Not my expertise at all but intrigued to learn more about this!
09.03.2026 22:32
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Not my expertise at all but intrigued to learn more about this!
Two decades of induced pluripotent stem cell research: From discovery to diverse applications
How do the H2A.Z histone variant and its dedicated chromatin remodeller SRCAP regulate gene expression ?
Beautiful work from @armelletollenaere.bsky.social now published @ www.nature.com/articles/s41...
Flyer for symposium: https://ctrlepiedit.sciencesconf.org/
Very excited to announce the FIRST symposium on epigenome editing! These tools are becoming widely used in mol bio, ag & therapy. It's time to bring leaders together to discuss this rapidly growing and exciting field. And why not in Paris! Please register & share! (1/2) ctrlepiedit.sciencesconf.org
Pls re-post: My department @oxfordbiochemistry.bsky.social are recruiting for several new faculty positions (links below). Broad search in molecular biology/biochemistry, across prokaryotes and eukaryotes. Interested in understanding life at the molecular level, this job might be for you!
1/n
Excellent opportunities in a top lab!
Figure 1.(A) Classical gel electrophoresis experiments showing mono-, di-, tri-, tetra-, and further multinucleosome bands upon chromatin digestion. (B) The nucleosome repeat length (NRL) is defined as the genomic distance between the centres of two neighbouring nucleosomes.
Figure 2.Nucleosome mapping using MNase-seq versus ATAC-seq. (A) In MNase-seq, nucleosomes in both open and tightly packed genomic regions are accessible to digestion. MNase preferentially cleaves DNA between nucleosomes and digests DNA until it encounters a histone octamer, which provides a footprint of nucleosome-protected DNA regions. (B) Bulk MNase-seq results in averaged maps across millions of cells, effectively capturing all possible nucleosome positioning configurations. (C) Single-cell MNase-seq (scMNase-seq) results in a noisier and sparser signal. The resulting footprints still represent nucleosome-protected regions, but not all nucleosomes are represented. (D) In ATAC-seq, open regions can be accessed by the enzyme Tn5 transposase, which can insert primers in regions free from the binding of nucleosomes and transcription factors (TFs). (E) For open chromatin regions, nucleosome maps can be obtained from ATAC-seq similar to MNase-seq. (F) Closed, tightly packed chromatin regions may be less represented in ATAC-seq nucleosome maps.
Figure 5.Molecular mechanisms affecting nucleosome spacing. (A) Linker histones H1 and nonhistone chromatin proteins which compete with H1s and modulate nucleosome spacing through structural and electrostatic mechanisms. (B) Chromatin remodellers actively reposition nucleosomes following context-dependent rules. (C) Cell state-dependent chromatin boundaries formed by CTCF and other structural proteins, as well as associated recruitment of chromatin remodellers which space nucleosomes. (D) Gene activity associated with remodeller action and RNA polymerases transcribing through the nucleosomes, leading to smaller distances between nucleosomes in regulatory regions and gene bodies. (E) DNA sequence repeats of different types.
![Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7rjg5hcnnloxgwuvwi23aixu/bafkreihl7mkdtxojw23qoqxm7yt57frzc24mjjllszhbohbvb67ffguccy)
Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).
Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/...
A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy!
@milena-bikova.bsky.social @chrsclrksn.bsky.social
Several COVID-19 severity associated genetic variants demonstrably change enhancer activity. Check out @gweykopf.bsky.social's preprint using STARR-seq and deep learning models to identify and get insight into some of these variants.
www.biorxiv.org/content/10.6...
I am very excited to host @danielibrahim.bsky.social for this talk “Enhancer-promoter specificity is determined by the promoter-proximal region” in our @enhancedgenomics.bsky.social seminar series ‘The 3D Regulatory Genome’
📅 05 March 2026 (today!)
⏰ 4 pm GMT
Please join us:
lnkd.in/eJ86KFNg
Excited to share our latest publication on interindividual variation of DNA methylation in human whole blood, spearheaded by the amazing Olivia Grant and co-led with @leo-schalkwyk.bsky.social and Meena Kumari.
link.springer.com/article/10.1...
Proud of @juruehle.bsky.social for getting her PhD paper on biorxiv! In it, we take synthetic enhancer screens to the single cell level, offering new insight into how transcription factors and enhancers interact 👀
1/ 🧵 In our new paper, we show that JARID2 and PALI1 mimic H3K27me3 to antagonise PRC2. www.cell.com/molecular-ce...
If you want to explore ncRNA dynamics during mammalian development, love microscopy, and are not afaraid of transposons biology, apply‼️
We are looking for a postdoc to join our team at @imbavienna.bsky.social
More details 👇🏻
Find our latest Perspective article in Nature Genetics on "The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements" at www.nature.com/articles/s41..., with implications for the future of research on the cause of human disease.
Delighted to share our paper, out today in @natplants.nature.com
Not all “wasted” carbon is lost: formate released during photorespiration can be reused to support DNA methylation. Our work reveals a metabolic link between CO₂ levels and epigenetic regulation in Arabidopsis.
doi.org/10.1038/s414...
I’m thrilled to share that my PhD work has been just published in Cell. After a long and bumpy ride, we uncovered the core function of nuclear speckles -splicing of GC-levelled exons- and traced the evolution of this gene architecture and condensates themselves to amniotes.
Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology.
www.science.org/doi/10.1126/...
🤩💪 Out now! 3D regulatory hubs in sex determination
With @mamartirenom.bsky.social & Capel labs, led by @imotagom.bsky.social & @jrotwitguez.bsky.social
1️⃣ METALoci – explore #3DGenome 🧬
2️⃣ Non-coding region controlling Fgf9 🧩
3️⃣ Meis genes = new key players 🌟
👉 rdcu.be/e5sm2
1/n Bluetorial 👇
We wrote a piece on how easy it is to write gene regulatory sequences. - Turns out, it isn't that easy even though we know a lot about cis-regulation.
huge credit to @carldeboer.bsky.social to seeing this through so our thoughts aren't lost. I promise, it's a worthwhile read!
Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...
🧬 @danielibrahim.bsky.social, moderated by @stefanschoenfelder.bsky.social, on enhancer-promoter specificity & how promoter-proximal regions act as molecular filters.
Register: us02web.zoom.us/webinar/regi...
March 5, 4PM UK.
#Genomics #GeneRegulation
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.
Join us tomorrow for two exciting enhancer talks!
Save the date!
We have an exciting conference coming up next year for the UK Mechanobiology community!
Our work on the interplay between loop extrusion and chromatin mechanics is finally out in @physrevresearch.bsky.social . Congrats @hosseinsalari.bsky.social for the hard work ! 👏
journals.aps.org/prresearch/a...
Sorry to clarify: the relatively low success rate (compared to our RNA-seq and ATAC-seq libraries) is something we see across antibodies; it’s not H3K27ac specific. They eventually all work - we just have to repeat more than I’d like.
Thanks Matthias. Our H3K27ac CUT&Tag libraries are definitely usable but we’ve found the FRiP scores are consistently lower than for ChIP-seq. We’ve tried several different antibodies. Might just be us though of course
Would love to hear if others have had similar experiences - many thanks for sharing in advance
2.) Even more frustratingly, our 'hit ratio' for CUT&Tag is still quite low. I would estimate 90-95% of our RNA-seq and ATAC-seq libraries are high quality, but for CUT&Tag it's closer to 60%. It's not a batch effect, it's not antibody-specific - frustratingly we've never been able to figure out why