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Yotam Drier

@yotamd.bsky.social
1.4K followers 788 following 10 posts

Epigenomics and chromosome topology in cancer • Assistant Professor, Faculty of Medicine, Hebrew University of Jerusalem • yotamdrier.ekmd.huji.ac.il

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Reposted by Yotam Drier
michalra.bsky.social @michalra.bsky.social · 05/08/2025
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/...
academic.oup.com
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
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Carl T. Bergstrom @carlbergstrom.com · 08/02/2025
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...
grants.nih.gov
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
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Mark Dawson @mafdawson.bsky.social · 02/01/2025
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...
cell.com
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.
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Lucas Farnung @lucas.farnunglab.com · 12/12/2024
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
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Davis McCarthy @davisjmcc.bsky.social · 10/12/2024
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... 🧪🧬💻
biorxiv.org
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...
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Laurence Ettwiller @ettwiller.bsky.social · 09/12/2024
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.
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Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
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
bmcgenomics.biomedcentral.com
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...
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Mark A. Hanson @hansonmark.bsky.social · 02/12/2024
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 🧵
A chart showing the explosion of special issues at for-profit gold Open Access publishers MDPI, Frontiers, and Hindawi.A chart showing that MDPI and Frontiers in particular massively increased their output of articles per journal between 2016-2022.
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024
🧬🔍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
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Raquel Fueyo @fueyoraquel.bsky.social · 03/12/2024
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...
cell.com
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...
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Luis G. Palma @luigalpal.bsky.social · 03/12/2024
Enhancer cooperativity can compensate for loss of activity over large genomic distances | Molecular Cell #chromatin #enhancers www.cell.com/molecular-ce...
cell.com
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...
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Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
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...
nature.com
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...
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Su-In Lee @suinlee.bsky.social · 24/11/2024
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included. go.bsky.app/QVPoZXp
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Christian Frezza @frezzalab.bsky.social · 24/11/2024
Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer 🧪 www.nature.com/articles/s43...
nature.com
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...
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Dave Shechner @shechnerlab.bsky.social · 21/11/2024
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)
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Manvendra Singh @manusingh.bsky.social · 21/11/2024
Plotting becomes tidy in R , good read for trainees. www.biorxiv.org/content/10.1...
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Eran Meshorer @meshorer.bsky.social · 20/11/2024
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.
nature.com
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Job Dekker @jobdekker.bsky.social · 14/11/2024
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...
cell.com
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Ben Hall @hallben.bsky.social · 12/11/2024
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
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Yotam Drier @yotamd.bsky.social · 17/11/2024
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.
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Yotam Drier @yotamd.bsky.social · 17/11/2024
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
t.co
https://www.genome.org/cgi/doi/10.1101/gr.278431.123
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Carmelo Ferrai @carmeloferrai.bsky.social · 17/11/2024
EpiSci - www.cell.com/molecular-ce...
cell.com
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.
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Isaac Yellan @downbythebayes.bsky.social · 15/11/2024
(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....
doi.org
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...
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Duncan Sproul @sproullab.bsky.social · 13/11/2024
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
embopress.org
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...
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Vijay Ramani @vram142.bsky.social · 15/11/2024
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
cell.com
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...
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Jon Henninger @jhenninger.bsky.social · 11/11/2024
First post! I am a new Assistant Professor at Carnegie Mellon University exploring how RNA molecules regulate transcription and cell fate. Check out our recent review in this space! www.cell.com/molecular-ce...
cell.com
An RNA-centric view of transcription and genome organization
RNA molecules are involved in diverse regulatory mechanisms that contribute to gene activation, gene repression, and genome structure. Henninger and Young discuss how the more traditional DNA-protein-...
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Maxim Greenberg @maxvcg.bsky.social · 12/11/2024
I've been meaning to write a lengthy thread about our experiences with DNA methylation editing in mouse ESCs if that would be useful (or interesting?) for a niche audience here. tl;dr: it was frustrating but we learned a lot, and it ended with our shiny new pub (1/17) www.nature.com/articles/s41...
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Francesca Mattiroli @fmattiroli.bsky.social · 12/11/2024
The peer-reviewed version of our paper is out! Thanks to all co-authors, editor and reviewers for the smooth process 🤓🎉 And don’t miss the chromatin haiku! www.cell.com/molecular-ce...
cell.com
Acute multi-level response to defective de novo chromatin assembly in S-phase
Dreyer et al. show the broad and rapid impact that acute inhibition of chromatin formation in S-phase has on DNA replication, chromatin stability, and cell-cycle progression. This study sheds light on...
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Robin Allshire 🇮🇪 🇪🇺✊🏿 ⬆️ Zak’s favourite nucleosome: K9me @allshire-lab.bsky.social · 13/11/2024
Our latest Preprint is now on BioRXiv: www.biorxiv.org/content/10.1... It explains how heterochromatin-dependent epimutations mediate resistance to caffeine & antifungals by imposing mitochondrial dysfunction. Thanks to all authors for their efforts especially Andreas Fellas & Alison Pidoux. Enjoy!
biorxiv.org
Heterochromatin epimutations impose mitochondrial dysfunction to confer antifungal resistance
Global health and food supply are endangered by an increasing frequency of antifungal resistance in pathogenic fungi. Wild-type fission yeast, Schizosaccharomyces pombe, can gain resistance to insults...
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Jackson Hoffman @jxhoffman.bsky.social · 13/11/2024
starter pack 2 for all things #chromatin, #transcription, and adjacent: go.bsky.app/Q5sXc6E - reply to self-nominate or suggest colleagues! check out pack 1: go.bsky.app/5zgpZfg and @sproullab.bsky.social's pack: go.bsky.app/TKp9YAn for more people to follow
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Fena Ochs @fenaochs.bsky.social · 13/11/2024
Hi Bluesky! I made a 3D chromatin starter pack. Let me know if you would like to be added. go.bsky.app/6tTQdqQ
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Duncan Sproul @sproullab.bsky.social · 12/11/2024
Hi all, just to say thanks for all the enthusiasm about the #epigenetics, Chromatin and Gene Regulation starter pack. The interface is a bit unreliable so a few people I added got missed off 😬. If you notice this applies to you, just message me and I'll try again. go.bsky.app/TKp9YAn
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Duncan Sproul @sproullab.bsky.social · 14/11/2024
Our 2025 MRC HGU PhD program is open for applications. Excellent human genetics projects in a friendly, #interdisciplinary environment. We have a project for those keen on the molecular mechanisms through which #epigenetics causes human disease: institute-genetics-cancer.ed.ac.uk/igc-graduate...
institute-genetics-cancer.ed.ac.uk
MRC four-year International PhD programme: Human Genetics, Genomics and Disease
Applications now open.
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zack chiang @zchiang.bsky.social · 11/11/2024
7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/
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Richard Sever @richardsever.bsky.social · 14/11/2024
Clarivate will strip eLife of its Impact Factor They never wanted one but will be interesting to see how this affects submissions given academia's obsession with it. retractionwatch.com/2024/11/13/e... But 1/2
retractionwatch.com
eLife won’t get an impact factor, says Clarivate
Clarivate, the data company for scholarly publications, has decided to continue indexing some content from eLife in Web of Science, after reevaluating the open-access biology journal’s unusual prac…
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Alper Akay @alperakay.bsky.social · 14/11/2024
We are advertising two PhD positions in our lab on RNA splicing and modifications in development and cancer. NRPDTP project is open to international applicants. UEA project is for UK applicants only. With Yiliang Ding and Mark Williams www.findaphd.com/phds/?Keywor...
findaphd.com
akay PhD Projects, Programmes & Scholarships
FindAPhD. Search Funded PhD Projects, Programmes & Scholarships in akay. Search for PhD funding, scholarships & studentships in the UK, Europe and around the world.
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Yotam Drier @yotamd.bsky.social · 14/11/2024
Final improved version now published at www.pnas.org/doi/full/10....
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Yotam Drier @yotamd.bsky.social · 25/11/2023
A new preprint in these difficult times: www.biorxiv.org/content/10.1... We profiled the cis-regulatory landscape of lung neuroendocrine tumors in collaboration with Prof. Grozinsky-Glasberg, head of the NET unit at Hadassah Medical Center.
biorxiv.org
Enhancer heterogeneity of lung neuroendocrine tumors reveals sensitivity to FGF signaling inhibition
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/10/2023
We are hiring a Senior Biomedical Data Scientist for our lab at CeMM & the Medical University of Vienna. This is a senior staff position within the Bock Lab (bioinformatics, single-cell, CRISPR, cancer), with tenure-track option via @MedUni_Wien . Details: medical-epigenomics.org/files/Senior...
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Richard Sever @richardsever.bsky.social · 28/09/2023
bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...
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