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Baptiste Rafanel

@baptisterafanel.bsky.social
92 followers 121 following 13 posts

Transposons, Transcription, piRNA, Drosophila PhD Student in the Brennecke lab at IMBA

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Reposted by Baptiste Rafanel
Cedric Feschotte @cedricfeschotte.bsky.social · 24/09/2026
Thrilled to see this published today! Truly special because we made the initial discovery >15 yrs ago! We found two copies of a human gene called BC200 embedded in a human poxvirus. BC200 blurs the line between gene & transposon—both functional & mutagenic! www.science.org/doi/10.1126/... 🧵1/n
science.org
Escape of the BC200 gene to a human poxvirus reveals its persistent transposition in primates
Transposable elements mobilize within and occasionally between genomes, including from host to virus. We identified two insertions of the human BC200 noncoding RNA gene in the poxvirus molluscum conta...
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Arjuna Rajakumar PhD @arjunarajakumar.bsky.social · 19/09/2026
So proud of my lab mate @sagrill.bsky.social (whose on the job market 👀) for this magnum opus from @remlehmann.bsky.social lab @whiteheadinstitute.bsky.social ScRNA-seq of 🪰 germ cells reveals new biology, answers age old questions, and proposes new paradigms! 1/8 www.biorxiv.org/content/10.6...
Drosophila stage 10b embryo w/HCR staining marking two germ cell clusters. One will successfully colonize the gonad and the other, like tears in the rain, will be lost forever
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Peter Andersen @germline.bsky.social · 02/09/2026
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! /+
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Peter Andersen @germline.bsky.social · 29/08/2026
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 :-)
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
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...
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Peiwei Chen @peiwei-chen.bsky.social · 17/07/2026
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...
biorxiv.org
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...
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Jakob Schnabl-Baumgartner @jakobschnabl.bsky.social · 17/07/2026
Cool study! TEs in the male Drosophila germline jump in bursts
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Jakob Schnabl-Baumgartner @jakobschnabl.bsky.social · 07/07/2026
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 👀 🧫 🧬
cell.com
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...
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Gainetdinov lab at NYU Biology @gainetdinov.bsky.social · 23/05/2026
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...
biorxiv.org
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The Cecere Laboratory @cecerelab.bsky.social · 22/05/2026
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
nature.com
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...
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Alejandro Burga @arburga.bsky.social · 18/05/2026
🧬 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:
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Baptiste Rafanel @baptisterafanel.bsky.social · 06/05/2026
I'm super happy to finally see the paper published ! Check out the full story here: link.springer.com/article/10.1...
link.springer.com
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Ralf Jansen @ralfjansen.bsky.social · 04/05/2026
Five years after a short rotation in the Peters lab, I’m happy to see this cool story spearheaded by Gordana Wutz finally published.
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Peter Andersen @germline.bsky.social · 17/04/2026
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! 🙏
Flyer for a PhD position in the Andersen Lab on Genetic Innovation at Aarhus University, Denmark. Title: "Transcriptional regulation in Drosophila germline development." Start date between August 2026 and January 2027, application deadline May 1, 2026. The flyer describes a project on germline-specific transcription factor paralogs, funded by the Novo Nordisk Foundation (PARAGLIDE programme). Includes example data figures: genomics browser tracks, a proximity-labeling proteomics volcano plot, and fluorescence microscopy of germline tissue. Contact: pra@mbg.au.dk. Apply via phd.nat.au.dk.
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Emilie Brasset @emiliebrasset.bsky.social · 09/04/2026
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 👇👇
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Peter Andersen @germline.bsky.social · 01/04/2026
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!
phd.nat.au.dk
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Dominik Handler @86dominik.bsky.social · 13/02/2026
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)
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 10/02/2026
A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements www.biorxiv.org/content/10.64898/20…
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Institute of Molecular Biology (IMB) @imbmainz.bsky.social · 09/02/2026
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...
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Jacob Schreiber @jmschreiber91.bsky.social · 10/12/2025
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...
biorxiv.org
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...
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Polina Tikanova @polinatikanova.bsky.social · 24/11/2025
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?
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Alejandro Burga @arburga.bsky.social · 24/11/2025
🪱 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.
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Ulrich Hohmann @hohmannulrich.bsky.social · 19/11/2025
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/
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Ulrich Hohmann @hohmannulrich.bsky.social · 19/11/2025
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
tinyurl.com
Research
IMB Mainz
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Julius Brennecke @juliusbrennecke.bsky.social · 07/11/2025
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
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Dominik Handler @86dominik.bsky.social · 14/10/2025
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)
Graphical abstract: The Drosophila OSC Genome as a resource for transposon and piRNA biology. The figure illustrates the workflow and key findings. Left: De novo genome assembly using Oxford Nanopore Technologies (ONT) long reads and Hi-C data generates a phased assembly distinguishing unique (blue) and repetitive (orange) sequences. Dot plot comparison between OSC-r1.01 and dm6 reference genomes shows overall synteny with extensive structural variation. Middle: A freely accessible UCSC genome browser session displays multi-omics data tracks including gene models, transposon insertions, chromatin accessibility, transcription, small RNAs, and histone modifications. Right: New insights into flamenco piRNA cluster biology reveal >730 kb transcribed from a single promoter without major splicing. Tethering assays demonstrate long-range silencing effects across the locus, and genome browser tracks show coordinated regulation of piRNA production, transcription, and chromatin state. This resource enables comprehensive studies of transposon regulation and piRNA pathway function in a widely-used Drosophila cell line.
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Ulrich Hohmann @hohmannulrich.bsky.social · 23/09/2025
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)
biorxiv.org
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...
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Júlia Portell Montserrat @julsportell.bsky.social · 17/09/2025
My first first-author paper is out!🎉 Here we propose a model where a silencing complex, PIWI*, assembles on target RNAs to recruit effectors and shut down transposon activity. Huge thanks to the Brennecke and Plaschka labs, especially Julius and Clemens, and all co-authors!
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Baptiste Rafanel @baptisterafanel.bsky.social · 14/08/2025
1/ How do animals develop immunity against a newly encountered transposable element from scratch? Our study reveals that the mobility of TEs is their Achilles heel, allowing hosts to develop a powerful small RNA-mediated silencing response. www.biorxiv.org/content/10.1...
biorxiv.org
Antisense transposon insertions into host genes trigger piRNA mediated immunity
Transposable elements pose a persistent threat to genome integrity, yet how host defense systems adapt to newly invading elements remains poorly understood. Here, we reveal how Drosophila melanogaster...
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