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

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...

tinyurl.com

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

A human-specific regulatory mechanism revealed in a pre-implantation model

Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.

rdcu.be

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.

The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs

The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...

biorxiv.org

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...

REST/NRSF Preserves muscle stem cell identity by repressing alternate cell fate - Nature Communications

Here the authors show that REST/NRSF represses non-muscle lineage genes in muscle stem cells and progenitors, preserving their identity and differentiation capacity. Loss of REST disrupts gene silenci...

nature.com

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/...

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage

A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

science.org

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)

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

nature.com

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

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression

Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

science.org

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!

TREnD@trendrna.bsky.social · last yr.

We are excited to announce that registration for this year's Toronto RNA Enthusiasts' Day (TREnD) is now open! July 10th, 1pm-4pm ET ONLINE for everyone July 11th, 9am-7pm ET ONLINE across Canada and IN PERSON in Toronto event.fourwaves.com/trend25/regi...

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

Perspective on recent developments and challenges in regulatory and systems genomics

Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul

doi.org

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 🧬🖥️

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

biorxiv.org

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!

Hani Goodarzi@genophoria.bsky.social · last yr.

Check out our latest preprint, led by Dr. Siyu Chen, that brings together an amazing team of scientists from several labs ( @vram142.bsky.social, Tavazoie, and Navickas) to tackle a fundamental problem in biology: how do cells regulate expression of their tRNAs? www.biorxiv.org/content/10.1...

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...

Dissecting the RNA binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport

RNA-binding proteins (RBPs) utilize multiple RNA-binding domains (RBDs) to engage with extensive mRNA networks. Understanding the intricate interplay of modular RBDs is essential for uncovering RBP fu...

biorxiv.org

@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...

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...

biorxiv.org

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...

Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression

Lung cancer remains the deadliest cancer in the United States, with lung adenocarcinoma (LUAD) as its most prevalent subtype. While computed tomography (CT)-based screening has improved early detectio...

biorxiv.org

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/... 👇

Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and a...

science.org

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...

A generative framework for enhanced cell-type specificity in rationally designed mRNAs

mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...

biorxiv.org

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/

Austin Wang@austintwang.bsky.social · 2y ago

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

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!

Hani Goodarzi@genophoria.bsky.social · 2y ago

@thejohnnyyu.bsky.social, @therealnima.bsky.social , Kevan Shokat, and I are excited to announce a historic achievement by our team at @vevotherapeutics.bsky.social: tinyurl.com/4rrvap3t

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!

A panoramic view of cell population dynamics in mammalian aging

To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...

tinyurl.com

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/...

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....

science.org