Marta Shahbazi dirige un grupo en el legendario Laboratorio de Biología Molecular de Cambridge, cuyos científicos han ganado una docena de premios Nobel. El equipo de la española ha iluminado los primeros días de la fecundación humana. Más información ➡ social.elpais.com/_bj…

Sharing our new preprint 🧬 *Generative design of functional disordered regions in a developmental TF*. Lance Denes @lancedenes.bsky.social sums it up nicely in this thread!

Lance Denes@lancedenes.bsky.social · 3d ago

New preprint. We extend generative protein design to the disordered proteome… A collaboration between the Lionnet, Holt, and Holehouse labs. @successprocess.bsky.social @liamholt.bsky.social @alexholehouse.bsky.social @remenecker.bsky.social www.biorxiv.org/content/10.6...

🚨Preprint from our lab🚨 How and when did TADs emerge during evolution? 🐁🐟🪰 HINT: the diversification of CTCF regulation and functions enabled new mechanisms of 3D chromatin folding 🧬 With Liene Astica & @rdacemel.bsky.social Link: www.biorxiv.org/content/10.6... Bluetorial 1/15👇

🎉 Our paper is out today in @science.org! How does the intestine maintain the right balance of cell types? We find that signalling rhythms matter! So proud of our three shared first authors, Sonja Weterings, @hiromuneeto.bsky.social & @jddeleede.bsky.social! 🔗 www.science.org/doi/10.1126/...

Are weak TF motifs important? Weilert et al use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong pioneer motifs to drive chromatin opening. Paper: www.cell.com/cell-genomic... Preview w/ Grace Bower: www.cell.com/cell-genomic...

Deep learning uncovers hidden power of low-affinity motifs

Low-affinity transcription factor binding sites are functionally important but difficult to map and mechanistically poorly understood. In this issue of Cell Genomics, Weilert et al. leverage sequence-...

cell.com

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 🧪 Experimental backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

Postdoc position in Moises Mallo's lab 👍. Super science in the great new GIMM institute in Lisboa. Please RT

Join our lab! We're hiring TWO positions: One Wellcome-funded postdoc to study how nutrition impacts male fertility. One Crick-PACE fellowship in collaboration with @taponlab.bsky.social to study the dynamics of mTOR signalling. More info on our website: www.amoyellab.com/join-the-team

Join the team | Amoyel Lab

amoyellab.com

1/ I’m excited to share our new work, now out in @natneuro.nature.com! This was a wonderful collaboration with my long-term collaborator @steinlab.bsky.social, led by two fantastic trainees, @nanamatoba.bsky.social and Jessica McAfee. www.nature.com/articles/s41...

Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants - Nature Neuroscience

A large-scale functional screen identified noncoding variants that regulate gene activity during human brain development, providing insights into the molecular mechanisms that shape differences in hum...

nature.com

Infertility affects ~1 in 6 people, and up to 30% of cases are unexplained. I am excited to present my postdoctoral work from @toddmacfarlan.bsky.social 's lab, now available as a preprint: tinyurl.com/yync6f2r addressing a possible role for the meiotic gene PRDM9 in infertility 🧵/1

Sharing ZATELLITE 🛰️ - a tool to visualize and manipulate repetitive loci in living cells using designer zinc fingers tinyurl.com/ZATELLITE led by Nestor Saiz, collab with Marcus Noyes, @teresadavoli.bsky.social, @glennislogsdon.bsky.social, @liamholt.bsky.social & @jefboeke.bsky.social (1/n)

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Noncoding transcription controls the developmental dynamics of long-range gene regulation

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

science.org

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

nature.com

Glad to see this out and happy that we could contribute to interesting study in which a surprising role for WAPL and WAPL/CTCF depletion in 2CLC conversion has been uncovered: link.springer.com/article/10.1... Congrats to Sergio and team!

Alterations in chromatin organization promote totipotent-like features in a DPPA2/DUX-dependent manner - The EMBO Journal

2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Although CTCF depletion induces 2CLC conversion in mouse ESC, whether this reprogramming is ...

link.springer.com

In a new (ish) preprint, we used CRISPR barcodes to label germline stem cell clones in zebrafish, then tracked their contributions to sperm production for 2 years. Instead of staying stable, individual clones rose, fell, and disappeared over time. www.biorxiv.org/content/10.6...

Clonal dynamics deviate from neutral drift in zebrafish spermatogenesis

Spermatogonial stem cells (SSCs) maintain male fertility, but how their clonal dynamics change with age remains poorly understood. Here, we use in vivo CRISPR barcoding in zebrafish to label SSCs and ...

biorxiv.org

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...

Nature Protocols@natprot.nature.com · 4mo ago

New Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

Introns have a hidden regulatory role! 🧬🎉 Delighted to share our latest paper showing that inefficiently spliced introns and spliceosomal proteins direct RNA methylation, engaging RNAi to silence retrotransposons and regulate gene expression nature.com/articles/s41...

bioRxiv alert! CoPhasing resolves haplotype-specific 3D chromatin structures from GAM data, revealing extensive structural heterogeneity between human homologous chromosomes and its interplay with histone modifications and gene expression! Thanks to all coauthors! www.biorxiv.org/content/10.6...

After some good funding news, we are hiring! Looking for a postdoc to join our team and lead our explorations into transposon repression by the nuclear lamina. Check out the full ad on our lab website at buchwalter-lab.github.io/postdoc-ad.pdf + contact me to learn more!

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

Interested in hearing about mechanisms of cohesin-dependent vs. -independent enhancer regulation? @karissalhansen.bsky.social will be presenting her work **Tues June 23rd 8am CET** www.biorxiv.org/content/10.6... www.science.org/doi/10.1126/... Thank you @genome-org-aus.bsky.social ! 👇

GOA - Genome Organisation Australia@genome-org-aus.bsky.social · 5mo ago

Only one week to go until our next GOA seminar! @karissalhansen.bsky.social will present here work on the mechanisms of long-range enhancer-promoter communication. Registration link: unimelb.zoom.us/webinar/regi...

🚨Preprint Drop🚨 We are very pleased to release our study on DNA methylation dynamics at enhancers during ESC differentiation! This work was led by Marlet Morales-Franco and Priscillia Lhoumaud 🧵(1/13) www.biorxiv.org/content/10.6...

Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency

Cis-regulatory elements, such as enhancers, play an essential role in coordinating gene expression programs during cellular transitions. As such, substantial efforts have been made to characterize enh...

biorxiv.org

1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...

We are over the moon! 🎈 Dr. Marieke Oudelaar joins the MPI-IE as a new #MaxPlanck Director, heading the newly established Department of Genome Biology She studies how the 3D folding of DNA controls gene expression – more details below ⬇️ Welcome to #Freiburg, @mariekeoudelaar.bsky.social!

Marieke Oudelaar becomes new Director at MPI-IE in Freiburg

ie-freiburg.mpg.de

📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...

High-dimensional data is hard to understand. But is it truly cursed? To help you build better intuition for high-dimensional datasets, @lekschas.de and I developed dtour, a visualization tool for smoothly navigating through data projections.

New preprint from my lab! Will Anderson developed a transgenic #zebrafish ubiquitously expressing an optogenetic FGF/ERK activator. We're having a lot of fun with it and think you will too! www.biorxiv.org/content/10.6...

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇