Excited to share our new paper on pseudouridine (ψ)! We find ψ acts in a density-dependent way: single sites ↑ protein, clustered sites ↓ protein (despite ↑ ribosome density). Suggests new ways to tune gene expression for RNA/gene therapies. tinyurl.com/psitranslation

Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation

Abstract. Pseudouridine (psi) is one of the most abundant mRNA modifications, yet its impact on translation is unclear, in part because existing modificati

tinyurl.com

Multi-Scale Kinetics Modeling and Advanced Assay for mRNA-Lipid Nanoparticle Potency Assessment https://www.biorxiv.org/content/10.1101/2025.09.29.679406v1

Protocol for differential analysis of pseudouridine modifications using nanopore DRS and unmodified transcriptome control #protocol #starprotocols #cellpress

Protocol for differential analysis of pseudouridine modifications using nanopore DRS and unmodified transcriptome control

In this protocol, we detect pseudouridine using nanopore direct RNA sequencing (DRS 002/004) and analyze dynamic changes to mRNA modifications in response to perturbation. We cover RNA extraction, poly(A) selection, DRS, unmodified transcriptome (in vitro transcribed [IVT]) library preparation, and knockdowns of writer proteins as critical controls. We detail preprocessing, psi-site identification, and differential analysis, quantifying the direction and magnitude of changes across cellular type...

dlvr.it

RNA modifications in T cells are more stable than expected—primary and immortalized cells share most sites, suggesting common regulatory features can be studied across systems bit.ly/3GP97C8

1/🧵 🚨 New paper published in RNA! Scientists often say anecdotally that RNA modifications are disrupted in immortalized cells — but no one’s really tested it. So we did: ψ-mapping in primary T cells vs. Jurkat cells using direct RNA-seq. 📄 tinyurl.com/TCellPsiRNA #nanopore #RNA #pseudouridine

In this incredible work, @srouhanifard.bsky.social developed a new catalyst, which makes CuAAC truly biocompatible rdcu.be/enfHz

inCu-click: DNA-enhanced ligand enables live-cell, intracellular click chemistry reaction with copper catalyst

Nature Communications - Tracking biomolecules in living cells requires fast but gentle labeling. Here, authors introduce inCu-click, a DNA-conjugated ligand that localizes copper to enable...

rdcu.be

Just published: “inCu-click: DNA-enhanced ligand enables live-cell click chemistry with copper catalyst” in @natcomms.nature.com! 🚀 A DNA-conjugated chelator locks Cu⁺ ions for in situ CuAAC at nanomolar doses—zero toxicity. Read the full paper here ➡️ rdcu.be/enfHz #clickchemistry

inCu-click: DNA-enhanced ligand enables live-cell, intracellular click chemistry reaction with copper catalyst

Nature Communications - Tracking biomolecules in living cells requires fast but gentle labeling. Here, authors introduce inCu-click, a DNA-conjugated ligand that localizes copper to enable...

rdcu.be

1/6 🧬New paper at @cp-cellsystems.bsky.social led by @sashafanari.bsky.social! Does pseudouridine (Ψ) dynamically respond to cell state? We used nanopore DRS + Mod-p ID to map Ψ in neuron-like cells under “normal” and “perturbed” conditions (healthy differentiation and unhealthy Pb2+ poisoning).

Sitting in a journal club-style class right now and after the main presenters present, there are "roles" from others in the group, like the "archeologist" who looks into the citation trail, the "private investigator" who tries to dig into the history, and the "industry practitioner", etc. Cool idea!

🧪🧬👩‍🔬🖥️ Do immortalized cells have a different RNA modification profile compared to primary cells? 🤔 @sashafanari.bsky.social @wanunupore.bsky.social @srouhanifard.bsky.social assess the most abundant RNA modification, pseudouridine, in primary and immortalized human T cells 👇 doi.org/10.1101/2025...

Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications.

Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T cell signaling, activat...

doi.org

Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications. https://www.biorxiv.org/content/10.1101/2025.03.02.641090v1

Office hours are starting

Online Now: Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens

Sood et al. used high-throughput screening to identify regulators of gene bursting and find both gene- and cell-type-specific effectors. Acetylation alters burst size in a gene-specific manner but is independent of promoter acetylation. Rather,…

dlvr.it

Single-molecule live-cell RNA imaging with CRISPR–Csm - @doudna-lab.bsky.social @qb3-berkeley.bsky.social @innovativegenomics.bsky.social go.nature.com/3EJPKsM

Single-molecule live-cell RNA imaging with CRISPR–Csm - Nature Biotechnology

Single-molecule live-cell fluorescence in situ hybridization uses an RNA-targeting CRISPR–Csm complex to image and track endogenous RNAs.

go.nature.com

Cool paper using LLM to discover a protein sequence code for subcellular localization 👏 www.science.org/doi/10.1126/...

Protein codes promote selective subcellular compartmentalization

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...

science.org

Gene editing technology began by people studying salt marshes. Ozempic began by folks studying the venom of Gila Monsters. Support for basic science has empowered us to understand our world. Tethering it to applications health has transformed and saved countless lives.

Check it out! Another novel RNA modification - ADP-ribosylation - that was previously only known on proteins. A cousin to #glycoRNA 👏 www.nature.com/articles/s41...

"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...

Liu, ... Rouhanifard have optimized nuclear FISH to the point where it's now possible to sort cells based on transcript production. They sort cells into bins and measure chromatin state at the locus whose tx was sorted on. www.biorxiv.org/content/10.1...

NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis

Transcriptional bursts refer to periods when RNA polymerase interacts with a DNA locus, leading to active gene transcription. This bursting activity can vary across individual cells, and analyzing the...

biorxiv.org