Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025

Transcriptional interferences ensure one olfactory receptor per ant neuron www.nature.com/articles/s41... Caviar for RNA-Seq nerds! Check this out

📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...

🚨 New paper alert on telomeres! 🚨 Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.

Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK. Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD

www.biorxiv.org/content/10.1... Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

Delighted to share our latest paper out @NatureComms. REST/NRSF is essential for muscle stem cell identity, blocking alternate cell fates—huge congrats to the first author @KorinSahinyan and the rest of the fantastic coauthors. www.nature.com/articles/s41...

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/...

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in @natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

Hello out there! Are you looking for a friendly community to share your RNA research and hear about some cool RNA biology? Register for @trendrna.bsky.social on July 10-11 now! Oral abstract deadline is May 30th! Co sponsored by @rnacanada.bsky.social!

Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models. 🔗 doi.org/10.1093/bioa... #Genomics #Bioinformatics #RegulatoryGenomics

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Delighted to see this out! Fun fact: I actually started my lab @ UCSF w/ goal of understanding tRNA txn regulation, which aligned perfectly w/ @genophoria.bsky.social & Sohail! 6+ years of amazing collaboration & stellar work by Siyu, Albertas, & co & we're making real progress w/ more to come!

Alternative splicing (AS) is common, but its impact on the proteome remains debated, especially in primary cells. What determines which AS isoforms result in abundant proteins ? We find that proteoform-specific ... 🧵 www.biorxiv.org/content/10.1...

our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell! key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity many are "negative regulators" & misexpressed in cancer www.sciencedirect.com/science/arti...

Why do RBPs need multiple RNA-binding domains? We show transcriptome-wide that the endosomal mRNA transporter Rrm4 uses its three RRMs to differentiate functional binding sites from accessory ones. Great collaboration with @koenig-lab.bsky.social and Zarnack lab www.biorxiv.org/content/10.1...

@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...

How do early lung tumors evolve? Our latest preprint, led by Junbum Kim, maps early-stage cancer at single-cell resolution, revealing two key pathways: 🦠Driven by immune activity 🛠️ Driven by fibrosis These insights could refine detection & treatment. www.biorxiv.org/content/10.1...

Thrilled to share LUNA🌕 – our new generative AI model that reassembles tissue structures from dissociated cells! LUNA learns spatial priors over existing spatially resolved datasets with the aim to predict cell locations de novo. Check out our paper here: www.biorxiv.org/content/10.1...

I love this insight on building teams from @genophoria.bsky.social, Core Investigator at Arc Institute, which just released Evo 2: the largest AI model for biology to date. Catch the full conversation: + YouTube: youtu.be/sWcoslBueiE + Spotify: spoti.fi/4hLk3xo + Apple Podcasts: apple.co/40sQCu9

Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin? By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient! #chromatin #3Dgenome #generegulation www.science.org/doi/10.1126/... 👇

The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...

Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/

On December 6, we remember: Geneviève Bergeron Hélène Colgan Nathalie Croteau Barbara Daigneault Anne-Marie Edward Maud Haviernick Maryse Laganière Maryse Leclair Anne-Marie Lemay Sonia Pelletier Michèle Richard Annie St-Arneault Annie Turcotte Barbara Klucznik-Widajewicz

This is bound to be an amazing resource!

Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!

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/...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

(1/n) What better way to start posting on Bluesky than to share our recent preprint, in collaboration with @timhughesto.bsky.social, on characterization of the intrinsic DNA binding specificities of 179 human transcription factors using a new assay, GHT-SELEX: www.biorxiv.org/content/10.1...