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

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

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

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. 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

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

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

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...