Ralf Jansen
@ralfjansen.bsky.social
BIF PhD fellow in the Brennecke lab (@juliusbrennecke.bsky.social) at IMBA (@imbavienna.bsky.social), Vienna
Interested in transcription and RNA export.
http://www.oeaw.ac.at/imba/research/julius-brennecke
Interested in transcription and RNA export.
http://www.oeaw.ac.at/imba/research/julius-brennecke
Reposted by Ralf Jansen
I’m happy to share the main result of my PhD, which you can find on bioRxiv www.biorxiv.org/content/10.6.... If you are interested in learning about a new way to perform DNA-PAINT multiplexing, which we call Combi-PAINT, or if you are interested in the study of mRNA conformation, keep reading! 1/10
January 26, 2026 at 11:31 AM
I’m happy to share the main result of my PhD, which you can find on bioRxiv www.biorxiv.org/content/10.6.... If you are interested in learning about a new way to perform DNA-PAINT multiplexing, which we call Combi-PAINT, or if you are interested in the study of mRNA conformation, keep reading! 1/10
Reposted by Ralf Jansen
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
TLDR; TFIID behaves differently depending on promoter type. More below:
High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo
TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with and functions at different promoter types in vivo ...
www.biorxiv.org
January 9, 2026 at 6:30 PM
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
TLDR; TFIID behaves differently depending on promoter type. More below:
Reposted by Ralf Jansen
Do transcriptional activators work on any promoter? Our data says no. 🙅♂️
Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬
Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬
December 29, 2025 at 7:30 PM
Do transcriptional activators work on any promoter? Our data says no. 🙅♂️
Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬
Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬
Reposted by Ralf Jansen
Very happy to share my postdoc work (on preprint), where we try to understand a long-standing transcription-silencing paradox, and uncovered a hidden RNA decay arm of nuclear piRNA pathway, see detailed threads quoted from @juliusbrennecke.bsky.social
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1
December 22, 2025 at 7:38 PM
Very happy to share my postdoc work (on preprint), where we try to understand a long-standing transcription-silencing paradox, and uncovered a hidden RNA decay arm of nuclear piRNA pathway, see detailed threads quoted from @juliusbrennecke.bsky.social
Reposted by Ralf Jansen
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1
December 22, 2025 at 6:14 PM
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
Reposted by Ralf Jansen
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
www.science.org
December 4, 2025 at 8:18 PM
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Reposted by Ralf Jansen
🪱 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 Ralf Jansen
Congrats to Dr. @julsportell.bsky.social
on her PhD! Her journey as a joint student (Brennecke/Our Lab) led to key insights into gene silencing. Paper: www.cell.com/molecular-ce.... Journey: www.viennabiocenter.org/about/news/t.... CP.
on her PhD! Her journey as a joint student (Brennecke/Our Lab) led to key insights into gene silencing. Paper: www.cell.com/molecular-ce.... Journey: www.viennabiocenter.org/about/news/t.... CP.
November 20, 2025 at 3:56 PM
Congrats to Dr. @julsportell.bsky.social
on her PhD! Her journey as a joint student (Brennecke/Our Lab) led to key insights into gene silencing. Paper: www.cell.com/molecular-ce.... Journey: www.viennabiocenter.org/about/news/t.... CP.
on her PhD! Her journey as a joint student (Brennecke/Our Lab) led to key insights into gene silencing. Paper: www.cell.com/molecular-ce.... Journey: www.viennabiocenter.org/about/news/t.... CP.
Reposted by Ralf Jansen
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 Ralf Jansen
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 Ralf Jansen
New paper alert! Scientists in Julius Brennecke’s lab at IMBA and Clemens Plaschka’s lab at @impvienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: https://imba.science/3Xl2hJ3
November 6, 2025 at 4:00 PM
New paper alert! Scientists in Julius Brennecke’s lab at IMBA and Clemens Plaschka’s lab at @impvienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: https://imba.science/3Xl2hJ3
Reposted by Ralf Jansen
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Wilkinson Lab
We discover and study reverse transcriptases
wilkinsonlab.bio
October 31, 2025 at 7:00 PM
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Reposted by Ralf Jansen
What’s it like doing a PhD between two labs? In our latest Behind the Science, Júlia Portell i de Montserrat, shared PhD student in the Plaschka lab at the IMP and the Brennecke lab at @imbavienna.bsky.social, tells us more about her unusual but rewarding PhD journey: bit.ly/3IHXtdp
October 13, 2025 at 3:07 PM
What’s it like doing a PhD between two labs? In our latest Behind the Science, Júlia Portell i de Montserrat, shared PhD student in the Plaschka lab at the IMP and the Brennecke lab at @imbavienna.bsky.social, tells us more about her unusual but rewarding PhD journey: bit.ly/3IHXtdp
Reposted by Ralf Jansen
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 Ralf Jansen
Thrilled to share that I’ll be joining @imbmainz.bsky.social in February 2026 to start my own group!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
October 12, 2025 at 8:19 PM
Thrilled to share that I’ll be joining @imbmainz.bsky.social in February 2026 to start my own group!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
Reposted by Ralf Jansen
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)
Reposted by Ralf Jansen
I am excited to announce that I will be moving to IMB Mainz next year! The Winter call for the IPP PhD program is now open; if you are interested in maternal #mRNA regulation and #translation in early vertebrate development, please apply! Deadline: 16 October.
More info: www.imb.de/students-pos...
More info: www.imb.de/students-pos...
Laura Lorenzo Orts
IMB Mainz
www.imb.de
September 15, 2025 at 12:13 PM
I am excited to announce that I will be moving to IMB Mainz next year! The Winter call for the IPP PhD program is now open; if you are interested in maternal #mRNA regulation and #translation in early vertebrate development, please apply! Deadline: 16 October.
More info: www.imb.de/students-pos...
More info: www.imb.de/students-pos...
Reposted by Ralf Jansen
Love RNA biology?
Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇).
PhD student/postdoc position co-supervised by Clemens Plaschka & myself.
DM or email us if you’d like to know more!
@vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇).
PhD student/postdoc position co-supervised by Clemens Plaschka & myself.
DM or email us if you’d like to know more!
@vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 18, 2025 at 2:34 PM
Love RNA biology?
Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇).
PhD student/postdoc position co-supervised by Clemens Plaschka & myself.
DM or email us if you’d like to know more!
@vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇).
PhD student/postdoc position co-supervised by Clemens Plaschka & myself.
DM or email us if you’d like to know more!
@vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
Reposted by Ralf Jansen
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!
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!
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 17, 2025 at 1:00 PM
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!
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!
Reposted by Ralf Jansen
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 17, 2025 at 10:39 AM
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
Reposted by Ralf Jansen
Close inter-lab collaborations with shared PhD students and postdocs are the future!
Julia is the hero of this work, she is currently looking for postdoc labs …
Julia is the hero of this work, she is currently looking for postdoc labs …
📰 New paper alert!
In a collaborative project with the lab of Clemens Plaschka at the IMP, the lab of Julius Brennecke has revealed how PIWI proteins kickstart transposon silencing in reproductive cells.
The findings are published in Molecular Cell: www.sciencedirect.com/science/arti...
In a collaborative project with the lab of Clemens Plaschka at the IMP, the lab of Julius Brennecke has revealed how PIWI proteins kickstart transposon silencing in reproductive cells.
The findings are published in Molecular Cell: www.sciencedirect.com/science/arti...
How cells lock down “jumping genes”:
Researchers from IMBA and IMP identify the first protein interactions that trigger PIWI–piRNA–mediated transposon silencing, using AlphaFold predictions, genetics, biochemistry and cell biology.
Read more: www.viennabiocenter.org/about/news/t...
Researchers from IMBA and IMP identify the first protein interactions that trigger PIWI–piRNA–mediated transposon silencing, using AlphaFold predictions, genetics, biochemistry and cell biology.
Read more: www.viennabiocenter.org/about/news/t...
September 9, 2025 at 10:59 AM
Close inter-lab collaborations with shared PhD students and postdocs are the future!
Julia is the hero of this work, she is currently looking for postdoc labs …
Julia is the hero of this work, she is currently looking for postdoc labs …
Reposted by Ralf Jansen
Target RNA recognition drives PIWI∗ complex assembly for transposon silencing
Target RNA recognition drives PIWI∗ complex assembly for transposon silencing
Portell-Montserrat et al. reveal that target RNA recognition by PIWI-piRNA complexes triggers the assembly of conserved PIWI∗ complexes, molecular platforms that recruit silencing effectors in both the nucleus and cytoplasm. This mechanism, conserved across animals, explains how piRNA pathways couple target recognition to transposon silencing.
dlvr.it
September 8, 2025 at 11:33 AM
Target RNA recognition drives PIWI∗ complex assembly for transposon silencing
Reposted by Ralf Jansen
New paper by our Plaschka lab with Brennecke’s lab at IMBA!
Researchers at the Vienna BioCenter have solved a 20-year-old mystery in genome biology, revealing how PIWI proteins engage partner molecules to silence “jumping genes” that threaten genetic stability.
Researchers at the Vienna BioCenter have solved a 20-year-old mystery in genome biology, revealing how PIWI proteins engage partner molecules to silence “jumping genes” that threaten genetic stability.
How cells lock down “jumping genes”:
Researchers from IMBA and IMP identify the first protein interactions that trigger PIWI–piRNA–mediated transposon silencing, using AlphaFold predictions, genetics, biochemistry and cell biology.
Read more: www.viennabiocenter.org/about/news/t...
Researchers from IMBA and IMP identify the first protein interactions that trigger PIWI–piRNA–mediated transposon silencing, using AlphaFold predictions, genetics, biochemistry and cell biology.
Read more: www.viennabiocenter.org/about/news/t...
September 8, 2025 at 9:10 AM
New paper by our Plaschka lab with Brennecke’s lab at IMBA!
Researchers at the Vienna BioCenter have solved a 20-year-old mystery in genome biology, revealing how PIWI proteins engage partner molecules to silence “jumping genes” that threaten genetic stability.
Researchers at the Vienna BioCenter have solved a 20-year-old mystery in genome biology, revealing how PIWI proteins engage partner molecules to silence “jumping genes” that threaten genetic stability.
So happy to see the PhD work of Emilio Santillán published—what an amazingly elegant piece of work!!
Working with him and Luisa at the IMP was a great and formative experience.
Working with him and Luisa at the IMP was a great and formative experience.
Our work on the function of miR-51/miR-100 is out! miR-100 is widely conserved across eumetazoans but its function has been mysterious. Emilio Santillán found in worms it regulates signaling and extracellular matrix genes, some of which seem to be conserved targets! www.science.org/doi/10.1126/...
An ancient and essential miRNA family controls cellular interaction pathways in C. elegans
A microRNA that arose at the origin of eumetazoans regulates cell adhesion and signaling in C. elegans through conserved targets.
www.science.org
September 3, 2025 at 7:46 PM
So happy to see the PhD work of Emilio Santillán published—what an amazingly elegant piece of work!!
Working with him and Luisa at the IMP was a great and formative experience.
Working with him and Luisa at the IMP was a great and formative experience.
Reposted by Ralf Jansen
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...
www.biorxiv.org/content/10.1...
August 14, 2025 at 5:09 PM
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...
www.biorxiv.org/content/10.1...