iiinova — where your digital self keeps evolving

Alan Gerber @alangerber.bsky.social · 28/09/2026

Preprint alert 🚨: We built a CRISPRi screen for a part of the genome that is unusually awkward to perturb: the RNA Pol III transcriptome. Hundreds of tRNA genes, lots of sequence similarity, plenty of redundancy... Turns out the biology had a few surprises for us 👇 www.biorxiv.org/content/10.6...

biorxiv.org

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains uncl...

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Reposted by Alan Gerber

Alex Palazzo @ribonucleicacids.bsky.social · 13/02/2026

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

science.org

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation

Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

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Reposted by Alan Gerber

Evelina Tutucci @anilevetu.bsky.social · 15/10/2025

And it's out! Our paper on the optimization of smFISH to quantify cytokine mRNAs in T cells is published in EMBO Journal. Using this protocol, we gathered interesting insights on cytokine mRNAs co-expression and localization in these teeny tiny human cells. www.embopress.org/doi/full/10....

embopress.org

Single-molecule imaging of transcription dynamics, RNA localization and fate in human T cells | The EMBO Journal

imageimageT cells produce pro-inflammatory cytokines like IFN-γ and TNF. This study presents an optimized single-molecule FISH workflow in primary human T cells for studying how (post)-transcriptional...

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Evelina Tutucci @anilevetu.bsky.social · 26/02/2025

It's out! Beautiful work led by Loreto Oyarte Gálvez & @cbisot.bsky.social! Do you want to learn more about how Mycorrhizal fungi extraordinary networks form and function? Read the open-access publication! Link below 👇

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Evelina Tutucci @anilevetu.bsky.social · 21/12/2024

I am giving a lecture at the EMBO practical course: "FISHing for RNAs: classical to single molecule approaches" Check out this hands-on EMBO course!

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Anders Sejr Hansen @andersshansen.bsky.social · 20/12/2024

Excited to share @domenicnarducci.bsky.social 's paper now out in Mol Cell published back-to-back with the paper from @dewitlab.bsky.social‬ - despite lots of prior work, we find that ZNF143 has no looping function www.sciencedirect.com/science/arti... www.sciencedirect.com/science/arti...

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Alan Gerber @alangerber.bsky.social · 20/12/2024

MDPI & Frontiers journals blacklisted in Finland, I wonder if this will indeed spread further? Never considered any of these journals for publication, but MDPI surely send funny emails... Maybe I will introduce myself like this 👇 from now on 😂.

The picture shows a screenshot of an email from a MDPI journal creatively addressing me by fusing part of the title of a paper and my last name...

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Alejandro Montenegro @aemonten.bsky.social · 12/12/2024

"We report that numerous “miRNAs” previously reported in EMT and cancer contexts are not incorporated into RISC and are not capable of endogenously silencing target genes, despite the fact that hundreds of publications in the cancer field describe their roles" www.biorxiv.org/content/10.1...

biorxiv.org

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Yago Arribas @yarribas.bsky.social · 12/12/2024

Not easy to describe the emotions of seeing our work published in @cellpress.bsky.social ! We explored how novel isoforms emerge during evolution through the exonization of Transposable Elements. Exonized TEs modify the functions and structures of host proteins. www.cell.com/cell/fulltex...

cell.com

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.

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Reposted by Alan Gerber

Alexis A. Jourdain @jourdainlab.bsky.social · 16/12/2024

📢We're recruiting📢 Our lab at the University of Lausanne is looking for a postdoctoral associate to study #nucleotide metabolism in physiology and cancer in vivo! Please share #uridine #cancermetabolism #immunometabolism @unil.bsky.social 🔗(PDF): www.jourdainlab.org/wp-content/u...

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Olivier Duss @olivierduss.bsky.social · 11/12/2024

Excited to share our new work on the earliest steps of Pol-III transcription: We provide structural and kinetic insights into tRNA promoter engagement by yeast transcription factor TFIIIC ! Cool collaboration with the Müller and Eustermann Labs @embl.org ! academic.oup.com/nar/advance-...

academic.oup.com

Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC

Abstract. Transcription of transfer RNA (tRNA) genes by RNA polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes

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Scott McGrath @smcgrath.phd · 09/12/2024

🧪 Your eyes may deceive you. A study of 3,387 life-science papers from 2023 found nearly 1/3 of bar charts distorted data, often by not starting the y-axis at zero or misusing log scales.

nature.com

Bad bar charts are pervasive across biology

Scientific ‘shorthand’ could be introducing data distortions into published papers.

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Reposted by Alan Gerber

Alex Palazzo @ribonucleicacids.bsky.social · 26/11/2024

Very cool - snoRNA73 acts as a bridge between mRNAs and 7SL (i.e. the SRP ncRNA) to facilitate the synthesis of the encoded secreted protein.

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Reposted by Alan Gerber

Molecular Biosystems Conference @molbiosystems.bsky.social · 25/11/2024

Did you know that at our conference, we record our Keynote Lectures and make them freely available? You can find them all in our Youtube page! To get started, check out the 2023 IUBMB Jubilee Lecture, given by Prof. Rachel Green.

youtube.com

Rachel Green - IUBMB Jubilee Lecture - 3rd Molecular Biosystems Conference (2023)

YouTube video by Molecular Biosystems Conference

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Reposted by Alan Gerber

Artem @rtviii.bsky.social · 25/11/2024

Post a non-religious photo you think of as holy. Not necessarily holy, just cool contrast between "then and now" in ribosome assembly landscape understanding. Nierhaus map from the 80s / AV Broeck & Sebastian Clinge in Science 2023.

https://www.science.org/doi/10.1126/science.adh3892?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

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Evelina Tutucci @anilevetu.bsky.social · 24/11/2024

This 👇 is happening. Change is coming!

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Alan Gerber @alangerber.bsky.social · 24/11/2024

Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 by Ueli Laemmli! The paper which introduced SDS-page to the world!!! 💯

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 24/11/2024

💯 February 14th 1969, RNA polymerases' day. The pioneering experiment that laid the foundation for the eukaryotic transcription field by Robert Roeder.

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Ben Long @botbml.bsky.social · 24/11/2024

Post a non-religious photo you think of as holy

A TEM image of structural carboxysomes in a tobacco chloroplast

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Alan Gerber @alangerber.bsky.social · 23/11/2024

Post a non-religious photo you think of as holy.

Figure showing the chromatographic resolution of the three nuclear DNA-dependent RNA polymerases from
Sea urchin embryos (Bob Roeder, 18 Feb 1969).

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Reposted by Alan Gerber

The Lewis Lab @peterlewislab.bsky.social · 22/11/2024

IDH-mutant gliomas evolve from slow-cycling OPC-like cells to proliferative NPC-like cells through chromatin reprogramming and genetic alterations. This transition reveals key mechanisms of tumor progression. www.nature.com/articles/s43...

nature.com

Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer

Wu et al. perform single-cell analyses to explore the switch from low-grade to high-grade isocitrate-dehydrogenase-mutant glioma and show that it is characterized by oligodendrocyte progenitor cell-li...

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Nils Blüthgen @molsysbio.bsky.social · 21/11/2024

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...

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Sam Rodriques @sgrodriques.bsky.social · 20/11/2024

New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Paper here: www.biorxiv.org/content/10.1... 1/

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Craig Kaplan @triggerloop.bsky.social · 21/11/2024

This is a very cool paper that I will add to my Mol Bio course. Specific tRNA recruitment of mRNA degradation complex to ribosome through the P site tRNA interactions with CCR4-NOT complex 1/ www.science.org/doi/10.1126/...

science.org

Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes

The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation....

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Reposted by Alan Gerber

Will Allen @weallen1.bsky.social · 21/11/2024

In collaboration with Reuben Saunders, @jswlab.bsky.social, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform for pooled multimodal genetic screens in intact mammalian tissue. Check it out! www.biorxiv.org/content/10.1...

biorxiv.org

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the...

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Reposted by Alan Gerber

Laura White @laurakwhite.bsky.social · 19/11/2024

New preprint on our method aa-tRNA-seq: chemically capturing aminoacylated tRNA molecules & pulling them through nanopores. It’s been a blast working with my collaborator Aleks Radakovic to take this from idea to promising pilot data to some looking exciting biology to chase down in future work.

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Reposted by Alan Gerber

Ivana Gasic @ivanagasic.bsky.social · 18/11/2024

Hello Bluesky community! What a better way to introduce myself and my research team than post our lab’s first paper freshly off press 🥳🍾 We reveal how tubulins regulate the stability of their mRNA via reversible sequestration of TTC5. Bravo A. Batiuk and all coauthors 👏🏻🥂 doi.org/10.1038/s414...

doi.org

Soluble αβ-tubulins reversibly sequester TTC5 to regulate tubulin mRNA decay - Nature Communications

When tubulin proteins are present in excess, their encoding mRNAs are selectively degraded in a process initiated by the protein TTC5. Here, the authors show that tubulins themselves reversibly seques...

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Reposted by Alan Gerber

Denis Wirtz @deniswirtz.bsky.social · 16/11/2024

Download our database of 313 different postdoctoral fellowships. For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship). Download our database here: research.jhu.edu/rdt/funding-...

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Luijsterburglab @luijsterburglab.bsky.social · 16/11/2024

Happy to share our new paper with Goran Kokic and the Svejstrup lab in Cell! We show that STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair. Great teamwork by Diana, Marta and Paula! www.cell.com/cell/fulltex...

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Mark Peifer (He, him) @peiferlabunc.bsky.social · 16/11/2024

In September the world lost one of the great biologists of our time: Joe Gall. He bridged the transition from the histology era of cell biology to our molecular present, contributing a remarkable set of insights in his 9 decades 1/n 🧪 rupress.org/jcb/article-...

Title and abstract of the memoriam in the Journal of Cell Biology in the link

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Isaac Yellan @downbythebayes.bsky.social · 15/11/2024

(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....

doi.org

Extensive binding of uncharacterized human transcription factors to genomic dark matter

Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...

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Reposted by Alan Gerber

Evelina Tutucci @anilevetu.bsky.social · 12/11/2024

New preprint 📣📣 Together with Monika Wolker's lab @sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification. www.biorxiv.org/content/10.1...

biorxiv.org

Single molecule imaging of transcription dynamics, RNA localization and fate in T cells

T cells are critical effector cells against infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-gamma and TNF. Cytokine production is a tightly regulat...

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