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Lucas Farnung

@lucas.farnunglab.com

1.7K followers 120 following 120 posts

Assistant Professor of Cell Biology at Harvard Medical School | HHMI Freeman Hrabowski Scholar | Nexus of chromatin, transcription, replication, and epigenetics. farnunglab.com

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Lucas Farnung @lucas.farnunglab.com · Apr 6

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

Lucas Farnung @lucas.farnunglab.com · 9h

Della Syau successfully defended her PhD thesis today. Congrats, Dr. Syau. Strike #3!

Farnung Lab with newly minted Dr. Della Syau!

Lucas Farnung @lucas.farnunglab.com · 4d

We have added additional functionalities including a collapsible protein pane and zoom scrolling. domaindesigner.farnunglab.com

Lucas Farnung @lucas.farnunglab.com · 9d

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

Reposted by Lucas Farnung

Harvard Med Cell Biology @harvardcellbio.bsky.social · 6d

Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life

In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...

www.biorxiv.org

Lucas Farnung @lucas.farnunglab.com · 9d

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

Reposted by Lucas Farnung

Quartzy @quartzy.com · 12d

🌟 Our customers never stop innovating.
This NFC-to-Quartzy workflow is a perfect example of why we built an API — so labs can create the exact tools they need to make science run smoother. Check out how they did it.

Lucas Farnung @lucas.farnunglab.com · 12d

🚀 Ordering lab supplies just got way easier in our lab.
We built a workflow (github.com/farnunglab/N...) where tapping an NFC tag on a reagent bottle automatically triggers an order request in Quartzy. No more scribbling notes or hunting for a computer. Here’s how 👇

Lucas Farnung @lucas.farnunglab.com · 12d

Amazing idea by @sophiero.bsky.social and implemented in just three days.

Lucas Farnung @lucas.farnunglab.com · 12d

✅ Benefits:
Fast: takes seconds
Context-aware: order reagents where you actually use them
Reliable: less chance of forgetting to order later
🛠️ Implementation details:
We use NFC tags programmed with URLs that call our Cloudflare Worker. The Worker authenticates & sends the request to Quartzy’s API.

Lucas Farnung @lucas.farnunglab.com · 12d

📱 The idea:
What if a physical action—like tapping a reagent bottle with your phone—could trigger the digital ordering process directly?
🔗 Our solution:
Each common reagent gets an NFC tag
Tap the tag with your phone
The tag hits a Cloudflare Worker
The Worker submits the order request to Quartzy

Lucas Farnung @lucas.farnunglab.com · 12d

🧪 The problem:
Labs constantly run out of common reagents. But ordering them is tedious—usually you need a computer, login, and multiple clicks. Often you realize something is low while you’re at the bench, not at your desk.

Lucas Farnung @lucas.farnunglab.com · 12d

🚀 Ordering lab supplies just got way easier in our lab.
We built a workflow (github.com/farnunglab/N...) where tapping an NFC tag on a reagent bottle automatically triggers an order request in Quartzy. No more scribbling notes or hunting for a computer. Here’s how 👇

Lucas Farnung @lucas.farnunglab.com · 13d

Find up to date links to the Farnung lab's cloning, experiment designer, and buffer preparation software tools here: www.farnunglab.com/tools

Services 3 — Farnung Lab

www.farnunglab.com

Reposted by Lucas Farnung

Oli Clarke @olibclarke.bsky.social · 26d

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

Lucas Farnung @lucas.farnunglab.com · Sep 4

Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.

The Farnung Lab celebrates Martin Filipovski's thesis defense.

Lucas Farnung @lucas.farnunglab.com · Sep 4

Congrats, Hanneke! Fantastic achievement.

Lucas Farnung @lucas.farnunglab.com · Sep 3

In our IWS1 story, we also visualize the histone reader LEDGF PWWP domain on a transcribed downstream nucleosome. Because the PWWP requires both DNA gyres for binding, it binds to the promoter-distal side of the nucleosome during transcription through the nucleosome.

LEDGF PWWP (pink) binds the transcribed downstream nucleosome. A cryo-EM map (grey) verifies the positioning of the activated transcription elongation complex in relation to the downstream nucleosome.

Reposted by Lucas Farnung

Harvard Med Cell Biology @harvardcellbio.bsky.social · Aug 29

New insights into transcriptional elongation by IWS1 from the @lucas.farnunglab.com lab. This work establishes IWS1 as a scaffold to organiz the elongation complex, illustrating how disordered regions regulate transcription elongationhttps://www.biorxiv.org/content/10.1101/2025.08.28.672863v1

Structure and function of IWS1 in transcription elongation

Transcription elongation by RNA polymerase II is a tightly regulated process that requires coordinated interactions between elongation factors. IWS1 (Interacts with SPT6) has been implicated as a core...

www.biorxiv.org

Lucas Farnung @lucas.farnunglab.com · Aug 29

Also check out related work: www.nature.com/articles/s41...

IWS1 positions downstream DNA to globally stimulate Pol II elongation - Nature Communications

Although IWS1 has been implicated in transcription-coupled processes, its direct role in RNA polymerase II function remained undefined. Here, the authors demonstrate that IWS1 enhances Pol II elongati...

Lucas Farnung @lucas.farnunglab.com · Aug 29

🛡️ IWS1 shields the elongation complex from RECQL5 inhibition & helps position LEDGF on transcribed nucleosomes 📖. Together, we present the most complete structure of a mammalian elongation complex to date.

Lucas Farnung @lucas.farnunglab.com · Aug 29

⚡ Structure–function assays reveal a division of labor: some motifs anchor IWS1 to Pol II ⚓, while others directly boost transcription processivity 🚀 across DNA & chromatin.

Lucas Farnung @lucas.farnunglab.com · Aug 29

Using cryo-EM, we discovered that the disordered C-terminal tail of IWS1 contains short linear motifs (SLiMs) 🎯 that engage Pol II subunits (RPB1, RPB2, RPB5) & elongation factors DSIF, SPT6, ELOF1

Lucas Farnung @lucas.farnunglab.com · Aug 29

🧬 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...

Reposted by Lucas Farnung

Sarah Hainer @hainerlab.bsky.social · Aug 28

Our collaborative paper with the Arndt lab is out today: doi.org/10.1093/nar/... (originally bioRxiv: www.biorxiv.org/content/10.1...). Here we asked the question of how CHD1 localizes to chromatin.

A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes

Abstract. The nucleosome remodeler Chd1 is required for the re-establishment of nucleosome positioning in the wake of transcription elongation by RNA Polym

Lucas Farnung @lucas.farnunglab.com · Aug 17

Publication date? The column system hasn’t changed at all!

Reposted by Lucas Farnung

Harvard Med Cell Biology @harvardcellbio.bsky.social · Aug 7

New work from the @sshaolab.bsky.social lab with Gu and Elledge labs reveals structure of TXNL1 bound to proteasome and mechanism of its ubiquitin-independent degradation www.nature.com/articles/s41...

Structure of the TXNL1-bound proteasome - Nature Structural & Molecular Biology

Gao, Nardone et al. report the cryo-EM structure of human TXNL1 bound to the proteasome and reveal interactions required for the stress-induced degradation of TXNL1, an abundant protein that may regul...

Reposted by Lucas Farnung

Ryan Flynn @raflynn5.bsky.social · Aug 6

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...