203.341!

Transposons and Genetic

Conflict!
Lectures 23 and 24!
!

Prak and Kazazian, 2000. Nature Reviews

Genetics 1:134-!
Cordaux & Batzer, 2009 Nature Reviews Genetics
10:691!

Austen Ganley, October 12th, 2015

Barbara McClintock
Barbara McClintock is famous for
discovering transposons in maize!
However, she was a brilliant
cytogeneticist, who made many
other important discoveries!

Controlling elements/transposons
McClintocks discovery of transposons showed that the
genome was not static, but dynamic!
She thought these jumping genes controlled the expression
of many genes in the genome, and called them controlling
elements!
This was the first suggestion that suites of genes can be
regulated to control processes such as development!

www.bbc.co.uk/scotland/education/bitesize/higher/
biology/control_regulation/
genetic_control1_rev.shtml

She was also probably the

first one to understand the
idea of epigenetics (she
called this phase changes)!
Many of her ideas were
ignored, but with the advent
of molecular biology, people
recognised their importance
and she won the Nobel
Prize in 1983!

Ac/Ds elements in maize

The break is
caused by a
transposon
at that site!
Requires an
element
called Ac
(activator)!
Sometimes,
yellow corn
with purple
spots were
found!
Led to
evidence for
a jumping
gene!

 The original line

was produced
by the Ds
element jumping
(transposing)
into the C
gene!

Ds/Ac mechanism

Weaver, Molecular Biology, 2008

The gene can continue

transposing with the help of
the Ac element, thus some
patches of tissue will have
the purple colour reappear!
McClintock showed that the
Ac element itself can
transpose, too!

Feschotte et al., 2002. Nature Reviews Genetics 3: 329-

Transposons are found throughout life

Transposons are found
throughout life!
In bacteria, often called
IS (insertion sequences)!
Many are related to viruses:
move between genomes, using
viruses as a vector!
Many different kinds of
transposons; divided into families,
with each family thought to have
a common origin!

gydb.uv.es/phylogeny.php?tree=gagpol

Transposon types

Slotkin & Martienssen, 2007. Nature

Reviews Genetics 8: 272-

Three classes of transposon class I (retrotransposons),

class II (DNA transposons and
MITEs), and helitrons!
Class I and II transposons can
both be further divided into
two types: autonomous and
non-autonomous!
Autonomous transposons
encode proteins that catalyse
their transposition!
Non-autonomous transposons
do not, and rely on proteins
from autonomous transposons
of the same family for their
transposition!

Autonomous vs Non-autonomous

Feschotte et al., 2002.

Nature Reviews Genetics 3: 329-

Usually more non-autonomous versions of transposons than

autonomous within a genome!
Only a few autonomous transposons can catalyse the
transposition of many non-autonomous transposons!

Class II transposons

www.math.princeton.edu/~jgevertz/
public_html_Pelement/
three_transposition_methods.htm

All DNA-based
transposons have small
(10-200bp) inverted
repeats at their ends.
There are two types:!
Conservative transposons
move by cutting
themselves out of the
DNA, and re-inserting at a
new site (cut-and-paste)!
Replicative transposons
move by making a copy of
themselves, and
integrating the copy into a
new site (copy-and-paste)!
Which is more mutagenic?!

Conservative transposition
You should recognise that
the Ds/Ac system in maize
must work through
conservative transposition!
In the Ds/Ac system, the Ac
transposase binds to the
inverted repeats of the
transposon, !
It cuts the transposon out
(hence sometimes resulting
in broken chromosomes)!
It then catalyses its insertion
into a new, essentially
random, integration site!

Replicative transposition
The replicative transposition
mechanism is a bit more complex!
Transposase makes cuts in the DNA
containing the transposon and the
target site, joining these together, and
then replicating the transposon DNA!
Results in the transposon remaining in
its original site, and a copy being made
to the target site!
Mechanism is related to homologous
recombination; DNA synthesis
produces two copies of the transposon
from one!

Target site duplications

When transposons move,
they integrate into a new
site by making staggered
cuts at the integration site!
Transposon then inserts,
and the single-strand gaps
are filled!
Results in duplications of
the target site!
Duplications are typically
small (3-30 bp), but are
diagnostic of transposons!
www.sbs.utexas.edu/herrin/bio344/

Class I transposons - retroposons

Retrotransposons
transpose through
an RNA intermediate!
Autonomous
retrotransposons
contain a reverse
transcriptase gene!
Retrotransposon is
transcribed, reverse
transcribed, and the
DNA copy integrates
elsewhere in the
genome!
What type of
transposon must all
class I transposons
be?!

www.sbs.utexas.edu/herrin/bio344/

Evidence for
retrotransposons
Retrotransposition is
fairly-easily demonstrated
experimentally!
An intron can be inserted
into the retrotransposon,
e.g. into a Ty element in
yeast!
When this element
transposes, the new copy
no longer has the intron!

Effects on the genome - summary

Insertion
mutation!
Target site
mutation!
Movement of
genes!
Recombination
duplicates or
deletes genes;
genomic
instability!
Deletion or
duplication of
genes between
transposons!
The cell tries to
control
transposition,
Prak & Kazazian, Nature Reviews Genetics, 2000, 1: 134-
e.g. siRNA!

Effects on the genome - summary

Retroposons in the human genome

International Human Genome Sequencing Consortium, Nature 409: 860-921 (2001)

Retrotransposons make up the vast majority of

repetitive elements in the human genome!
Also make up almost half of the human genome!

LINEs/SINEs/LTRs

Han & Boeke, 2005. BioEssays 27: 775-

Three main types of retrotransposons:!

LINEs (long interspersed nuclear elements)!
SINEs (short interspersed nuclear elements)!
LTRs (long terminal repeat retrotransposons)!

LINEs

biol.lf1.cuni.cz/ucebnice/en/repetitive_dna.htm

LINEs have a 5 UTR that acts as a promoter!

Encode two proteins: a DNA-binding protein, and a
reverse transcriptase with endonuclease activity!
Have a 3 UTR region, followed by a poly-A tail!
Create 7-20 bp target site duplications!
Both autonomous and non-autonomous LINEs exist!

LINE transposition

LINEs are
transcribed
into RNA, and
then move into
the cytoplasm
and are
processed,
and bind to the
two
transposase
proteins!
They then
move back into
Ostertag et al., 2007. Genome Biology 8:
the nucleus!
The transposase proteins catalyse the integration of the
LINE into a new target site, using a mechanism called
target-primed reverse transcription!

S16

Target-primed
reverse transcription

The endonuclease cuts the

target site, which has a short
region that can anneal to the
poly-A tail!
The LINE RNA anneals to the
single-strand DNA here, and
reverse transcriptase starts
synthesizing DNA using the
LINE RNA as the template!
A second (staggered) cut is
made in the target site, and the
newly-synthesized DNA joins
onto this!
DNA polymerase then replaces
the LINE RNA with DNA,
therefore completing insertion
of the LINE at the new site with
target site duplications!
Truncated copies occur
predominantly at the 5 end! biol.lf1.cuni.cz/ucebnice/en/repetitive_dna.htm

SINEs

Prak & Kazazian, Nature Reviews

Genetics, 2000, 1: 134-

Almost all SINEs

(apart from Alu) are
derived from tRNA
genes!
They contain a 3 UTR
region that is related
to LINEs, and also
have a poly-A tail!

They are 100-300 bp in size!

All SINEs are transcribed into RNA, and are believed to
use the LINE transposase machinery to catalyse their
transposition; therefore their transposition mechanism is
the same as that for LINEs!
They make target-site duplications!

Alus
biol.lf1.cuni.cz/ucebnice/en/repetitive_dna.htm

Most abundant SINE in the human genome is

called Alu (have an AluI restriction site)!
Derived from a small RNA called 7SL RNA;
SINE RNA forms a distinct secondary
structure, similar to 7SL RNA!

LTRs

biol.lf1.cuni.cz/ucebnice/en/repetitive_dna.htm

LTR = long terminal repeats; these have long direct repeats

(100 bp - several kb) at each end!
Contains gag and pol genes; the pol protein contains reverse
transcriptase, RNase, and integrase activities!
Related to retroviruses; difference is presence of an env
gene (allows production of the viral particle) and the prt gene!
Mechanism of transposition: recombination of the cDNA into
the genome using the LTRs!
Makes target site duplications, but very short!
No known autonomous LTRs in the human genome!

Effects on the genome - mutation

Hartwell, Genetics: From Genes to Genomes, 2008

Transposons cause mutations by inserting into

genes and regulatory sequences, etc.!
Even if the transposon is a conservative
transposon, it can leave behind target site
duplications, which are a form of mutation!

Effects on the genome - rearrangement

Recombination
between
transposons at
different sites can
cause duplications
& deletions!
This is dangerous
with transposons
on different
chromosomes;
causes genomic
instability!

Hartwell, Genetics: From Genes to Genomes, 2008

Transposition with two nearby transposons can move

intervening genes; can duplicate or delete these genes!

Effects on the genome - duplication

Exon duplication via SINE mobilization
exon 1

SINE

exon 2

intron

SINE transcript

SINE

exon 2

SINE transcription can extend past the

normal stop signal!
Reinsertion occurs elsewhere in the genome!
Reverse transcription duplicates both the
SINE and exon 2!

Effects on the genome summary I

Insertion
mutation!
Target site
mutation!
Movement of
genes!
Recombination
duplicates or
deletes genes;
genomic
instability!
Deletion or
duplication of
genes between
transposons!
The cell tries to
control
transposition,
Prak & Kazazian, Nature Reviews Genetics, 2000, 1: 134-
e.g. siRNA!

Effects on the genome summary II

In addition, the
double-strand breaks
introduced by
transposons can
cause mutations!