Download LINEs

‘mobile’ DNA: transposable elements
Transposable elements

Discrete sequences in the genome that have
the ability to translocate or copy itself
across to other parts of the genome without
any requirement for sequence homology by
using a self-encoded recombinase called
transposase
Transposable elements move from
place to place in the genome

1930s Marcus Rhoades and 1950s
Barbara McClintock – transposable
elements in corn

1983 McClintock received Nobel
Prize

Found in all organisms

Most 50 – 10,000 bp

May be present hundreds of times in
a genome
TEs can generate mutations in adjacent genes
TEs in Maize
Fig 15.19 Genes VII by B. Lewin
Common mechanism of transposition


Transposons encode transposases that
catalyse transposition events
Regulation of transposase expression
essential
Fig13.24a: Hartwell
Common mechanism of transposition
Common mechanism of transposition
2 sequential steps
Site specific cleavage of
DNA at the end of TE
Complex of transposasetranspososome
element ends
(transpososome)
brought to DNA target
where strand transfer is
carried out by covalent
joining of 3’end of TE to
target DNA
Common mechanism of transposition


transposase (blue) binds and assembles a paired end complex
(PEC) by dimerization, a process that might involve divalent
metal ions (Me2+).
PEC is then active for the cleavage reactions that remove
flanking donor DNA (thin black lines) and transfer of the
transposon ends into target DNA (black dotted line).
Trends in Microbiology 2005 Vol13(11) pp 543-549
Catalytic domain of transposase involved in a transphosphorylation
reaction that initiates DNA cleavage & strand transfer
Fig 15.14
Fig 15.10
GenesVII Lewin
Transposition can occur via
RNA intermediates
 Class I TEs –
Use a ‘copy & paste’
mechanism

DNA intermediates
Class II TEs
Use a ‘cut and paste’ mechanism
Generally short sequences
See interspersed repeats from the repetitive elements lecture
How transposons move
Classes of transposable elements
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Interspersed repeats (transposon-derived)
major types
class
size
Copy
%
number genome*
LINE L1 (Kpn family)
L2
~6.4kb
0.5x106
0.3 x 106
16.9
3.2
SINE
Alu
~0.3kb
1.1x106
10.6
LTR
e.g.HERV
~1.3kb
0.3x106
8.3
mariner
~0.25kb
1-2x104
2.8
DNA
transposon
family
* Updated from HGP publications
HMG3 by Strachan & Read pp268-272
LINEs (long interspersed elements)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
LINEs
Most ancient of eukaryotic genomes
 Autonomous transposition (reverse trancriptase)
 ~6-8kb long, located mainly in euchromatin
 Internal polymerase II promoter and 2 ORFs
 3 related LINE families in humans
– LINE-1, LINE-2, LINE-3.
LINE-1 still active (~17% of human genme)
 Believed to be responsible for retrotransposition
of SINEs and creation of processed pseudogenes
LINEs (long interspersed elements)
HMG3 by Strachan & Read pp268-272
SINEs (short interspersed elements)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
SINEs
Non-autonomous (successful freeloaders!
‘borrow’ RT from other sources such as LINEs)
 ~100-300bp long
 Internal polymerase III promoter
 No proteins
 Share 3’ ends with LINEs
 3 related SINE families in humans
– active Alu, inactive MIR and Ther2/MIR3.

100-300bp
1,500,000
13%
LINES and SINEs have preferred insertion sites

In this example,
yellow represents the
distribution of mys (a
type of LINE) over a
mouse genome where
chromosomes are
orange. There are
more mys inserted in
the sex (X)
chromosomes.
Try the link below to do an online experiment
which shows how an Alu insertion
polymorphism has been used as a tool to
reconstruct the human lineage
http://www.geneticorigins.org/geneticorigins/p
v92/intro.html
Long Terminal Repeats (LTR)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Long Terminal Repeats (LTR)
Repeats on the same orientation on both sides of element
e.g. ATATATnnnnnnnnnnnnnnATATAT
• contain sequences that serve as transcription
promoters as well as terminators.
• These sequences allow the element to code for an
mRNA molecule that is processed and polyadenylated.
• At least two genes coded within the element to supply
essential activities for retrotransposition.
• RNA contains a specific primer binding site (PBS) for
initiating reverse transcription.
• small direct repeats formed at the site of integration.
Long Terminal Repeats (LTR)
Autonomous or non-autonomous
 Autonomous LTR encode retroviral genes gag,
pol genes e.g HERV
 Non-autonomous elements lack the pol and
sometimes the gag genes e.g. MaLR

Ancestral repeats (AR)
‘transpositional fossils’
Comprise ~ 25% of the genome
~780 classes
Largely nonfunctional
Sporadic cases where AR have
acquired anew function after
insertion
MER121 is highly conserved among
mammals!!
DNA transposons
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
DNA intermediate
Class II TEs
IS elements and transposons
bounded by inverted terminal repeats (ITR)
e.g. ATGCNNNNNNNNNNNCGTA
Class II TEs
DNA intermediate
Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner)
encode only transposase sequences
eukaryotic transposons encode additional genes such
as antibiotic resistance genes
Some types of rearrangements mediated by DNA
transposons
Gene (2005)345 pp91-100
Transposons move in different
ways
Classified into 5 families on the basis of their
transposition pathways
1)
2)
3)
4)
5)
DDE-transposases
RT/En transposases
(reverse transcriptase/endonuclease)
Tyrosine (Y) transposases
Serine (S) transposases
Rolling circle (RC) or Y2 transposases
Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
Transposons can be used to transfer
DNA between bacterial cells
Transposons
(pink) integrate
into new sites on
the chromosome
or plasmids by
non-homologous
recombination.
Integrons (dark
green) use
similar
mechanisms to
exchange single
gene cassettes
(brown).
Nature Reviews Microbiology 3, 722-732 (2005)
Some transposons can encode
integrons

Integrons are assembly platforms — DNA
elements that acquire open reading frames
embedded in exogenous gene cassettes and convert
them to functional genes by ensuring their correct
expression.
e.g. bacterial Tn7 also encodes an integron — a
DNA segment containing several cassettes of
antibiotic-resistance genes. These cassettes can
undergo rearrangements in hosts that express a
related recombinase, leading to alternative
combinations of antibiotic-resistance genes.
Integrons
Mobile Integrons
Superintegrons
Mazel Nature Reviews Microbiology 4, 608–620 (August 2006)
Reading
1)
Chapter 9 pp 265-268
HMG 3 by Strachan and Read
2)
Chapter 10: pp 339-348
Genetics from genes to genomes
by Hartwell et al (2/e)