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Reposted by John Prensner

Megan Dennis @mydennis.bsky.social · 2d

Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.

bioRxiv Genomics @biorxiv-genomic.bsky.social · 3d

Influence of cis-regulatory elements on regulatory divergence in human segmental duplications https://www.biorxiv.org/content/10.1101/2025.10.03.680410v1

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Reposted by John Prensner

Edda Schulz @eddaschulz.bsky.social · 2d

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology

Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

www.nature.com

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Reposted by John Prensner

MaRtiNA Hallegger @martinahallegger.bsky.social · 4d

Stress granules have a limited impact on global translation regulation but serve to protect small ribosomal subunits and preinitiation complexes from degradation

David Kuster @rnadavid.bsky.social · 4d

Translation landscape of stress granules | Science Advances

www.science.org/doi/10.1126/...

Translation landscape of stress granules

Cryo–electron tomography visualizes stress granules in situ, revealing their spatial interplay with translation machinery.

www.science.org

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Reposted by John Prensner

Susan Shao @sshaolab.bsky.social · 5d

Beautiful reconstitution of amino acid stress-dependent ISR activation by my @harvardcellbio.bsky.social colleagues presenting a unifying mechanism for GCN2 activation, which requires ribosome collisions and is enhanced by cognate uncharged tRNA in the A site! www.science.org/doi/10.1126/...

GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling

During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular stres...

www.science.org

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Reposted by John Prensner

Hassan uz Zaman @hassanzaman.bsky.social · 12d

After testing virtually all reasonable permutations of sample prep, spectra acquisition, database selection, data processing...

This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵

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John Prensner @johnprensner.bsky.social · 10d

Supporting the #chadtough run to support #DMG/DIPG research for children with #childhoodcancer. What a great run!

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Reposted by John Prensner

bioRxiv Genomics @biorxiv-genomic.bsky.social · 15d

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors https://www.biorxiv.org/content/10.1101/2025.09.22.676906v1

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Reposted by John Prensner

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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Reposted by John Prensner

Yun S. Song @yun-s-song.bsky.social · 17d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Reposted by John Prensner

Javier Santoyo @jsantoyo.bsky.social · 24d

The reference genome of the human diploid cell line RPE-1. #HumanReferenceGenome #HumanDiploidCellLine @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...

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Reposted by John Prensner

Steven Corsello @corsello.bsky.social · Sep 2

Excited to share our discovery of potent TRIM21 molecular glues with anticancer activity, online today @CD_AACR: "Defining the antitumor mechanism of action of a clinical-stage compound as a selective degrader of the nuclear pore complex". 1/18

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Reposted by John Prensner

Maxim Greenberg @maxvcg.bsky.social · Sep 1

"Honey, wake up. New CUT protocol just dropped" www.biorxiv.org/content/10.1...

CUT&TIME captures the history of open chromatin in developing neurons

Chromatin structure plays a central role in defining cell identity by regulating gene expression. During development, shifts in chromatin structure facilitate changes in gene expression needed to spec...

www.biorxiv.org

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John Prensner @johnprensner.bsky.social · Aug 30

Back to school shopping with kids, and seeing the 90s baggy sign, and remembering that my 90s baggy pants are actually from the 90s, and reflecting on how time passes….

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Reposted by John Prensner

Mia Farrow @miafarrow.bsky.social · Aug 30

Pediatric Brain Cancer Group to Lose Federal Funding.
A respected network of hospitals and cancer centers is halting enrollment in clinical trials for children with brain cancer after the federal government said it would no longer provide funding to the group.

www.nytimes.com/2025/08/28/w...

Pediatric Brain Cancer Group to Lose Federal Funding

www.nytimes.com

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John Prensner @johnprensner.bsky.social · Aug 29

@debbiedingell.house.gov As my elected representative, please continue to fight for childhood cancer research.

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John Prensner @johnprensner.bsky.social · Aug 29

Thank you @nytimes.com for featuring this upsetting news about the loss of #childhoodcancer funding for #braintumors. It was my pleasure to speak with #NinaAgrawal for this piece. But I wish circumstances were different and we didn't need this article at all.

www.nytimes.com/2025/08/28/w...

Pediatric Brain Cancer Group to Lose Federal Funding

www.nytimes.com

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Reposted by John Prensner

Liam Faller @liamfaller.bsky.social · Aug 28

Very cool stuff on the co-translational folding of dimers by Sander Tans and his team @amolf-nl.bsky.social:

www.nature.com/articles/s41...

Co-translational ribosome pairing enables native assembly of misfolding-prone subunits - Nature Communications

Protein complexes are essential for cell function. Here, authors show that paired ribosomes can help each other’s nascent chains fold correctly, enabling proper dimer assembly and preventing misfoldin...

www.nature.com

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Reposted by John Prensner

Laura White @laurakwhite.bsky.social · Aug 22

Our paper is out in its final form! Back in April 2023, my coauthor Aleks Radakovic, then a PhD student, approached me after a talk in Chicago to ask what I thought an aminoacylated tRNA would look like if we pulled it through a @nanopore.
doi.org/10.1038/s414...

Nanopore sequencing of intact aminoacylated tRNAs - Nature Communications

Accurate protein synthesis depends on aminoacylated tRNAs, but their identities have been hard to measure. Here, authors present aa-tRNA-seq, a nanopore-based method that reveals the amino acid, seque...

doi.org

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John Prensner @johnprensner.bsky.social · Aug 22

Either way I turn, it looks like home 😉

Airport terminals for Boston and Detroit flights

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John Prensner @johnprensner.bsky.social · Aug 22

Saying goodbye to Giraffe the cat at the conclusion of the first ever #GRC on #microproteins #darkproteome. What a FANTASTIC meeting with worldwide and world class experts on all domains of the dark proteome. Get ready for 2027 because that is when the next of these fantastic meetings will occur!

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John Prensner @johnprensner.bsky.social · Aug 21

Day 5 of the Gordon Conference on #Microproteins! Ask yourself the question, does your conference have a cat apparently named “giraffe”?

@rna-julie.bsky.social

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John Prensner @johnprensner.bsky.social · Aug 20

If #PBTC cannot continue, children with brain cancer lose. Really sad.

*Please help advocate to your elected officials if you can*

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John Prensner @johnprensner.bsky.social · Aug 20

Sadly, clinical trials for children with brain cancer sometimes struggle to get the financial support they deserve. That is why federal investment is so critical. It's not just about funding clinical trials, but about funding clinical trials that *would not* otherwise have financial support.

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John Prensner @johnprensner.bsky.social · Aug 20

The #PBTC is a core consortium of over a dozen leading childhood cancer hospitals in the United States and Canada. The #PBTC runs and supports critical clinical trials that help to bring treatments to patients.

While I was training at #DanaFarber, we regularly hosted PBTC trials.

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John Prensner @johnprensner.bsky.social · Aug 20

#HiWorld
I am getting a flurry of messages that the #PediatricBrainTumorConsortium is at risk of closing due to changes/losses in US-based federal funding through the #NIH and others.

*Please help advocate to your elected officials if you can*

#Cancer
#pediatrics
#childhoodcancer
#DIPG
#CANsky

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