Long time no see

Lab meeting

Guillaume - 13/11/18

Guess who's back...

What changed ?

What changed ?

But most importantly...

3 new questions (family meetings / saturday night parties)

1 - Why a PhD ?

2 - What's your PhD about ??

and...

• "As you work in informatics, can you fix my printer ?" (No)

Why a PhD

What's the PhD going to be about ?

Explained to my parents, who still think I'm a med student

Explained to fellow scientists (and to random people, drunk, on a saturday night)

Ciliates: A 340 years old story

Christopher Hooke

1665 - "Micrographia"

30x microscope

First Cell description

Antoni Van Leeuwenhoek

1678 - "Animalcules"

First observation of single-cell organisms

Infusoria, Paramecium

The storytelling in biology

... And we love great stories

Very rare picture of me (right), explaining my PhD project during the lab meeting Pere Castor et Al. (Flammarion FR - Circa 2018 - Colourized)

Apocalypse now...

AC : Activator

DS  : Destabilization

Ac is required for DS activity

DS literally "moves" in the genome

Ac/Ds elements

Barbara McClintock - 1960's

Nobel Prize in 1968

"Jumping Genes"

Composite-sketch of a  transposon

Identification of the Ac/Ds sequences identified a few years later:

• Some transposons encode a transposase: They are autonomous (ex: Ac)
• Some others are dependant of a transposase (ex: Ds)

Class I & II TE

Copy/Paste

Cut/Paste

Both can be autonomous or dependant

Horizontal transfer of TE

• TE are considered as "sharing an ancestor with viruses"
• They could transfer horizontally by their own or through pathogens, pollinators, symbiosis, plasmids...

... And many others

Autonomous copy/paste + horizontal transfer = Global Invasion

TE = Chaotic invasion ? Yes !

Genome Biol Evol. 2017

"Evolution and Diversity of Transposable Elements in Vertebrate Genomes" (Cibele G.)

Extreme case 1)

Maize

Up to 86%

He dead ?

Extreme case 2)

• Prokaryote
• One of the smallest genome ever sequenced
• No TE, no transposase
• Only known exception to day

Prochlorococcus marinus SS120

The invasion seems total in eucaryotes

No known exception

The selfish gene - 1976

• Finalist/Anthropomorphist analogy: "The DNA is selfish and only 'wants' to reproduce itself" --> Parasitic DNA

• With limited resources, the best DNA replicators "win"

• The evolution and natural selection could be better described by "DNA replicators" rather than species

Quick maths won't stand the distance

Fruit flies:

• Speciation ~65 million years ago
• 1 generation / 30 days
• 1 initial TE
• 1 duplication.10^-5 /TE/Generation

About 2^7800 = 10^2348 transposons

Homo Sapiens:

• ~300.000 years ago
• 1 generation / 35 years
• 1 duplication.10^-5 /TE/Generation
• 100 initial TE

100 +[ 3/ 35 * 100 ] = 108 transposons

Evolution of TE must be different than trivial

• Even considering the low level of one transposition event every 10^5 generations
• Even considering a 99% transposition success rate after excision

They should have disappeared a long time ago in many species

Hypothesis why the calculus don't work

• Transposable elements degenerate quickly if the host has no benefit and therefore don't replicate anymore
• Autonomous element become easily dependant, so... the higher the copy number, the higher the dependant copies, the lesser transposition efficiency
• The most aggressive types of TE invaded and extincted their host, so we just observe under-active TE
• The most vulnerable species got extincted because of the TE, so we just observe the most-protected species (those who have repressive systems)
• During their own horizontal transfer, transposons can also carry their associated defense-system (otherwise the host extincts)
• Some TE families could have appeared more than once, so their age is maybe not so old
• Transmission rate is unknown, and insertion is biaised

Hints of a hidden past

Reconstruct TE's story is something feasible

The global story remains a mystery

• A wide range of strategies exist
• Eucaryotes, procaryotes and archea have very different mechanisms
• This suggest a progressive, separate, even constant adaptation

A wide range of strategies to fight transposons

P-M Hybrid dysgenesis

1982 - Identification of a mechanism of defense in multicellular animals, later identified as piRNA

The piRNA mechanism

Methylation of DNA and maintenance

Histone modifications

Cis/Trans Repression

The modification itself seems guided by small RNA

• In fungi, methylation the Copy Number Variants (CNVs) seem to be one (still debated) mechanism or repression
   
• In procaryotes, apparently random genes are regularly excised, which avoids accumulation of TE

• ORFs are not conserved in TE mutants. Non-sens RNA-mediated decays could be helpfull for eucaryotes

To be continued...

Other mechanisms

The ciliates: a specific case

MIC/MAC Differenciation

Transposable elements are suppressed in the MAC, where the transcription occurs

Avoids the negative effect of TE

PiggyMac

Excision of IES: ScanRNA pathway

• SCAN-RNA --> Excision of 60% of IES max  (shown by DICER-like silencing)

• Piwi shuttle

• What about the 40% remaining ?

What's to be discovered ?

• New TE seem to be excised by PGM + ScRNA


• Old and degenerated TE (= IES) accumulate in genes and seem to be excised very precisely by another system

2 Hypothesis:

1) Paramecium's methylation (started in Master's internship)

2) mtF-Like proteins

DNA Methylation

Methylation analysis needs local > 25X

• Analogy with known-systems
• 6mA reported to be abundant
• 5mC = MYSTERY !
• Contradiction between techniques... Including PacBio

mtF-Like

The PhD project

1 - Methylation: A lot remains to be done !

2 - mtF-Like analysis

3 - Building a model of excision

4 - Reconstructing the story of "How Paramecium is different than other ciliates ?", and why it's unique

Other tasks: Some annotation or assembly work to have a higher resolution in analysis

Thank you

Eric

Mathieu

Auguste

And everyone else :) ...

Variety of TEs discovered