The function of nuclear speckles is revealed! This is an incredibly important paper with absolutely beautiful data! Wow! www.cell.com/cell/fulltex...
25.02.2026 17:43
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The function of nuclear speckles is revealed! This is an incredibly important paper with absolutely beautiful data! Wow! www.cell.com/cell/fulltex...
Please check out our new review on emerging oligo-based imaging methods in studying chromatin organization, which summarizes recent advances in DNA FISH and its applications in chromatin tracing, live-cell imaging, lineage reconstruction, and optical pooled screening.
Link: bit.ly/46YV3Qb
π¨New preprint from the labπ¨
𧬠What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK.
www.biorxiv.org/content/10.1...
π¨ Preprint alert π¨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A π§΅π
doi.org/10.1101/2025...
Our new findings on how chromosomes get ready for cell division are now published in @cellpress.bsky.social!
Congratulations, Kai, @andibrunner.bsky.social and everyone else involved! π€©
www.sciencedirect.com/science/arti...
Brown University Professor and kidney transplant expert is deported despite valid visa, judge's order, and petition.
www.nytimes.com/2025/03/16/u...
Graphical abstract for Binan et al., Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits
Fantastic work from my soon-to-be neighbour LoΟc Binan (and all)! Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits
www.cell.com/cell/fulltex...
UMASS IS RESCINDING ALL GRAD POSITIONS FOR THIS YEAR
Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1
Amid concerning times, sharing a bit of positivity: our 1st preprint of 2025 (funded VIA NIH COMMON FUND), heroically led by Marty Yang (@martyyang.bsky.social) w/ huge assist from @genophoria.bsky.social lab. Lots to cover so letβs get this tweetorial started (1/n)! www.biorxiv.org/content/10.1...
Thermodynamic principles link in vitro transcription factor affinities to singlemolecule chromatin states in cells
www.biorxiv.org/content/10.1...
Every once in a while we publish a paper that moves a whole field forward. I think that's the case for this one from the Bugaj lab, where they describe proteins for THERMOGENETIC control of cellular behavior. www.nature.com/articles/s41...
Itβs official π I am excited to share that I will start my lab this spring at the Max Planck Institute for Immunobiology and Epigenetics @mpi-ie.bsky.social in beautiful Freiburg π€©π»βοΈ I am looking forward to new collaborations and working with the fantastic community in Freiburg & its surroundings!
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: <loops> are generally rare (2.3%)
www.biorxiv.org/content/10.1...
Enhancer scrambling strategy
We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels π§΅
www.biorxiv.org/content/10.1...
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
How to test the functional impact of non-coding variants in vivo? We developed a new method called dual-enSERT, which can quantitatively compare the effects of enhancer variants in live mouse embryos in under two weeks. www.nature.com/articles/s41... 1/n
𧬠Weβre excited to introduce D&D-seq, a single-cell technology that maps DNA:Protein interactions through molecular footprinting. Check it out here: biorxiv.org/content/10.1... #Genomics #Epigenetics
Is chromatin ordered or disordered? It all depends on the linker DNA length.
Check our latest work with Mike Rosen and Sy Redding. We explore how changes in linker DNA length (as small as 1 bp) fine-tune chromatin structure, between order and disorder, and the properties of chromatin droplets
Deaminase-mediated chromatin accessibility profiling with single-allele resolution www.biorxiv.org/content/10.1...
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, π¬ focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
1/π Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! π§΅π
biorxiv.org/content/10.1101/2024.12.11.627935v1
πΊπΊπΊRED TRIANGLE ALERT πΊπΊπΊ
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!
Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!
SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...
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...
Thrilled to announce that our latest work has been published in Science and featured on the front cover!
www.linkedin.com/posts/scienc...
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)
Our paper on a centromere-enriched retroelement is out! link.springer.com/article/10.1... Congratulations to all the authors! Comments and reposts welcome and appreciated π§¬π¬
PCP maps 3D genome organization at the nucleosome level. (a) Schematic of the PCP reaction on chromatin. Crosslinked chromatin is digested into nucleosomes by Caspase Activated DNAse (CAD) and then immobilized onto magnetic beads. Digested chromatin is ligated by seed and receptor molecules to the ratio of 1/10. The PCP reaction takes place on the beads where RNA tags will diffuse from the seeds and tag nearby receptors. The chromatin is then decrosslinked, the proteins and RNA removed, and a sequencing library generated by PCR. Molecules sharing the same UMI are grouped. Tag groups can be analyzed in several ways, including individual multiway tag groups or pairwise interaction matrices. (b) Plot showing the relative frequency of receptor tagging as a function of distance from the seed, the midpoints of the tagged molecules is shown. Seeds that self-tag are excluded from this analysis. (c) Plot showing the number of reads per seed tag groups for G1 data. (d) Distance decay interaction plots of PCP (orange) and Micro-C (Costantinto et al. 2020, 15 min 23Β°C sample) (res = 50bp).
Regularly spaced nucleosome arrays are prevalent over the genome. (a) Meta analysis of PCP matrices relative to the dyad of the +1 nucleosome of genes longer than 2Kb, 50 least expressed genes (res = 10bp). (b) As a, but for the 50 most expressed genes (res = 10bp). (c) PCP map of low expressed gene RNR3 (middle, res = 25bp), Nucleosome profile (grey). Note the grid-like pattern across the entire gene body. (d) PCP map of the expressed gene FMP27 (res = 25bp), Nucleosome profile (grey). Note the grid-like pattern at the 5β end of the gene and parallel stripes at towards the middle and 3β end of gene. (e) Schematic of the results observed. No pattern is obtained with poorly spaced, poorly positioned nucleosomes. Dotted pattern is obtained with regularly spaced, well positioned nucleosome arrays. Striped pattern is obtained with regularly spaced delocalized arrays. The number of parallel stripes indicates the number of nucleosomes in the array. (f) Meta plot of highly transcribed, ribosomal protein genes. The genes are organized with respect to the Rap1 protein at position 0. Top panel, Rap1 ChIP-MNase in blue (Gutin et al. 2018), All reads size, Mono-nucleosomal (Nuc.) reads only and Sub-nucleosomal reads only (Sub. 20 bp < insert size < 90 bp) are represented. Medium panel represent the density of read by position relative to insert size from mapped PCP data. The bottom panel is a pile-up analysis of PCP matrix oriented relative to the RP genes (res = 10bp). Note that the gene body contains short, delocalized nucleosome arrays. (g) Frequency of tagging relative to the seed position for the subset of genes used in a and b. The most expressed genes are in red and least expressed genes in blue. (h) Frequency of tagging relative to the seed position for gene of at least 600bp. The most expressed are in orange and the least expressed is in blue.
Interesting new method to map nucleosomes in 3D, "Proximity Copy Paste (PCP)". www.biorxiv.org/content/10.1...
βΆοΈ mapped connectivity of nucleosomes in S. cerevisiae
βΆοΈ chromatin is predominantly organized into regularly spaced nucleosome arrays
βΆοΈ metaphase chromosomes packed by arrayed cohesin hubs
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