Monitoring the Impact of Transposable Element activity on genome structure and function, in response to environmental - and chemical Stresses ...
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Monitoring the Impact of Transposable Element activity on
genome structure and function, in response to environmental
and chemical Stresses
TE
Anna-Sophie Fiston-Lavier, TE Séverine Chambeyron,
MCF, INEE DR, INSB
Présentation MITI – 16 février 2021
~90%
Transposable Elements (TEs)
Mobile DNA
>60%
TEs are ubiquitous DNA sequences
Mostly dispersed repeats
Highly repetitive sequences (over ~million copies)
Highly diverse (Classes, Superfamilies, Families…)
~20%
~17%
TIR TIR LTR LTR
Adapted from Wessler 2006
Biémont C, 2010
Introduction
TE dynamics
Structural and functional impact of the
TE activity due to their :
● Mechanism,
● Repetitiveness,
● Insertion site.
Introduction
1) Most of the TE
insertions are deleterious Drosophila melanogaster natural populations
Functional enrichment analysis
of genes nearby TEs
3) 300 adaptive-TEs
2) Recombination is the stronger detected using T-lex
evolutionary force explaining the TE (Fiston-Lavier
distribution (Fiston-Lavier et al 2009; 2011,2015,2020;
Petrov et al 2011) Reich et al 2019)
Green: stress response, Red: behavior, Blue: development
Introduction
piRNA mediated silencing in somatc ovarian tssues
Egg chamber
piRNA
X
Piwi 1
Follicle cells
TE
germ line
A genetic tool to activate Oocyte infecton
control Piwi-KD mobilization of TEs over
generations maintaining Oocyte nucleus
fertile progenies 2
3
Piwi-knockdown (KD) induces a New TE
Reverse
insertion
reduction in fertility (ovaries) Transcripton (RT)
Introduction
TE
TE
Can we activate the transposition after one generation ?
Can we activate the transposition after one generation ?
G0
TE piRNA
1 TE transcription
2 Germ line infection and TE RT
G1
3 New TE insertions
Introduction Previous
Can we activate the transposition after one generation ?
TE piRNA
1 TE transcription
G1
2 Germ line infection and TE RT
3 New TE insertions
G0
● 9 TE families with less small RNA
● 4 out of 9 TE families with a higher TE expression level
Barckmann et al, 2018
Introduction Previous
germ line
Oocyte infecton
Does TE soma-to-germline transfer
lead to genome integration ? Oocyte nucleus
2
3
New TE
insertion
Reverse
Transcripton (RT)
Mobile-seq: sequencing of
the eccDNA (circular DNA)
from Drosophila embryos
hallmarks of TE insertions
TE piRNA
1 TE transcription
Piwi-sKD
G1
2 Germ line infection and TE RT
Barckmann et al, 2018
3 New TE insertions
normalized TE reads
G0
Introduction Previous
Germ line infection results in de novo TE
integrations in the next generation
DNA-seq: Short read PE sequencing of G0 and G1
Ratio de novo insertions piwi-KD / control
Piwi-sKD (G1) / control ratio (G0)
TE piRNA of putative de novo TE insertions
1 TE transcription
Barckmann et al, 2018
2 Germ line infection and TE RT
3 New TE insertions
Introduction PreviousTE
TE
Monitoring the Impact of Transposable Element activity on
genome structure and function, in response to environmental
and chemical Stresses
● Aim1 : How to reactivate the transposition over
generations ?
● Aim2 : Investigate the TE dynamics based on the
detection of novel TE insertions over time
● Aim3: Analysis of the functional impact of the TE insertions
over time and under different stress conditionsTE load over generations of somatic Piwi-KD
G0 G1 G11 G17 G30 G41 G72
qPCR
Number of TE copies relative to Rpl32 Somatic piwi-KD at each generation
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ZAM and gtwin show strongly increased transposition rate
that stays stable over generations
Introduction Previous ResultsTE
TE
Monitoring the Impact of Transposable Element activity on
genome structure and function, in response to environmental
and chemical Stresses
● Aim1 : How to reactivate the transposition over
generations ?
● Aim2 : Investigate the TE dynamics based on the
detection of novel TE insertions over time
● Aim3: Analysis of the functional impact of the TE insertions
over time and under different stress conditionsIn-depth analysis of the TE dynamics Introduction Previous Results
In-depth analysis of the TE dynamics
Experimental G0 G1 G11 G17 G30 G41 G72
Pooled
sequencing (x100) G0 G31 G73 G88
REF
73 generations of TE
no TE mobilization mobilization
ZAM
Introduction Previous ResultsStep1 : Identification of new TE insertions using long-reads
in G73 compared to G0
Assumption : Global TE insertions, expected
to be common insertions should be present in
the assemblies while minor insertions, less
frequent, need to be saved.
274 new TEs
ERV
Mohamed et al, 2020
Introduction Previous ResultsStep 2 : In depth analysis of the new TE insertions detected
Target site duplication,
hallmarks of new TE insertions
Intron Exon Intergenic
43% 27% 31%
Master TE insertions can be
detected
Introduction Previous ResultsStep 3 : TE population frequency using long-read pooled data
Frequency spectrum
of non-reference TEs
Publication of the
Bioinformatics tool in process
Introduction Previous ResultsConclusion & next Others stresses
(Paraquat)
Experimental G0 G1 G11 G17 G30 G41 G72
With stress
Without stress
Pooled
sequencing (x100) G0 G31 G73 G88
REF
● Aim1 : How to reactivate the transposition over generations ?
2019 Publication #1 : Mohamed et al 2020
● Aim2 : Investigate the TE dynamics based on the detection of
2020 novel TE insertions over time
Publication #2 : Mansour et al 2021
Publication #3 : How to estimate the TE frequency in long read pooled data
2021
● Aim3 : Analysis of the functional impact of the TE insertions over time
and under different stress conditions (RNA-seq and Paraquat test in
process) Master 2 student / Publication #4
Introduction Previous Results 2021Merci pour votre attention
Anna-Sophie Fiston-Lavier, MCF Chambeyron Séverine, Dr CNRS
Mansour Yasmine, PhD student Alain Pelisson, Dr CNRS
Mohamed Mourdas, Bioinformatican
Yuki Ogiyama, CR CNRS
Bruno Mugat, Techician
François Sabot, DrYou can also read
