Jakob Schnabl-Baumgartner
@jakobschnabl.bsky.social
Postdoc at the FMI (@fmiscience.bsky.social) in Basel, interested in chromatin, biochemistry and SINE transposons
Pinned
ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment
Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence feature...
www.biorxiv.org
📖 Happy to share our recent preprint! www.biorxiv.org/content/10.1... We discovered how SINEs are kept silent: the ChAHP protein complex acts as a molecular brake on POL III transcription retrotransposons. A 🧵:
Reposted by Jakob Schnabl-Baumgartner
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.
(Please repost to reach a broad audience.)
(Please repost to reach a broad audience.)
November 12, 2025 at 4:49 AM
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.
(Please repost to reach a broad audience.)
(Please repost to reach a broad audience.)
Reposted by Jakob Schnabl-Baumgartner
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 6, 2025 at 4:04 PM
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
Reposted by Jakob Schnabl-Baumgartner
great to be at the #EMBOMobileGenome meeting in Heidelberg with a wonderful bunch of colleagues, speakers and attendees.
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
Welcome to Day 1 of 'The mobile genome: genetic and physiological impacts of transposable elements'! 🧬
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
November 4, 2025 at 8:25 PM
great to be at the #EMBOMobileGenome meeting in Heidelberg with a wonderful bunch of colleagues, speakers and attendees.
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
Reposted by Jakob Schnabl-Baumgartner
Now in @embojournal.org: Researchers in @labgrosshans.bsky.social & UCSC found that similar molecular machineries control daily circadian rhythms & developmental timing—showing that evolution can repurpose core timing systems to coordinate both daily cycles & growth. www.fmi.ch/news-events/...
One clock, two functions: from daily rhythms to development
Scientists at the FMI and the University of California-Santa Cruz have found that similar molecular machineries control daily circadian rhythms and developmental timing. Their work in worms shows that...
www.fmi.ch
November 4, 2025 at 8:28 AM
Now in @embojournal.org: Researchers in @labgrosshans.bsky.social & UCSC found that similar molecular machineries control daily circadian rhythms & developmental timing—showing that evolution can repurpose core timing systems to coordinate both daily cycles & growth. www.fmi.ch/news-events/...
Reposted by Jakob Schnabl-Baumgartner
Three FMI researchers—Nanci Winke, @neuramos.bsky.social & @lukas-anneser.bsky.social—have received @snsf.ch Ambizione Grants! Their projects explore how emotions shape behavior, how the brain responds to anxiety treatments, and how brain states affect learning & memory 🧠 www.fmi.ch/news-events/...
Three FMI researchers awarded coveted SNSF Ambizione Grants
Three FMI researchers — Nanci Winke, Arnau Ramos Prats, and Lukas Anneser — have been awarded a prestigious Ambizione Grant from the Swiss National Science Foundation (SNSF). Their work spans from unc...
www.fmi.ch
October 29, 2025 at 9:06 AM
Three FMI researchers—Nanci Winke, @neuramos.bsky.social & @lukas-anneser.bsky.social—have received @snsf.ch Ambizione Grants! Their projects explore how emotions shape behavior, how the brain responds to anxiety treatments, and how brain states affect learning & memory 🧠 www.fmi.ch/news-events/...
Reposted by Jakob Schnabl-Baumgartner
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
October 23, 2025 at 5:10 PM
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
Reposted by Jakob Schnabl-Baumgartner
And the next one: dx.doi.org/10.1038/s44318-025-00585-z . Super-fun collaboration with @partchlab.bsky.social & @gotworms.bsky.social to find similarities between developmental and circadian clocks – supported by @fmiscience.bsky.social Facilities and, financially, @snsf.ch and @erc.europa.eu . 1/n
October 20, 2025 at 1:25 PM
And the next one: dx.doi.org/10.1038/s44318-025-00585-z . Super-fun collaboration with @partchlab.bsky.social & @gotworms.bsky.social to find similarities between developmental and circadian clocks – supported by @fmiscience.bsky.social Facilities and, financially, @snsf.ch and @erc.europa.eu . 1/n
Reposted by Jakob Schnabl-Baumgartner
what you always wanted to know about the molecular choreography of nuclear mRNA packaging and export.
thought-provoking review by our colleagues (local or in the RNA community).
@plaschkalab.bsky.social
@rupertfaraway.bsky.social
@thezenklusen.bsky.social
www.annualreviews.org/content/jour...
thought-provoking review by our colleagues (local or in the RNA community).
@plaschkalab.bsky.social
@rupertfaraway.bsky.social
@thezenklusen.bsky.social
www.annualreviews.org/content/jour...
Mechanisms of Messenger RNA Packaging and Export
The packaging and export of messenger RNA (mRNA) are essential cellular pathways that bridge the nuclear and cytoplasmic phases of eukaryotic gene expression. During their nuclear maturation, mRNAs ar...
www.annualreviews.org
October 18, 2025 at 3:08 PM
what you always wanted to know about the molecular choreography of nuclear mRNA packaging and export.
thought-provoking review by our colleagues (local or in the RNA community).
@plaschkalab.bsky.social
@rupertfaraway.bsky.social
@thezenklusen.bsky.social
www.annualreviews.org/content/jour...
thought-provoking review by our colleagues (local or in the RNA community).
@plaschkalab.bsky.social
@rupertfaraway.bsky.social
@thezenklusen.bsky.social
www.annualreviews.org/content/jour...
Reposted by Jakob Schnabl-Baumgartner
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
www.keystonesymposia.org
October 17, 2025 at 2:36 PM
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
Congratulations, looking forward to more insights into this really unusual flamenco transcript!
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 15, 2025 at 3:55 AM
Congratulations, looking forward to more insights into this really unusual flamenco transcript!
Reposted by Jakob Schnabl-Baumgartner
Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n
October 10, 2025 at 2:17 PM
Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n
Reposted by Jakob Schnabl-Baumgartner
Just out in @science.org: Together with the lab of @wilhelmpalm.bsky.social, we used sequential in-vitro/in-vivo CRISPR screens to decipher metabolic adaptations in tumors. We find that acidosis is a dominant factor that shapes energy metabolism and stress resilience. www.science.org/doi/10.1126/...
October 9, 2025 at 7:37 PM
Just out in @science.org: Together with the lab of @wilhelmpalm.bsky.social, we used sequential in-vitro/in-vivo CRISPR screens to decipher metabolic adaptations in tumors. We find that acidosis is a dominant factor that shapes energy metabolism and stress resilience. www.science.org/doi/10.1126/...
Reposted by Jakob Schnabl-Baumgartner
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Jakob Schnabl-Baumgartner
⚡⚡Excited to announce I'll be starting my lab at the Max Planck Institute of Molecular Genetics (@molgen.mpg.de) in Berlin in December! Leaving sunny California to join a fantastic environment with colleagues who do super cool work.
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab
October 6, 2025 at 1:46 PM
⚡⚡Excited to announce I'll be starting my lab at the Max Planck Institute of Molecular Genetics (@molgen.mpg.de) in Berlin in December! Leaving sunny California to join a fantastic environment with colleagues who do super cool work.
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab
Reposted by Jakob Schnabl-Baumgartner
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
rdcu.be
October 1, 2025 at 6:08 PM
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Reposted by Jakob Schnabl-Baumgartner
We’re looking for a #postdoc to join Lori Passmore’s group, within a programme aimed at understanding addition of mRNA poly(A) tails
More info: www.nature.com/naturecareer...
Closes 06 OCT
#ScienceJobs #PostdocJobs
More info: www.nature.com/naturecareer...
Closes 06 OCT
#ScienceJobs #PostdocJobs
September 18, 2025 at 9:36 AM
We’re looking for a #postdoc to join Lori Passmore’s group, within a programme aimed at understanding addition of mRNA poly(A) tails
More info: www.nature.com/naturecareer...
Closes 06 OCT
#ScienceJobs #PostdocJobs
More info: www.nature.com/naturecareer...
Closes 06 OCT
#ScienceJobs #PostdocJobs
Reposted by Jakob Schnabl-Baumgartner
Do you research endogenous retroviruses (ERVs) or want to learn more about them? 🧬🤔
Consider presenting at or attending AuusiERV - an inaugural online symposium for ERV research in Australia 🇦🇺 (and abroad) 🗺️
Abstracts due 1st October!
events.humanitix.com/aussierv-2025
#ERV #retrovirus
Consider presenting at or attending AuusiERV - an inaugural online symposium for ERV research in Australia 🇦🇺 (and abroad) 🗺️
Abstracts due 1st October!
events.humanitix.com/aussierv-2025
#ERV #retrovirus
AussiERV 2025
AussiERV: Australia’s first symposium dedicated to endogenous retroviruses. Join us for this one-day virtual event on November 7th!
events.humanitix.com
September 27, 2025 at 7:28 AM
Do you research endogenous retroviruses (ERVs) or want to learn more about them? 🧬🤔
Consider presenting at or attending AuusiERV - an inaugural online symposium for ERV research in Australia 🇦🇺 (and abroad) 🗺️
Abstracts due 1st October!
events.humanitix.com/aussierv-2025
#ERV #retrovirus
Consider presenting at or attending AuusiERV - an inaugural online symposium for ERV research in Australia 🇦🇺 (and abroad) 🗺️
Abstracts due 1st October!
events.humanitix.com/aussierv-2025
#ERV #retrovirus
Reposted by Jakob Schnabl-Baumgartner
We’re excited to host the next TriRhena Gene Regulation Club on November 5!
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Attendance is free, but registration (by October 20) is mandatory 👇🏽
👉 The next TriRhena Gene Regulation Club takes place at the Friedrich Miescher Institute @fmiscience.bsky.social in Basel.
📅 Nov. 5th, 2025 (14:00-20:00)
📌 FMI, Basel
✍️ Registration deadline: Oct. 20th, 2025
Attendance is free 💸 , but registration mandatory:
www.ie-freiburg.mpg.de/gene-regulat...
📅 Nov. 5th, 2025 (14:00-20:00)
📌 FMI, Basel
✍️ Registration deadline: Oct. 20th, 2025
Attendance is free 💸 , but registration mandatory:
www.ie-freiburg.mpg.de/gene-regulat...
TriRhena Gene Regulation Club
The TriRhena Gene Regulation Club is a one-day symposium that brings together researchers from France (IGBMC), Germany (MPI-IE) and Switzerland (FMI) who share a common interest in gene regulation.
www.ie-freiburg.mpg.de
September 26, 2025 at 8:25 AM
We’re excited to host the next TriRhena Gene Regulation Club on November 5!
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Reposted by Jakob Schnabl-Baumgartner
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 24, 2025 at 9:45 PM
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
Reposted by Jakob Schnabl-Baumgartner
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 Jakob Schnabl-Baumgartner
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 Jakob Schnabl-Baumgartner
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
September 20, 2025 at 4:10 PM
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
Reposted by Jakob Schnabl-Baumgartner
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 Jakob Schnabl-Baumgartner
wrong bioRxiv link here, sorry.
the correct link to the collaboration with Torben and Clemens is:
www.biorxiv.org/content/10.1...
the correct link to the collaboration with Torben and Clemens is:
www.biorxiv.org/content/10.1...
September 17, 2025 at 4:55 PM
wrong bioRxiv link here, sorry.
the correct link to the collaboration with Torben and Clemens is:
www.biorxiv.org/content/10.1...
the correct link to the collaboration with Torben and Clemens is:
www.biorxiv.org/content/10.1...
Reposted by Jakob Schnabl-Baumgartner
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...