Longer transcript is incorrectly processed, removing
an exon from the mRNA and producing a
nonfunctional protein.
iv. Neither parent had this sequence in the
neurofibromatosis gene.

23. LINEs (Long interspersed elements)
(Li elements)
 LINEs are one of the most ancient and successful inventions in
eukaryotic genomes
 In humans, are about 6 kb long
 encode two open reading frames (ORFs)
 Most LINE-derived repeats are short, with an average size of 900 bp
- 1,070 bp
 cases of hemophilia have been shown to result from newly transposed
Li insertions into the factor VIII gene. (Factor VIII is required for normal
blood clotting.)

24. Pseudogene
“false” genes , which look like real genes but have no apparent
function
Pseudogene is a DNA sequence that is nearly identical to that of
a functional gene, but contains one or more mutations, making
it non-functional
Much of the intron material in the genomes of organisms is
composed of recognizable pseudogenes.
 Pseudogenes are the molecular remains of broken genes which
are unable to function because of lethal injury to their
structures.
 The great majority of pseudogenes are damaged copies of
working genes and serve as genetic fossils that offer insight
into gene evolution and genome dynamics.

25. There are three main types of pseudogenes :
1. Processed Pseudogenes: Lack introns, have small flanking direct repeats
and a 3’ polyadenine tail
portion of the mRNA transcript of a gene is spontaneously reverse transcribed
back into DNA and inserted into chromosomal DNA.
Once these pseudogenes are inserted back into the genome, they usually
contain a poly –A tail, and usually have had their introns spliced out
2. Duplicated Pseudogenes : A copy of a functional gene may arise as a result
of a gene duplication event and subsequently acquire mutations that cause
it to become nonfunctional.
The loss of a duplicated gene's functionality usually has little effect on an
organism's fitness, since an intact functional copy still exists.
3. Disabled genes, or unitary pseudogenes :
Various mutations can stop a gene from being successfully transcribed or
translated, and a gene may become nonfunctional or deactivated if such a
mutation becomes fixed in the population.