Baptiste Rafanel
@baptisterafanel.bsky.social
Transposons, Transcription, piRNA, Drosophila
PhD Student in the Brennecke lab at IMBA
PhD Student in the Brennecke lab at IMBA
Reposted by Baptiste Rafanel
Finally - the 🧵!
So, the piRNA pathway defends the animal germline from transposons. But most of what we know comes from narrow developmental windows like late oogenesis, where it's easiest to study.
We asked if the pathway is the same across development.
It is not!
/+
So, the piRNA pathway defends the animal germline from transposons. But most of what we know comes from narrow developmental windows like late oogenesis, where it's easiest to study.
We asked if the pathway is the same across development.
It is not!
/+
We watched piRNAs and transposons across development, saw them dance tightly and wrote a paper about it.
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
A developmental switch in the piRNA pathway ensures stage-specific transposon silencing https://www.biorxiv.org/content/10.64898/2026.08.28.747770v1
September 2, 2026 at 3:10 PM
Finally - the 🧵!
So, the piRNA pathway defends the animal germline from transposons. But most of what we know comes from narrow developmental windows like late oogenesis, where it's easiest to study.
We asked if the pathway is the same across development.
It is not!
/+
So, the piRNA pathway defends the animal germline from transposons. But most of what we know comes from narrow developmental windows like late oogenesis, where it's easiest to study.
We asked if the pathway is the same across development.
It is not!
/+
Reposted by Baptiste Rafanel
We watched piRNAs and transposons across development, saw them dance tightly and wrote a paper about it.
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
A developmental switch in the piRNA pathway ensures stage-specific transposon silencing https://www.biorxiv.org/content/10.64898/2026.08.28.747770v1
August 29, 2026 at 5:09 PM
We watched piRNAs and transposons across development, saw them dance tightly and wrote a paper about it.
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
Reposted by Baptiste Rafanel
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 25, 2026 at 9:18 AM
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Baptiste Rafanel
How do transposons jump when they’re released from host control?
I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs.
Here’s what we found & excited to share my 1st postdoc paper:
“piRNA loss unleashes episodic transposition bursts”
www.biorxiv.org/content/10.6...
I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs.
Here’s what we found & excited to share my 1st postdoc paper:
“piRNA loss unleashes episodic transposition bursts”
www.biorxiv.org/content/10.6...
piRNA loss unleashes episodic transposition bursts
In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...
www.biorxiv.org
July 17, 2026 at 2:07 PM
How do transposons jump when they’re released from host control?
I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs.
Here’s what we found & excited to share my 1st postdoc paper:
“piRNA loss unleashes episodic transposition bursts”
www.biorxiv.org/content/10.6...
I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs.
Here’s what we found & excited to share my 1st postdoc paper:
“piRNA loss unleashes episodic transposition bursts”
www.biorxiv.org/content/10.6...
Reposted by Baptiste Rafanel
Cool study! TEs in the male Drosophila germline jump in bursts
piRNA loss unleashes episodic transposition bursts https://www.biorxiv.org/content/10.64898/2026.07.11.737971v1
July 17, 2026 at 8:25 AM
Cool study! TEs in the male Drosophila germline jump in bursts
Reposted by Baptiste Rafanel
www.cell.com/molecular-ce...
I'm happy to see our work published! If you are interested in transposons, transcriptional regulation and Pol III come and check it out 👀 🧫 🧬
I'm happy to see our work published! If you are interested in transposons, transcriptional regulation and Pol III come and check it out 👀 🧫 🧬
ChAHP silences SINE retrotransposons by inhibiting TFIIIB recruitment
SINEs are short transposable elements that make up large fractions of mammalian genomes.
Known to be transcribed by RNA polymerase III, their regulation has remained largely
unexplored. Schnabl-Baumga...
www.cell.com
July 7, 2026 at 3:06 PM
www.cell.com/molecular-ce...
I'm happy to see our work published! If you are interested in transposons, transcriptional regulation and Pol III come and check it out 👀 🧫 🧬
I'm happy to see our work published! If you are interested in transposons, transcriptional regulation and Pol III come and check it out 👀 🧫 🧬
Reposted by Baptiste Rafanel
Our new work with Eric Lai's lab shows that endogenous RNAi represses only a few genes in D.melanogaster, but hundreds of mRNAs in D. simulans testis. Our data suggest that gene regulation by RNAi is essential for D.simulans spermatogenesis.
@lucksmith.bsky.social
www.biorxiv.org/content/10.6...
@lucksmith.bsky.social
www.biorxiv.org/content/10.6...
May 23, 2026 at 3:04 PM
Our new work with Eric Lai's lab shows that endogenous RNAi represses only a few genes in D.melanogaster, but hundreds of mRNAs in D. simulans testis. Our data suggest that gene regulation by RNAi is essential for D.simulans spermatogenesis.
@lucksmith.bsky.social
www.biorxiv.org/content/10.6...
@lucksmith.bsky.social
www.biorxiv.org/content/10.6...
Reposted by Baptiste Rafanel
Our latest work is now online in NSMB: maternal yolk carries microRNAs from the intestine to embryos, shaping gene regulation and stress resilience in the next generation.
rdcu.be/fj8Er
#Epigenetics #microRNA #Inheritance @pasteur.fr @devstempasteur.bsky.social @erc.europa.eu
rdcu.be/fj8Er
#Epigenetics #microRNA #Inheritance @pasteur.fr @devstempasteur.bsky.social @erc.europa.eu
Soma-to-germline miRNA inheritance through yolk promotes stress resilience in progeny - Nature Structural & Molecular Biology
In this study, the authors use the Caenorhabditis elegans model organism to show that maternal microRNAs are delivered from the intestine to embryos by the yolk, where they regulate gene expression an...
www.nature.com
May 22, 2026 at 11:36 AM
Our latest work is now online in NSMB: maternal yolk carries microRNAs from the intestine to embryos, shaping gene regulation and stress resilience in the next generation.
rdcu.be/fj8Er
#Epigenetics #microRNA #Inheritance @pasteur.fr @devstempasteur.bsky.social @erc.europa.eu
rdcu.be/fj8Er
#Epigenetics #microRNA #Inheritance @pasteur.fr @devstempasteur.bsky.social @erc.europa.eu
Reposted by Baptiste Rafanel
🧬 New research from the Burga lab! We took a closer look at a rogue selfish protein and caught evolution in the act of turning something old into something radically new 💡 (a.k.a. neofunctionalization) @imbavienna.bsky.social
www.biorxiv.org/content/10.6...
Curious? Here’s a breakdown:
www.biorxiv.org/content/10.6...
Curious? Here’s a breakdown:
May 18, 2026 at 1:49 PM
🧬 New research from the Burga lab! We took a closer look at a rogue selfish protein and caught evolution in the act of turning something old into something radically new 💡 (a.k.a. neofunctionalization) @imbavienna.bsky.social
www.biorxiv.org/content/10.6...
Curious? Here’s a breakdown:
www.biorxiv.org/content/10.6...
Curious? Here’s a breakdown:
I'm super happy to finally see the paper published ! Check out the full story here: link.springer.com/article/10.1...
May 6, 2026 at 10:28 AM
I'm super happy to finally see the paper published ! Check out the full story here: link.springer.com/article/10.1...
Reposted by Baptiste Rafanel
Five years after a short rotation in the Peters lab, I’m happy to see this cool story spearheaded by Gordana Wutz finally published.
🧬 Inside the cell nucleus, two meters of DNA are folded into shape by cohesin—a protein complex that forms DNA loops. But how is this process controlled?
Our Peters’ lab and collaborators have discovered how cells put the brakes on DNA loop formation: www.sciencedirect.com/science/arti...
Our Peters’ lab and collaborators have discovered how cells put the brakes on DNA loop formation: www.sciencedirect.com/science/arti...
May 4, 2026 at 6:07 PM
Five years after a short rotation in the Peters lab, I’m happy to see this cool story spearheaded by Gordana Wutz finally published.
Reposted by Baptiste Rafanel
Reminder: PhD position in my lab is open for two more weeks.
How do germ cells use their own private transcription factors? Come help us find out.
Fully funded. Deadline May 1.
Flyer attached — please boost! 🙏
How do germ cells use their own private transcription factors? Come help us find out.
Fully funded. Deadline May 1.
Flyer attached — please boost! 🙏
April 17, 2026 at 11:48 AM
Reminder: PhD position in my lab is open for two more weeks.
How do germ cells use their own private transcription factors? Come help us find out.
Fully funded. Deadline May 1.
Flyer attached — please boost! 🙏
How do germ cells use their own private transcription factors? Come help us find out.
Fully funded. Deadline May 1.
Flyer attached — please boost! 🙏
Reposted by Baptiste Rafanel
Love Drosophila genetics — this journal club was a great way to share that enthusiasm and pay tribute to the pioneers of transposons regulation 🪰 How classical genetics uncovered key determinants of TE silencing #transposon @igred.fr
@igred.fr
👇👇
@igred.fr
👇👇
New online! How classical genetics uncovered key determinants of TE silencing
How classical genetics uncovered key determinants of TE silencing
Nature Reviews Genetics, Published online: 25 March 2026; doi:10.1038/s41576-026-00951-5In this Journal Club, Emilie Brasset highlights a 1995 publication by Prud’homme et al., who designed a clever genetic assay to identify a gene important for TE silencing, which provided a crucial foundation for later studies to unravel the underlying mechanisms.
dlvr.it
April 9, 2026 at 9:16 AM
Love Drosophila genetics — this journal club was a great way to share that enthusiasm and pay tribute to the pioneers of transposons regulation 🪰 How classical genetics uncovered key determinants of TE silencing #transposon @igred.fr
@igred.fr
👇👇
@igred.fr
👇👇
Reposted by Baptiste Rafanel
Germ cells have their own versions of core transcription factors and fertility depends on them.
We're hiring a PhD student to figure out how! 📢
Fly genetics + proteomics + genomics. Fully funded.
Aarhus University 🇩🇰
Deadline May 1 👇
Please share with anyone who might be interested!
We're hiring a PhD student to figure out how! 📢
Fly genetics + proteomics + genomics. Fully funded.
Aarhus University 🇩🇰
Deadline May 1 👇
Please share with anyone who might be interested!
phd.nat.au.dk
April 1, 2026 at 7:51 AM
Germ cells have their own versions of core transcription factors and fertility depends on them.
We're hiring a PhD student to figure out how! 📢
Fly genetics + proteomics + genomics. Fully funded.
Aarhus University 🇩🇰
Deadline May 1 👇
Please share with anyone who might be interested!
We're hiring a PhD student to figure out how! 📢
Fly genetics + proteomics + genomics. Fully funded.
Aarhus University 🇩🇰
Deadline May 1 👇
Please share with anyone who might be interested!
Reposted by Baptiste Rafanel
How does the piRNA pathway solve the self vs. non-self problem? 🧬
Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements https://www.biorxiv.org/content/10.64898/2026.02.07.704324v1
February 13, 2026 at 3:11 PM
How does the piRNA pathway solve the self vs. non-self problem? 🧬
Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
Reposted by Baptiste Rafanel
A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements https://www.biorxiv.org/content/10.64898/2026.02.07.704324v1
February 10, 2026 at 5:17 AM
A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements https://www.biorxiv.org/content/10.64898/2026.02.07.704324v1
Reposted by Baptiste Rafanel
Ulrich’s research will help advance our understanding of RNA biology & gene regulation, as well as how these mechanisms might be altered during viral infections & other diseases.
@hohmannulrich.bsky.social comes from the @impvienna.bsky.social / @imbavienna.bsky.social
www.imb.de/about-imb/ne...
@hohmannulrich.bsky.social comes from the @impvienna.bsky.social / @imbavienna.bsky.social
www.imb.de/about-imb/ne...
February 9, 2026 at 11:14 AM
Ulrich’s research will help advance our understanding of RNA biology & gene regulation, as well as how these mechanisms might be altered during viral infections & other diseases.
@hohmannulrich.bsky.social comes from the @impvienna.bsky.social / @imbavienna.bsky.social
www.imb.de/about-imb/ne...
@hohmannulrich.bsky.social comes from the @impvienna.bsky.social / @imbavienna.bsky.social
www.imb.de/about-imb/ne...
Reposted by Baptiste Rafanel
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...
www.biorxiv.org
December 10, 2025 at 3:18 PM
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
Reposted by Baptiste Rafanel
Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis 🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis - Nature Ecology & Evolution
In Caenorhabditis tropicalis, three toxin–antidote elements arose via gene duplication from the essential tRNA-synthetase subunit FARS-3. The ancestral antidote probably acquired affinity for FARS-3, ...
www.nature.com
November 24, 2025 at 9:10 PM
Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Reposted by Baptiste Rafanel
🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.
November 24, 2025 at 1:03 PM
🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.
Reposted by Baptiste Rafanel
Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/
November 19, 2025 at 11:22 PM
Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/
Reposted by Baptiste Rafanel
Lastly, I’m excited to join @imbmainz.bsky.social in 2026 to start my own lab. We'll explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology. tinyurl.com/y4x29ctt
Thanks for reading! 20/20
Thanks for reading! 20/20
Research
IMB Mainz
tinyurl.com
November 19, 2025 at 11:22 PM
Lastly, I’m excited to join @imbmainz.bsky.social in 2026 to start my own lab. We'll explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology. tinyurl.com/y4x29ctt
Thanks for reading! 20/20
Thanks for reading! 20/20
Reposted by Baptiste Rafanel
just in time for the opening of the @hohmannulrich.bsky.social group at @imbmainz.bsky.social
what started as a project on how cells export piRNA precursors, ended up as a tour de force in mRNA export. truly wonderful collaboration with @plaschkalab.bsky.social at the @viennabiocenter.bsky.social
what started as a project on how cells export piRNA precursors, ended up as a tour de force in mRNA export. truly wonderful collaboration with @plaschkalab.bsky.social at the @viennabiocenter.bsky.social
New paper alert! Scientists in Clemens Plaschka’s lab at the IMP and @juliusbrennecke.bsky.social's lab at
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
November 7, 2025 at 6:03 PM
just in time for the opening of the @hohmannulrich.bsky.social group at @imbmainz.bsky.social
what started as a project on how cells export piRNA precursors, ended up as a tour de force in mRNA export. truly wonderful collaboration with @plaschkalab.bsky.social at the @viennabiocenter.bsky.social
what started as a project on how cells export piRNA precursors, ended up as a tour de force in mRNA export. truly wonderful collaboration with @plaschkalab.bsky.social at the @viennabiocenter.bsky.social
Reposted by Baptiste Rafanel
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
October 14, 2025 at 8:34 PM
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
Reposted by Baptiste Rafanel
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)
Molecular basis of polyadenylated RNA fate determination in the nucleus
Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs[1][1],[2][2], that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, in...
www.biorxiv.org
September 22, 2025 at 11:23 PM
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)