Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos Abstract. As embryos transition from maternal to zygotic control, precise clearance of pre-loaded maternal mRNAs is essential for initiating new zygotic ge

How embryos stay “on time” as they grow?
Happy to share our recent publication: Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
(1/7)

academic.oup.com/nar/article/...

1. Today the NIH director issued a new directive slashing overhead rates to 15%.

I want to provide some context on what that means and why it matters.

grants.nih.gov/grants/guide...

mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription Transcription inhibitors also disrupt nuclear export. Here, Williams et al. reveal that mRNA export factors sense transcription inhibition and adapt by storing mature export-competent mRNA in nuclear speckles. This enables rapid release when transcription resumes and ensures retention of cellular identity and viability during a transient global transcription insult.

Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!

So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!

www.cell.com/molecular-ce...

Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data? Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)

Luckily for you, @aaronkwc.bsky.social has!

Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?

Check it out 👇
www.biorxiv.org/content/10.1...

🧪🧬💻

www.biorxiv.org/content/10.1...
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8

There's been some interest in this PLOS announcement, so despite it being light on details, here's why it's big. In our recent study 'The strain on scientific publishing' we showed how certain groups took off in total articles published.

Why? And why now?

direct.mit.edu/qss/article/...

1/n 🧵

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience

Long-range regulation of transcription scales with genomic distance in a gene-specific manner Jensen et al. show that targeting dCas9-VPR using a multiplexed array of RNA guides results in effective activator recruitment to promoter-distal, previously inaccessible genomic sites, allowing for l...

Today in Molecular Cell the work of one of my favorite (ex)PhD students in the Wysocka Lab: Dr. Christina Jensen. I saw this project develop throughout the years and it has kept me engaged in hypothesizing scenarios in every lab meeting. Congratulations to the authors!
www.cell.com/molecular-ce...

Enhancer cooperativity can compensate for loss of activity over large genomic distances Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex regulatory landscapes. Integrating the same enhancer at different distances from a promoter uncovered that activ...

Enhancer cooperativity can compensate for loss of activity over large genomic distances | Molecular Cell

#chromatin #enhancers

www.cell.com/molecular-ce...

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.

go.bsky.app/QVPoZXp

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...

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

www.nature.com/articles/s43...

Hi, can you please add me? Thank you, Yotam.

It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)

Plotting becomes tidy in R , good read for trainees.

www.biorxiv.org/content/10.1...

Our paper with Carmel lab, the work of PhD student Yoav Mathov was just published in Nat Ecol Evol. www.nature.com/articles/s41....
Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific.

Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it"

www.cell.com/action/showP...

Great list! Can you add me too? Thanks.

I’ve started making a starter pack for computational #cancer! Let me know if you’d like to be added or know someone who should be go.bsky.app/N6moBmG

DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis SMCHD1 loss drives FSHD pathogenesis by disrupting DNMT3B splicing, leading to D4Z4 hypomethylation and DUX4 overexpression.

Eden showed how SMCHD1 regulates the splicing of DNMT3B1, and how the promoted isoform changes DNA methylation at the D4Z4 satellite repeat to induce DUX4 expression, explaining how SMCHD1 mutations lead to FSHD. More details at: dx.doi.org/10.1126/scia...

#Epigenetics #Splicing #SMCHD1

Importing some of our recent updates from Twitter to facilitate the great migration. Happy to report our results on the role of SMCHD1 in facioscapulohumeral muscular dystrophy (FSHD). A very close and fun collaboration with Prof. Salton, this work was led by our amazing joint student, Eden Engal.

Importing some of our recent updates from Twitter to facilitate the great migration. Interested in inferring pathway activity in the single cell level from #SingleCell RNAseq data? check out SiPSiC. Details at: t.co/zeLafAiMHg
Available on bioconductor: t.co/CyK0YVokV9 and github: t.co/EzSWAUFeel

Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms Euchromatic and heterochromatic regions of the genome tend not to interact inside the nucleus. Stutzman et al. investigate the role of HP1a binding to histone H3K9 methylation in restricting these interactions. They observe weakening, but not a complete loss, of separation between euchromatin and heterochromatin when the H3K9-HP1a interaction is disrupted.

EpiSci -

www.cell.com/molecular-ce...

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...

(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....

#Cancer #Epigenomics

The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment | EMBO reports imageimageA UDR motif in DNMT3A acts in concert with other chromatin reading regions to promote chromatin recruitment. A cryo-EM structure reveals that DNMT3A1 binds to H2AK119ub-marked nucleosomes th...

Pleasure to continue our collaboration with Marcus Wilson and group and play a small part in this study which is now out in the paper version. Read on to learn more about DNMT3A's interaction with H3K36me2 and H2AK119Ub modified nucleosomes:
www.embopress.org/doi/full/10....
#epigenetics

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

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