When the genome lowers its epigenetic shield: Transposable elements on the move
Etienne Bucher IRHS, Angers, France
www.plantepigenetics.ch @methylcytosine MAIN ACTIVITIES OF THE GROUP
Basic research identifying novel epigenetic regulators in Arabidopsis
Epigenetic regulation of flowering in rose
Genomics and epigenomics in apple
Transposable element biology WHY CARE ABOUT TRANSPOSONS?
What are transposable elements (TEs or jumping genes)? - TEs are mobile repetitive sequences in the genome - All organisms have TEs
Why are TEs important? - TEs drive evolution - epigenetic regulation - crop domestication - regulate stress response CROP TRAITS INFLUENCED BY TRANSPOSONS
What is the relation between stress and TEs? Vezzulli, S. et al. J Exp Bot 63 Butelli, E. et al. Plant Cell 24 Walker, A.R. et al. Plant J 49 SILENCING OF TRANSPOSABLE ELEMENTS
TE bursts are repressed by silencing
silencing
TE burst
TE chromosome centromere TRANSPOSONS AND EPIGENETICS
MuLE Dfr-B
MuLE Dfr-B
IAP
Agouti
Slotkin RK & Martienssen R Nat Rev Genet 2007, 8:272–285. Cubas P et al. Nature 1999, 401:157–161. TRANSPOSONS ARE EFFICIENTLY SILENCED
Matzke, M.A., and Mosher, R.A. (2014). Nat Rev Genet 15, 394–408. STRESS AND EPIGENETICS
Does stress induce stable heritable epigenetic changes in plants? STRESS AND EPIGENETICS
So far there is no true stress-induced epi-mutation Holeski et al. (2012) TRANSIENT ACTIVATION OF ENDOGENOUS REPEATS
MULE- F19G14
18S rRNA
106B
5S-210
180 bp
18S rRNA RT minus
Tittel-Elmer (PLOS Gen 2010) TRANSCRIPTOME AFTER HEAT STRESS
Chr 1 Chr 2 Chr 3 Chr 4 Chr 5
ITS
ITS+2d
ATCOPIA78 Tittel-Elmer (PLOS Gen 2010) SILENCING BY RNA POL IV
ATCOPIA78
Ito H et al. Nature 2011, 472:115–119. RETROTRANSPOSON LIFE CYCLE
DNA LTR polyprotein LTR DNA
Pol II LTR polyprotein LTR
RNA RT L A M O S O M O R H C A R T X E F O N O I T A L U M DNA U C C A
ATCOPIA78 copy number Ito H et al. Nature 2011, 472 :115 – 119. N E W A T C O P I A 7 8 INSERTIONS IN THE MUTANT LINE
Ito H et al. Nature 2011, 472:115–119. ONSEN : JAPANESE FOR HOT SPRING ONSEN REGULATES HEAT STRESS RESPONSE
LTR poOlyNpSroENtein LTR host gene
Ito H et al. Nature 2011, 472:115–119. POL IV AND POL V LIMIT TE MOBILITY
Ito H et al. Nature 2011, 472:115–119. TE SILENCING MECHANISMS: POL II?
Matzke, M.A., and Mosher, R.A. (2014). Nat Rev Genet 15, 394–408. POL II REPRESSES THE ACTIVATION OF ONSEN
A= a-amanitin (Pol II inhibitor) Z= zebularine (DNA methylation inhibitor) Amanita phalloides death cap Thieme, M. et al Genome Biol; 2017;18: 134. INHIBITION OF POL II REDUCES DNA METHYLATION IN PLANTS
Thieme, M. et al Genome Biol; 2017;18: 134. MOBILIZATION OF ONSEN I N W I L D - TYPE ARABIDOPSIS PLANTS
HS control HS+A+Z
Thieme, M. et al Genome Biol; 2017;18: 134. N E W ONSEN INSERTIONS ARE STABLE
90
80 F1 F2 F3
70
60 copy number copy 50
40 ONSEN 30
20
10
0 a b c I II III IV V VI VII control lines treated lines
Thieme, M. et al Genome Biol; 2017;18: 134. INDUCED PHENOTYPIC DIVERSITY
wild-type ONSEN high-copy lines a b c I II III IV V VII
Thieme, M. et al Genome Biol; 2017;18: 134. INDUCED PHENOTYPIC DIVERSITY (SD)
Thieme, M. et al Genome Biol; 2017;18: 134. TE MOBILIZATION IN RICE
irri.org
WT
control A Z A&Z A
Z
A+Z confirmation by PCR
Houba whole genome sequencing of circular DNA
Thieme, M. et al Genome Biol; 2017;18: 134. B U N G E E : BREEDING USING JUMPING GENES
stress
TE gene active gene
stress BUNGEE and controlled TE burst
selection
step 1 step 2
The stress defines which set of TEs will be activated ONSEN - MEDIATED HEAT - S T R E S S TOLERANCE?
control ONSEN high copy lines
We can use TEs for plant breeding it is fast, directed and stable CONCLUSIONS AND A QUESTION
RNA Pol II plays an important role in TE defense
ONSEN mobility results in phenotypic diversity
We can use TEs to breed stress tolerance in crops!
Evolutionary question: How important is adaptive evolution? WHY TRANSPOSONS COULD BE A GREAT TOOL TO MONITOR RADIATION
TEs are definitely heritable!
They react to virtually all stresses
Easy to identify active TEs
One can date the age of TE insertions PLANT EPI/GENETICS MEETING
save the date: 29-31st October 2018
Invited Speakers: Isabel Bäuerle, Claude Becker, Tetsuji Kakutani, Marie Mirouze, Olivier Panaud, Bob Schmitz, Nathan Springer, Clémentine Vitte, Jian-Kang Zhu
https://symposium.inra.fr/plantepigenetics2018 ACKNOWLEDGEMENTS
Michael Thieme Nicolas Daccord Sandrine Balzergue Sophie Lanciano Marie Mirouze MOBILOME SEQUENCING
developed by Marie Mirouze
Lanciano S, et al. PLoS Genet. 2017;13 POL II ACTS UPSTREAM OF DCL2/3/4
Thieme, M. et al Genome Biol; 2017;18: 134. CURRENT CHALLENGES IN CROP BREEDING
Climate change stress objective
temperature rapid breeding of drought stress-tolerant crops salt
Current breeding tools
Classic genetic crosses slow
GMOs no public acceptance
Transposable elements fast, directed, not GMO POL II PLAYS A ROLE IN DNA METHYLATION AND TE SILENCING
release of a TE transcript in nrpb2
Pol II AGO4
Zheng, B et al Genes Dev 23, 2850–2860.