Outline

General characteristics of transposable elements

Mechanisms of transposition

Effects & regulation of transposition

Transposable elements in bacteria

Transposable elements in eukaryotes

Lecture 3 1
 What are transposable elements?
• Transposable elements are mobile DNA sequences
found in the genomes of all organisms.
• Transposable elements often cause mutations by
inserting into another gene & disrupting its function
or by promoting DNA rearrangement.
• Different types of transposable elements:
– Simple structure with necessary sequences for
transposition
– Complex structure and functional sequences not
directly related to transposition
Lecture 3 2
 Common characteristics

• Short flanking direct repeats from 3 to 12 bp long

are present both sides of most transposable
elements
– Not a part of a transposable element
– Generated in the process of transposition
– Sequences of repeats vary, but the length is
constant for each type of transposable element

Lecture 3 3
 Common characteristics

• Terminal inverted repeats

– End of transposable elements (not all)
– Length of 9-40 bp
– Two sequences are inverted & complementary
– Recognized by enzyme for transposition taking
place

Lecture 3 4
Lecture 3 5
Lecture 3 6
Lecture 3 7
Classification of transposable
elements

DNA transposons Retrotransposons

(Class I) (Class II)

Lecture 3 8
 Outline
General characteristics of transposable elements

Mechanisms of transposition

Effects & regulation of transposition

Transposable elements in bacteria

Transposable elements in eukaryotes

Lecture 3 9
 DNA transposons

Nonreplicative
Replicative transposition
transposition

A new copy inserts in a The old copy

new location while the excises from the
old one remains behind old site and inserts
at original site. at a new site.

The number of copies of

Number of copies
the transposable
stays the same.
element increases.
Lecture 3 10
 Replicative transposition
(copy-and-paste)
• First step, the two DNA molecules are joined, and the
transposable element is replicated, producing the
cointegrate structure
• Second step is known as resolution of the cointegrate.
• Number of transposable elements increases by
transposition
• Enzymes:
–Cointegration: cellular enzymes function as
replication & DNA repair
–Resolution: resolvase
Lecture 3 11
Lecture 3 12
 More detailed replicative
transposition

Lecture 3 13
Lecture 3 14
 Nonreplicative transposition (cut-
and-paste)
• The transposable element moves from one site to
another without replication of the entire transposable
element.
• It requires only that the transposable element and the
target DNA be cleaved and joined together.
– Cleavage requires transposase enzyme
– Joining likely takes place by normal replication &
repair enzymes
• Number of transposable elements will tend to increase by
DNA repair mechanism
Lecture 3 15
 Transposition through an RNA
intermediate

Lecture 3 16
Lecture 3 17
 Outline
General characteristics of transposable elements

Mechanisms of transposition

Effects & regulation of transposition

Transposable elements in bacteria

Transposable elements in eukaryotes

Lecture 3 18
 Mutagenic effects of transposition
• Transposable elements may insert into other genes &
disrupt their function
• Most mutations from transposition are detrimental
• Transposition may activate a gene or change the
phenotype of the cell in a beneficial way. Example:
color of grape varieties

Lecture 3 19
Lecture 3 20
 Mutagenic effects of transposition
• DNA rearrangement is due to:
– Transposition entails exchange of DNA sequences
& recombination
– Excision of transposable elements

Lecture 3 21
Lecture 3 22
Lecture 3 23
Lecture 3 24
 Mutagenic effects of transposition
• Transposable elements insert randomly into DNA
sequences is a powerful tool for inducing mutations
throughout genome
• A known sequence of transposable elements are
used as a ‘tag’. Ex: Sleeping Beauty
• Transposable elements may insert into a gene that
protects against cancer and destroys the gene. By
looking for the location of the Sleeping Beauty, a
number of genes that protect against cancer
identified
Lecture 3 25
 Regulation of transposition
• When first transposable element enters a cell,
transposition is frequent
• The number of copies of transposable element
increases, the frequency of transposition decreases
until reaching a steady-state number
• Limiting the production of transposase enzyme
– Regulation of gene expression at transcription or
translation (more frequently)

Lecture 3 26
 Outline
General characteristics of transposable elements

Mechanisms of transposition

Effects & regulation of transposition

Transposable elements in bacteria

Transposable elements in eukaryotes

Lecture 3 27
 Insertion sequence (IS)
• IS carries only necessary sequence for its movement
• ISs are typically from 800 to 2000 bp in length and &
possess two features: terminal inverted repeats and
the generation of flanking direct repeats at the site
of insertion
• Contain one or two genes that encode transposase

Lecture 3 28
Lecture 3 29
Lecture 3 30
 Composite transposons
• DNA becomes flanked by 2 copies of an insertion
sequence & may itself transpose
• The insertion sequences are responsible for
transposition
• Terminal inverted repeats & flanking direct repeats
at the sites of insertion
• Additional genetic information in between the
insertion sequences

Lecture 3 31
Lecture 3 32
Lecture 3 33
 Noncomposite transposons
• Lack of insertion sequences
• Carrying genes for transposase & other enzymes
• Flanking direct repeats at the sites of insertion

Lecture 3 34
 Outline
General characteristics of transposable elements

Mechanisms of transposition

Effects & regulation of transposition

Transposable elements in bacteria

Transposable elements in eukaryotes

Lecture 3 35
 Type of transposable elements
Eukaryotic transposable elements can be divided into
two groups:
• One group is structurally similar to transposable
elements found in bacteria: ending in short inverted
repeats & transposing as DNA
• Retrotransposons:
– Use RNA intermediates
– Structure and movement are similar to retroviruses.

Lecture 3 36
Ty elements in yeast (retrotransposon)
• End of a Ty element is direct repeats called delta
sequences
• Delta sequences contain:
– Several genes related to gag & pol genes
• gag (coding for structural proteins of the viral particle)
• pol (coding for a reverse transcriptase/integrase
protein)
– Promoters required for the transcription of Ty
genes, and may also stimulate the transcription of
genes that lie downstream of the Ty element.
Lecture 3 37
Lecture 3 38
 Ac and Ds elements in maize
(DNA transposon)

• DNA transposons: terminal inverted repeats +

flanking direct repeats
• Ac (Activator Factor) contains a single gene encoding
a transposase enzyme
• Ds (Dissociation Factor) elements are Ac with one or
more deletions inactivating the transposase gene
• Ds can transpose in the presence of Ac

Lecture 3 39
Ac and Ds elements

Lecture 3 40
Ac and Ds elements

Lecture 3 41
Ac and Ds elements in corn

Lecture 3 42
Ac and Ds elements in corn

Lecture 3 43
 Ac and Ds elements in corn

Lecture 3
44
 Ac and Ds elements in corn

Lecture 3
45
Transposable elements in Drosophila

• P elements as DNA transposons: terminal inverted

repeats + flanking direct repeats

• P element encodes both a transposase enzyme & a

repressor of transposition

• Repressor controlling transposition is demonstrated

by hybrid dysgenesis

Lecture 3 46
 No hybrid dysgenesis

Lecture 3
47
 Hybrid dysgenesis

Lecture 3
48
 Transposable elements in humans
• The human genome is populated by a diverse array of
transposable elements that collectively account for
44% of all human DNA
• The L1 element is a retroposon belonging to a class of
sequences known as the long interspersed nuclear
elements (LINEs)
• The human genome contains 3000-5000 complete L1
elements and more than 500,000 truncated L1
elements.

Lecture 3 50
 Transposable elements in humans
• SINEs retroposons are the second most abundant
class of transposable elements in the human genome.
SINE families are the Alu, MIR, and Ther2/MIR3
elements
• SINEs (Alu) are usually less than 400 base pairs long
and do not encode proteins
• The reverse transcriptase required for SINE
transposition is provided by a LINE-type element

Lecture 3 51
 The evolutionary status of
transposable elements
• Do transposable elements perform any useful
function, or are they merely genetic parasites?

• Where did transposable elements come from?

• What mechanisms have evolved to control and limit

their movement?