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Ed Chuong

@edchuong.bsky.social

1.8K followers 1.2K following 19 posts

Assistant Professor at the University of Colorado Boulder - Genome regulation, Transposons, Immunity - https://chuonglab.colorado.edu

chuonglab.colorado.edu

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Ed Chuong @edchuong.bsky.social · Dec 12

I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪

Regulation of human interferon signaling by transposon exonization

Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.

www.cell.com

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Reposted by Ed Chuong

Ivan Zanoni @lozanzi.bsky.social · Aug 21

#InterferonPower! Thrilled for our latest work @cp-cell.bsky.social! With @danielboehmer.bsky.social, we dug into tons of papers & created what we hope will be a go-to resource for immunologists & non-immunologist about type I, II, III (& IV😉) #interferons! Free👉 authors.elsevier.com/a/1leKGL7PXu...

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Reposted by Ed Chuong

Guillaume Bourque @guilbourque.bsky.social · Jul 21

Is the annotation of viruses in the human genome accurate? We think not. Take a look at our new paper and let us know if you agree! www.science.org/doi/10.1126/...

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage

A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

www.science.org

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Ed Chuong @edchuong.bsky.social · Jul 17

Are you bravely deciding to do a postdoc in the US? And also interested in some combination of genomics, immunology, and transposons? If so, consider applying to my lab at the BioFrontiers Institute in Boulder, Colorado!

jobs.colorado.edu/jobs/JobDeta...

🧪🧬 #TESky #interferosky

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Reposted by Ed Chuong

Julius Brennecke @juliusbrennecke.bsky.social · Jul 16

Pls. share widely

Calling all transposon fans & lovers of genetic innovation

MOBILE GENOME welcomes you in Heidelberg, Nov. 4–7 2025

→ Vibrant & friendly community
→ Cutting-edge talks from mechanisms to physiology
→ Plenty of surprises (TEs never stop innovating)

submit abstract by July 29

EMBL Events @events.embl.org · Jun 18

⏰ Abstract deadline for 'The mobile genome' is 29 July!

👉 https://s.embl.org/mge25-01-bl

Join us 4–7 Nov 2025 at EMBL Heidelberg (or online) to explore the impact of TEs across biology. 🧬🔍

⭐🧑🏼‍🔬 24 talks + 15 flash talks from posters – don't miss out!

#EMBOMobileGenome

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Reposted by Ed Chuong

Mallory Harris, PhD @malar0ne.bsky.social · Jun 9

Ok fine I'll listen to the Bhattacharya/Huberman interview amd share my notes

a woman wearing a protective suit with experian written on it

Alt: a woman wearing a protective suit with experian written on it

media.tenor.com

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Reposted by Ed Chuong

Cedric Feschotte @cedricfeschotte.bsky.social · Apr 30

💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS

Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

www.pnas.org

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Reposted by Ed Chuong

Clément Canonne @ccanonne.github.io · Mar 20

If no single piece of the original ship remains in the current ship, is the ship still the Ship of Theseus?

And if one percent of all my body's cells get replaced every single day, is it really me who, two months ago, accepted your review request?

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Reposted by Ed Chuong

Annika Barber @annikabarber.bsky.social · Feb 24

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

2025 Study section tracking

docs.google.com

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Reposted by Ed Chuong

Carolyn Ibberson @cbibberson.bsky.social · Feb 22

I created a brief spreadsheet of reductions I've heard of so far. Any additions you know of (especially if you have the links/receipts) would be great: docs.google.com/spreadsheets...

Graduate Reductions Across Biomedical Sciences (2025)

docs.google.com

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Reposted by Ed Chuong

Patrick Murphy @pjmurphy249.bsky.social · Feb 5

PREPRINT! Park et al. makes the case that we may be misunderstanding heterochromatin for past 30 years due to ChIP-Seq biases... 1/n

bioRxiv Genomics @biorxiv-genomic.bsky.social · Feb 5

CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays https://www.biorxiv.org/content/10.1101/2025.02.03.636299v1

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Ed Chuong @edchuong.bsky.social · Feb 5

Congrats to the team, this is super important for studying TEs!

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Reposted by Ed Chuong

Marlies Oomen @marliesoomen.bsky.social · Jan 20

Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵

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Ed Chuong @edchuong.bsky.social · Jan 10

Awesome, congrats to the team! 🎉

Reposted by Ed Chuong

brumbaugh-lab.bsky.social @brumbaugh-lab.bsky.social · Jan 10

Our new paper defining the role of H3K36 methylation in regulating cell fate and plasticity is available online: rdcu.be/d5AEc
Thanks to our entire team for their tireless work and to the editors at @naturecellbiology.bsky.social for the opportunity!

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium

Nature Cell Biology - Pashos et al. show that H3K36 methylation maintains intestinal epithelial fate commitment, whereas its suppression, which is also observed upon injury, induces a plastic state...

rdcu.be

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Reposted by Ed Chuong

Todd Macfarlan @toddmacfarlan.bsky.social · Jan 8

I'm looking for a postdoc to join my fantastic team at the NIH in Bethesda, MD. Great resources. Competitive salary. www.training.nih.gov/jobs/pdf-mb-...

Postdoc: Molecular Biology/Genetics/Developmental Biology/Evolution/Computational Biology

www.training.nih.gov

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Reposted by Ed Chuong

Ivan Zanoni @lozanzi.bsky.social · Dec 26

#EveryCellIsAnImmuneCell!💥Thrilled for the final version of our paper @cp-cell.bsky.social! We show that type III #interferons control ZBP1 activation driving gasdermin C cleavage & delaying gut repair by inducing #pyroptosis in intestinal epithelial cells! 1/n www.cell.com/cell/abstrac...

Type III interferons induce pyroptosis in gut epithelial cells and impair mucosal repair

Intestinal damage following colitis or irradiation induces type III interferons (IFNs), which delay the healing of the intestinal epithelium. IFN-λ directs the sensing of Z-form nucleic acids generated during gut injury and repair, triggering cell death and altering healthy epithelial regeneration.

www.cell.com

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Reposted by Ed Chuong

Aaron Whiteley @aaronwhiteley.bsky.social · Dec 19

Check out this thread on the latest work from our lab, led by @emilykibby.bsky.social ! Here we used the power of computationally predicting protein-protein interactions to understand how a bacterial antiphage system senses infection.

Emily Kibby @emilykibby.bsky.social · Dec 18

I’m so excited to share that some of my grad work in the @aaronwhiteley lab is now available on bioRxiv! We used an AlphaFold-multimer screen to uncover how a bacterial NLR-related proteins senses multiple phage-encoded proteins to confer phage protection. Link: www.biorxiv.org/content/10.1...

A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection

Immune systems must rapidly sense viral infections to initiate antiviral signaling and protect the host. Bacteria encode >100 distinct viral (phage) defense systems and each has evolved to sense cruci...

www.biorxiv.org

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Reposted by Ed Chuong

Miguel V. Almeida @migueldvalmeida.bsky.social · Dec 19

First #bluetorial. 🎉🎉 We’re very happy to share our latest biorxiv #preprint, just in time before the holiday season. We explored how transposable elements (TEs) diversify eukaryotic proteomes and found a cool case in nematode F-box genes. #TEsky #evosky #Celegans

Short 🧵 with highlights.

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Ed Chuong @edchuong.bsky.social · Dec 12

Also in this same issue--a fantastic deep dive into the prevalence of transposon exonization by @yarribas.bsky.social !

www.cell.com/cell/fulltex...

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.

www.cell.com

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Reposted by Ed Chuong

Ivan Zanoni @lozanzi.bsky.social · Dec 12

#NotOnlyParasites! 2 Cell papers by @edchuong.bsky.social lab & Amigorena lab demonstrate that transposable elements #TEs can exonize giving rise to functional (often shorter) proteins with distinct functions: eg a decoy short IFNAR2 that inhibits #interferon signaling! www.cell.com/cell/fulltex...

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.

www.cell.com

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Reposted by Ed Chuong

Waggoner Lab @labwaggoner.bsky.social · Dec 12

Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2
www.cell.com/cell/fulltex...
@cellcellpress.bsky.social @edchuong.bsky.social

Regulation of human interferon signaling by transposon exonization

Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.

www.cell.com

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Ed Chuong @edchuong.bsky.social · Dec 12

All the credit for this discovery goes to postdoc @giuliapasquesi.bsky.social , who first noticed the isoform in her 2020 Lockdown Sideproject (tm). Her perseverance, creativity, and talent made this study possible and it was an honor to be a part of it. Watch out for her--she's on the job market! 😉

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Ed Chuong @edchuong.bsky.social · Dec 12

Beyond IFNAR2, our findings suggest that TE exonization may be a widespread yet hidden source of decoy isoforms that regulate immune signaling.

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Ed Chuong @edchuong.bsky.social · Dec 12

Our study shows how TE exonization gave rise to a primate-specific IFN decoy receptor, which acts as a dial to turn down IFN signaling in human cells. While IFN decoy receptors have evolved repeatedly in viruses (eg VACV B18), this is the first host-encoded IFN decoy receptor.

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Ed Chuong @edchuong.bsky.social · Dec 12

We also found that risk variants linked to severe COVID-19 in the IFNAR2 locus almost perfectly coincided with splicing QTLs associated with higher relative expression of the decoy. This suggests that variation in IFNAR2 splicing partly underlies individual variation in response to infection.

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