BIO353 Lecture8 (Transposition) SHF 2021

BIO353 – lecture 8: Transposition
BIO353.01 – Molecular Genetics shf – 2022

Transposition: a recombination mechanism
homologous site-specific
recombination recombination transposition
two identical sequences two identical specific sequences two identical specific sequences
and any other sequence

Transposition: two modes of transposition
cut and paste copy and paste
(ctrl X / ctrl V) (ctrl C / ctrl V)
mainly DNA transposons mainly retrotransposons

Transposition: variation of seed pigmentation in maize
pigmented
colorless
spotted
pigment variability in maize kernel phenotypes

pigmented
colorless
spotted
Barbara McClintock
(1902 – 1992)

pigmented colorless
wild type mutant
mobility
Ac Ds C
Ds
Ac Ds C Ac mutant C
dissociator color locus

pigmented colorless spotted
wild type mutant revertant
mobility activation mobility

Ds
Ac Ds C Ac mutant C
activator
Ds
Ac Ds C Ac mutant C Ac C
dissociator color locus reverted

Transposition: transposon diversity in maize
activator
autononmous Ac transposase (= recombinase)
terminal inverted terminal inverted
repeat repeat
deletion
Ds-a
deletion
dissociator
non-autononmous Ds-b
sequence substitution
Ds-c

Transposition: transposon prevalence in genomes
100
genome fraction [%]
75
50
25
0
chimp / human maize barley lilly

Transposition: transposon prevalence in genomes

Transposition: evolution of transposable elements

Transposition: three classes of transposable elements
DNA transposons
transposable element
host DNA
transposase
target-site terminal inverted

duplication repeat

DNA transposons
host DNA
transposase

duplication repeat
virus-like retrotransposons (endogenous retroviruses)
promoter promoter
integrase and RT
5’-LTR 3’-LTR

DNA transposons
host DNA
transposase

duplication repeat
virus-like retrotransposons (endogenous retroviruses)
promoter promoter
integrase and RT
RNA intermediates
5’-LTR 3’-LTR
move through
polyA retrotransposons
promoter
ORF1 ORF2
5’-UTR 3’-UTR

gag pol env

autonomous
TSD TSD
LTR genes LTR ERV
LTR (endogenous
retroviruses)
gag
RNA intermediate
non-
autonomous
class I
ORF1 ORF2 (pol)

autonomous AAA LINEs
(long interspersed nuclear elements)
non-LTR AAA SINEs

A B (short interspersed nuclear elements)
non- TSD
autonomous
(CCCTCT)n VNTR AAA SVA

Alu-like HERV-like (SINE, VNTR, ALU)
DNA transposons
autonomous
class II
transposase
DR DR
TIR TIR
non-
autonomous MITEs
(miniature inverted repeat transposable elements)

size copy number

ORF1 ORF2 (pol)
LINEs autonomous AAA 6 – 8 kb 850.000 21%
polyA
A B
SINEs non-autonomous AAA 100 – 300 bp 1.500.000 13%
gag pol env

autonomous 6 – 11 kb
retrovirus-like 1.500.000 8%
gag
non-autonomous 1.5 – 3 kb
transposase
autonomous 2 – 3 kb
DNA transposons 300.000 3%
non-autonomous 80 – 2.000 bp

full-length element most commonly found

in genome
gag pol env
TSD LTR LTR TSD LTR

RNA intermediate
class I
ORF1 ORF2 (pol) ORF1 ORF2 (pol)

AAA AAA
AAA
AAA A B
A B
DNA transposons
transposase
class II
DR TIR TIR DR TIR TIR DR

pol II promoter
ORF1 ORF2 (pol) polyA
LINEs AAAn
TSD TSD
help to transpose
pol III promoter

polyA
SINEs AAAn
TSD
A B no ORFs TSD

Transposition: mobility - Alu (SINE)
Alu transposition
1 in 21 births

Transposition: mobility - LINE 1
1 in 95 births
Transposition: mobility and genetic variability
each two genomes are polymorphic for about 1.000 transpositions
1.000
≠
1.000
≠
1.000
≠
1.000
≠
1.000
≠

transposons in the human genome
25 mya
37 mya
Mouse Genome Sequencing Consortium, Initial sequencing and comparative analysis of the mouse genome, Nature, 2002, 420:523
37 25

transposons in the mouse genome
25 mya
37 mya
Transposition: cut and paste mechanism of DNA transposons


Transposition: DNA strand transfer


Transposition: mechanism for second strand cleavage
transposase only cleaves one strand à 3’- OH group

= endonuclease

= endonuclease
transesterification

= endonuclease
transesterification transesterification

Transposition: replicative DNA transposons




Transposition: transposition, replication, and copy number
replicative transposition increases copy number
direction of
replication
replication
fork
DNA transposon

direction of
replication
replication transposition
fork to sister chromatid
DNA transposon

direction of
replication
fork to replicated site
DNA transposon
transposition
to unreplicated site
DNA transposon

direction of
replication
fork to replicated site
DNA transposon
transposition
DNA transposon
progression of replication fork

direction of
replication
fork gap repair to replicated site
DNA transposon
transposition
gap repair (homology repair)
DNA transposon
progression of replication fork

Transposition: retrotransposons
promoter
DNA integrase and RT
5’-LTR 3’-LTR
transcription
RNA
reverse transcription
cDNA

Transposition: retrotransposons

Transposition: polyA retrotransposons
promoter
LINE1 DNA ORF1 ORF2
5’-UTR 3’-UTR
transcription
LINE1 mRNA
translation
ORF1 / ORF2
proteins
binding to LINE1 mRNA

Transposition: polyA retrotransposons and copy number
transposition increases copy number
RNA transposon
ORF1 ORF2
AAA
TSD TSD
transcription
AAAAAAAA

RNA transposon
T-rich target in genome

ORF1 ORF2
AAA
TSD TSD AAAAAAAA
mobility in nucleus
transcription
AAAAAAAA
export to cytoplasm
AAAAAAAA

RNA transposon
integration
(target site-primed RT)
ORF1 ORF2
AAA
TSD TSD AAAAAAAA
mobility in nucleus
transcription
AAAAAAAA
import to nucleus
export to cytoplasm
translation
AAAAAAAA

RNA transposon
integration
ORF1 ORF2 ORF1 ORF2
AAA AAA
TSD TSD TSD TSD
mobility in nucleus
transcription
AAAAAAAA
import to nucleus
export to cytoplasm
translation
AAAAAAAA

Transposition: target site specificity
AAA
T-rich
sequence TTTTTT TTT TT

AAA
T-rich
AAA
upstream of
RNApol III transcipts
A B box

AAA
T-rich
AAA
upstream of
A B box
AAA
heterochromatin

AAA
T-rich
AAA
upstream of
A B box
AAA
heterochromatin
AAA
spreading spreading
silenced TE

AAA
T-rich
AAA
upstream of
A B box
AAA
heterochromatin
AAA
spreading spreading
silenced TE
AAA
antisense
into introns
AAA

AAA
T-rich
AAA
upstream of
A B box
AAA
heterochromatin
AAA
spreading spreading
silenced TE
AAA
antisense neutral
into introns
AAA
sense selected against

into introns

Transposition: consequences for genome integrity / stability
transposition GENOME

transposition
DSB
DNA repair
resection of DNA ends resection of DNA ends
lost DNA sequence
NHEJ

AAA AAA
A B A B
two transposon insertions with the same orientation
recombination
AAA
A B
AAA
A B
excision AAA
A B
AAA
A B

gene
two neighboring DNA transposon insertions
transposon excision
gene
original locus
gene
excised DNA
transposition may promote translocations by homologous recombination
duplication event (transposition)
uneven recombination / Xing over

uneven recombination / Xing over
insertion / translocation
deletion

Transposition: IS10 and copy number counting



Transposition: Mu and self-avoidance (transposition target immunity)



Transposition: and the immune system
adaptive immunity innate immunity

humoral cellular
(B-cell immunity) (T-cell immunity)

Transposition: and V(D)J recombination
B cell receptor T cell receptor

antigen binding (antibody)
domain
VH heavy chain
VL antigen binding domain
variable
region
CH1
constant CL
region Va Vb
light chain
CH2
Ca Cb
CH3 a chain b chain
B lymphocyte T lymphocyte



V(D)J recombination and the 12/23 rule

à additional variability

V(D)J recombination and junctional diversity

Huang S et al., Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination, Cell, 2016, 166:102-114.

Transposition: most common transposable elements

BIO353 Lecture8 (Transposition) SHF 2021

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BIO353 – lecture 8: Transposition

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

cut and paste copy and paste

(ctrl X / ctrl V) (ctrl C / ctrl V)

mainly DNA transposons mainly retrotransposons

BIO353.01 – Molecular Genetics shf – 2022

pigment variability in maize kernel phenotypes

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

wild type mutant

BIO353.01 – Molecular Genetics shf – 2022

pigmented colorless spotted

wild type mutant revertant

mobility activation mobility

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

target-site terminal inverted

BIO353.01 – Molecular Genetics shf – 2022

target-site terminal inverted

virus-like retrotransposons (endogenous retroviruses)

BIO353.01 – Molecular Genetics shf – 2022

target-site terminal inverted

virus-like retrotransposons (endogenous retroviruses)

BIO353.01 – Molecular Genetics shf – 2022

gag pol env

ORF1 ORF2 (pol)

non-LTR AAA SINEs

(CCCTCT)n VNTR AAA SVA

BIO353.01 – Molecular Genetics shf – 2022

size copy number

gag pol env

BIO353.01 – Molecular Genetics shf – 2022

full-length element most commonly found

gag pol env

TSD LTR LTR TSD LTR

ORF1 ORF2 (pol) ORF1 ORF2 (pol)

DR TIR TIR DR TIR TIR DR

BIO353.01 – Molecular Genetics shf – 2022

pol III promoter

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

each two genomes are polymorphic for about 1.000 transpositions

BIO353.01 – Molecular Genetics shf – 2022

transposons in the human genome

BIO353.01 – Molecular Genetics shf – 2022

transposons in the mouse genome

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

transposase only cleaves one strand à 3’- OH group

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022

BIO353.01 – Molecular Genetics shf – 2022