Jakob Farnung
@jakobfarnung.bsky.social
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PostDoc Schulman Lab, MPI Biochemistry; formerly Bode Lab, ETH Zürich
pinned post!
🎉Super excited to share our story on how the substrate receptor FBXO31 functions as a quality control factor by recognizing amides. This has been an amazing collaboration between Bode lab and
@jcornlab.bsky.social
. Special shutout goes to
@matthiasmuhar.bsky.social
www.nature.com/articles/s41...
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C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
https://www.nature.com/articles/s41586-024-08475-w
10 months ago
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Jakob Farnung
David Bartel's Lab
6 days ago
Check out the latest work from our lab, led by Daniel Lin and Lara Elcavage:
www.biorxiv.org/content/10.1...
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mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers the degradation of a microRNA. This target-directed microRNA degradatio...
https://www.biorxiv.org/content/10.1101/2025.11.06.686990v1
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Jakob Farnung
Leo Kiss
9 days ago
Have a look at this Tools of the Trade Article I wrote for
@natrevmcb.nature.com
on decoding
#ubiquitin
signals inside cells using UbiREAD! Many thanks to
@lisaheinke.bsky.social
for the opportunity to write this TotT!
add a skeleton here at some point
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Jakob Farnung
Nature Reviews Molecular Cell Biology
10 days ago
ICYMI: New Online! Decoding ubiquitin signals inside cells
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Decoding ubiquitin signals inside cells
Nature Reviews Molecular Cell Biology, Published online: 31 October 2025; doi:10.1038/s41580-025-00919-zIn this Tools of the Trade article, Kiss (Schulman lab) discusses the development of UbiREAD, a method that delivers in vitro-ubiquitinated protein reporters into cells to systematically assess how different ubiquitin chain configurations affect protein stability and degradation.
https://bit.ly/4oeUIzA
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Lucas Farnung
3 months ago
🧬 Transcription elongation by RNA polymerase II relies on a web of elongation factors. Our new work shows how IWS1 acts as a modular scaffold to stabilize & stimulate elongation. Fantastic work by Della Syau!
www.biorxiv.org/content/10.1...
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Carolin Klose
3 months ago
Excited to share our latest study in
@natcomms.nature.com
, where we characterize the chaperone function of the ER membrane protein complex (EMC)—supporting membrane protein biogenesis beyond insertion! 1/9
www.nature.com/articles/s41...
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The EMC acts as a chaperone for membrane proteins - Nature Communications
Membrane proteins are essential for any cell but difficult to fold. Here, the authors show that the EMC acts as a chaperone for membrane proteins. They dissect client recognition and provide a molecul...
https://www.nature.com/articles/s41467-025-62109-x#article-info
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Jakob Farnung
Leo Kiss
5 months ago
Excited about
#ubiquitin
and
#TPD
? Then join us tomorrow for the latest instalment of the
@danafarber.bsky.social
Targeted Protein Degradation Webinar where Kimberly Stegmaier and I will present our latest work.
dfci.zoom.us/webinar/regi...
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Jakob Farnung
Harvard Med Cell Biology
5 months ago
Congratulations to our own Lucas Farnung
@lucas.farnunglab.com
who has been named as one of 30 Freeman Hrabowski Scholars for 2025 by the Howard Hughes Medical Institute (HHMI). So well deserved deserved !!
www.hhmi.org/programs/fre...
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The 2025 Freeman Hrabowski Scholars | HHMI
Freeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields.
https://www.hhmi.org/programs/freeman-hrabowski-scholars/2025-scholars
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Jakob Farnung
Leo Kiss
5 months ago
Schulman lab is ready for the GRK2243 Symposium: Understanding ubiquitination: from molecular mechanisms to disease in würzburg
#wUeBI2025
@grk2243.bsky.social
@jakobfarnung.bsky.social
@samuelmaiwald.bsky.social
@hannahbkmpr.bsky.social
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Super cool story on branched UB chain formation. Congrats Sam!
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6 months ago
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Jakob Farnung
Samuel Maiwald
6 months ago
Excited to share our latest study on how K29/K48-branched
#ubiquitin
chains are forged by the
#E3
ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s!
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
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TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains - Nature Structural & Molecular Biology
Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation sha...
https://www.nature.com/articles/s41594-025-01561-1
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Jakob Farnung
Lucas Farnung
6 months ago
 🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link:
authors.elsevier.com/a/1l2ik3vVUP...
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Jakob Farnung
Haselbach Lab
7 months ago
New Preprint: We have solved the structure of the proteasome in complex with two different ubiquitin chains:
www.biorxiv.org/content/10.1...
This work is spearheaded by PhD Student Sascha Amann Let me walk you through it 🧵 1/9
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Structural basis for the ubiquitin chain recognition of the human 26S proteasome
Proteasomal degradation is a fundamental process for all eukaryotic life. A protein destined for degradation is first tagged with a polyubiquitin chain, which is selected by the proteasome. Different ...
https://www.biorxiv.org/content/10.1101/2025.04.07.647569v1
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If you are interested in Ubiquitin this paper is a must read! Congrats Leo!
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8 months ago
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Jakob Farnung
9 months ago
It's finally out – actually out and in print! Many thanks to
@jcornlab.bsky.social
@matthiasmuhar.bsky.social
@jakobfarnung.bsky.social
and all the fantastic collaborators. What started as pure curiosity lead to an amazing find!
www.nature.com/articles/s41...
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C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
https://www.nature.com/articles/s41586-024-08475-w
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Jakob Farnung
Brian Liau
9 months ago
Today in
@nature.com
we share our back-to-back stories with Ning Zheng’s lab revealing chemical-genetic convergence between a molecular glue degrader & E3 ligase cancer mutations. 1/5
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Jakob Farnung
Lucas Farnung
10 months ago
Excited about mechanistic biology and processes in the cell's nucleus? Join our lab as a post-doctoral researcher! We have a state-of-the-art cryo-EM facility (new microscopes coming!), a brand-new lab space, and a vibrant community at HMS! DM/email me or check
farnunglab.com
for more info.
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Farnung Lab
https://farnunglab.com
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Jakob Farnung
Lucas Farnung
10 months ago
Our story on the mechanism of co-transcriptional histone mark deposition is now officially out:
www.science.org/doi/10.1126/...
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Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription
During transcription, RNA polymerase II traverses through chromatin, and posttranslational modifications including histone methylations mark regions of active transcription. Histone protein H3 lysine ...
https://www.science.org/doi/10.1126/science.adn6319
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Jakob Farnung
Jacob Corn
10 months ago
Cells are filled with toxic stuff that damages healthy proteins. Is that garbage just left to rot on the curb? No way! Ubiquitin ligases have evolved to recognize chemical damage and clean it up!
www.nature.com/articles/s41...
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C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
https://www.nature.com/articles/s41586-024-08475-w
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reposted by
Jakob Farnung
Clausen Lab
10 months ago
scary but fascinating - cells have a degradation pathway that hunts down C-terminal scars (amides!) on damaged proteins. just wow. chemical biology plus CRISPR at its best. big congrats to all authors!
www.nature.com/articles/s41...
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C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
https://www.nature.com/articles/s41586-024-08475-w
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reposted by
Jakob Farnung
Micha Rapé Lab
10 months ago
Very excited to highlight @jcornlab's beautiful work on the E3 ligase SCF-FBXO31, which recognizes chemically damaged proteins. Mutations in FBXO31 cause disease by substrate-rewiring, really cool. Congratulations to all authors!
rdcu.be/d7WGc
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Signs of damage that drive protein degradation | Nature
Many environmental toxins damage proteins, which then must be removed to avoid dangerous protein aggregation and disease. How cells dispose of chemically modified proteins has been unclear, but a discovery offers some clues. How the stress-response machinery eliminates damaged proteins.
https://rdcu.be/d7WGc
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Jakob Farnung
Leo Kiss
10 months ago
Super exiting new work revealing a novel quality control pathway for c-terminal amides!
add a skeleton here at some point
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Jakob Farnung
Thomas Arnesen
10 months ago
On the degradation of damaged cellular proteins via C-terminal amidation. By Alfred Freeberg &
@micharapelab.bsky.social
.
@ispt-proteinterm.bsky.social
www.nature.com/articles/d41...
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Signs of damage that drive protein degradation
How the stress-response machinery eliminates damaged proteins.
https://www.nature.com/articles/d41586-025-00082-7
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🎉Super excited to share our story on how the substrate receptor FBXO31 functions as a quality control factor by recognizing amides. This has been an amazing collaboration between Bode lab and
@jcornlab.bsky.social
. Special shutout goes to
@matthiasmuhar.bsky.social
www.nature.com/articles/s41...
loading . . .
C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
https://www.nature.com/articles/s41586-024-08475-w
10 months ago
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Jakob Farnung
Seychelle Vos
11 months ago
Our paper describing a novel DNA binding mode for MORC2 is published! Congratulations to Nika Fendler on her first, first author paper. This was an epic effort and revealed many new and unpredicted functions for MORC2. You can read about it here:
tinyurl.com/MORC2-DNA
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Jakob Farnung
Clausen Lab
11 months ago
🎄 xmas preprint 🎄 we are excited to share our cryo-EM structure of UBR4 in complex with KCMF1 and CALM1. the PQC ligase forms a massive ubiquitination arena, primed to amplify ubiquitin chains (E4 activity) and boost degradation of defective proteins.
www.biorxiv.org/content/10.1...
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Jakob Farnung
Lucas Farnung
11 months ago
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of
@jonmarkert.bsky.social
!
tinyurl.com/setd2
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Nina Hartrampf
11 months ago
Our Synthesis Tag (SynTag) for the synthesis of aggregating peptides and proteins is now published in JACS 🥳 Congratulations to first authors Héloïse & Elyse and everyone else involved ✨✨
pubs.acs.org/doi/10.1021/...
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A Versatile “Synthesis Tag” (SynTag) for the Chemical Synthesis of Aggregating Peptides and Proteins
Solid-phase peptide synthesis (SPPS) and native chemical ligation (NCL) are powerful methods for obtaining peptides and proteins that are otherwise inaccessible. Nonetheless, numerous sequences are di...
https://pubs.acs.org/doi/10.1021/jacs.4c14247#
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SFB Targeted Protein Degradation
12 months ago
SAVE THE DATE 🗓️Ubiquitin & Friends Symposium: 8-9 May 2025 in Vienna! Registration will open🔜 Keep an eye out for the announcement 👀 ✨guest speaker lineup👇🧵 +talks from abstracts! Great chance for
#ECRs
to meet with peers & experts in a friendly setting! 🔗
www.protein-degradation.org/symposium/
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Jakob Farnung
Malte Gersch
12 months ago
Could't think of a better inaugural post here. Very excited to share that our manuscript on the "Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53" was published today at Nature Chemical Biology. Congratulations Kim, Kai, and all authors!
www.nature.com/articles/s41...
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