Excited to share our new preprint on in situ chromatin structure of the inactive X chromosome in differentiated female mouse embryonic stem cells. www.biorxiv.org/content/10.6... 🧵1/8
Joe Bowness
@joebowness.bsky.social
Postdoc @CRG.eu Velten lab 🥼🧬🩸 gene regulation & single-cell genomics | PhD from Brockdorff lab Oxford
Very happy to share the first pre-print from my postdoc work with @larsplus.bsky.social (which we also presented at the excellent @isehsociety.bsky.social Annual Meeting last weekend). Here we performed a CRISPRi Perturb-seq screen targeting >500 transcriptional regulators in ex vivo mouse HSPCs.
Do you want to move to Oxford and join our lab? There is a computational biologist position open atm to develop and implement tools to analyse TE expression in single cell long read data and more. Apply! #TEsky #UniversityofOxford #postdoc
Rebecca Berrens@rberrens.bsky.social · 7mo agoWe are looking for a Postdoc to join our lab at @oxfordbiochemistry.bsky.social. This is a dry-lab focused post on the computational analysis of long read single-cell sequencing data to understand the role of transposable elements (TEs) in early development. my.corehr.com/pls/uoxrecru... #TEsky
Very excited to re-share the new pre-print from @juruehle.bsky.social et al! A result of lots of hard work to get the method to work (includes 5' targeted transcript capture!), and some very cool analysis. Honoured to be involved a little ☺️
Julia Rühle@juruehle.bsky.social · 7mo agoThe main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...
Early bird registration is closing Feb 28! We will have an AMAZING party!
Lars Velten@larsplus.bsky.social · 10mo agoISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols
Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...
doi.org
I am very happy to have posted my first bioRxiv preprint. A long time in the making - and still adding a few final touches to it - but we're excited to finally have it out there in the wild: www.biorxiv.org/content/10.1... Read below for a few highlights...
Decoding cnidarian cell type gene regulation
Animal cell types are defined by differential access to genomic information, a process orchestrated by the combinatorial activity of transcription factors that bind to cis -regulatory elements (CREs) to control gene expression. However, the regulatory logic and specific gene networks that define cell identities remain poorly resolved across the animal tree of life. As early-branching metazoans, cnidarians can offer insights into the early evolution of cell type-specific genome regulation. Here, we profiled chromatin accessibility in 60,000 cells from whole adults and gastrula-stage embryos of the sea anemone Nematostella vectensis. We identified 112,728 CREs and quantified their activity across cell types, revealing pervasive combinatorial enhancer usage and distinct promoter architectures. To decode the underlying regulatory grammar, we trained sequence-based models predicting CRE accessibility and used these models to infer ontogenetic relationships among cell types. By integrating sequence motifs, transcription factor expression, and CRE accessibility, we systematically reconstructed the gene regulatory networks that define cnidarian cell types. Our results reveal the regulatory complexity underlying cell differentiation in a morphologically simple animal and highlight conserved principles in animal gene regulation. This work provides a foundation for comparative regulatory genomics to understand the evolutionary emergence of animal cell type diversity. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, ERC-StG 851647 Ministerio de Ciencia e Innovación, https://ror.org/05r0vyz12, PID2021-124757NB-I00, FPI Severo Ochoa PhD fellowship European Union, https://ror.org/019w4f821, Marie Skłodowska-Curie INTREPiD co-fund agreement 75442, Marie Skłodowska-Curie grant agreement 101031767
biorxiv.org
Fresh preprint by @flavia-con.bsky.social from our lab uncovers how SMCHD1 finds & binds chromatin using live-cell single-molecule imaging🔬 She reveals how SMCHD1 dynamically engages chromatin, including the inactive X chromosome, to maintain gene silencing. www.biorxiv.org/content/10.1...
Selective interaction of the protein SMCHD1 with specific chromatin regions is governed by the loading factor LRIF1 and SMCHD1 ATPase activity
The chromosomal protein SMCHD1 is a GHKL ATPase that plays important roles in epigenetic silencing, including on the inactive X chromosome (Xi) and at the D4Z4 macrosatellite linked to regulation of D...
biorxiv.org
Extremely proud of my sis for persevering through a huge number of roadblocks to get this article published! It's really important these stories are documented & get heard widely as stimuli to redress inequalities in systems of research doi.org/10.1186/s409... (she's now on a publishing 🔥 streak!)
Peer researchers in NHS research: approved in principle, undermined in practice? - Research Involvement and Engagement
Background Despite the increasing support and expectation for involving people with lived experience in healthcare research in England, challenges persist when navigating organisational structures. Th...
doi.org
Monumental work! Huge congrats to all involved
Lars Velten@larsplus.bsky.social · last yr.Out @nature.com: Clonal tracing with somatic epimutations 🧬 Single cell methylome encodes cell state & clonal identity 🔨 EPI-Clone reads out both (+mutations, +RNA) at scale 🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations doi.org/10.1038/s415... 🧵
It was such a pleasure to visit the beautiful cities of Bonn and Cologne, and have the opportunity to present my postdoc work at the @dzne.science. Thank you so much for hosting me @jsschrepping.bsky.social!
Great to see the final form of this huge effort from the lab now published! Congrats Robert @juruehle.bsky.social @larsplus.bsky.social and all 🎉🎉 Read all about it this really cool work below ⬇️
Lars Velten@larsplus.bsky.social · last yr.Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵
Excited to share this story from the “Chromatin Dream Team” in the @arnausebe.bsky.social lab on chromatin evo across eukaryotes! 12 histone mark profiles from 12 species, including rhizarians, discobans, and cryptomonads. Read on to see what we found! www.biorxiv.org/content/10.1... 1/n
Diversity and evolution of chromatin regulatory states across eukaryotes
Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. ...
biorxiv.org
Perfectly summarised! It was great to be part of such a fantastic event, and seamlessly cooperative organisation team. 😄
Chiara Azzi@azzichia.bsky.social · 2y ago🎉 That’s a wrap! The International CRG-BI Postdoc Symposium has come to an end after three incredible days of inspiring talks, engaging discussions, and valuable connections. I have to say I couldn’t be happier! #CRGBIpostdocs A 🧵 below 👇🏼
Preprint alert. Excited to share our latest work. We demonstrate that the primary function of m6A on Xist is to promote RNA degradation. www.biorxiv.org/content/10.1...