Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity.

MRC Laboratory of Medical Sciences@mrc-lms.bsky.social · yesterday

New research published today in Nature Genetics uses a technique called mini-Capture Hi-C to map 3D DNA folding in rare ILC3 immune cells, linking 100+ genes to immune disease risk in this cell type 🧬

Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

Jesse Engreitz@jengreitz.bsky.social · 2y ago

Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social Thread👇

Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...

Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback

In Schizosaccharomyces pombe , the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methy...

biorxiv.org

1/ New paper alert! 🎉🧬 Our study on #9p21 gene regulation is out in #CellGenomics: "Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes" (Torlai Triglia, Miller, et al. www.cell.com/cell-genomic... 🧵

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

Controlled blinking of upconverting nanoparticles - no bleaching means attractive potential as an SMLM probe! www.nature.com/articles/s41...

We know little about proteins required for long-range compartment 3D interactions, but this @kyleeagen.bsky.social lab preprint shows that NSD3 can make Mb-scale long-range compartment-like interactions: www.biorxiv.org/content/10.6...

Very interesting study showing that active non-equilibrium fluctuations are required to explain chromatin organization at the 10-100kb scale:

Ranjith Padinhateeri@ranjithpa.bsky.social · 3mo ago

Our new preprint: Chromatin at ~10–100 kb scales behaves very differently from standard polymer expectations. DNA-PAINT data reveal broad fluctuations and sharp local bends. Our study suggests emergent active forces at these scales and quantifies the nature and strength of this activity

our paper starts with an analysis of the dynamics of 3D chromatin in cardiac differentiation, for ventricular and atrial cardiomyocytes. They are different! And by single cell methyl-HiC we can discern subtype differences. www.science.org/doi/10.1126/...

Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor

Dosage-sensitive transcription factors (TFs) underlie altered gene regulation in human developmental disorders, and cell type–specific gene regulation is linked to the reorganization of three-dimensio...

science.org

Masahiro and I were fortunate to contribute some RCMC analyses to this beautiful paper from Koska and Wysocka that comprehensively dissects the determinants of promoter competition: www.nature.com/articles/s41...

The number of secretaries in Rhode Island correlates with Customer satisfaction with UPS (r=0.926)

Genome Research has just announced an exciting call for spatial 'omics related papers! I am thrilled to be co-editing this special issue with Jian Ma (@jianma.bsky.social) and Christina Leslie!

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

doi.org

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · last yr.

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

An encyclopedia of enhancer-gene regulatory interactions — online today! nature.com/articles/s4158… Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model 1/

Andreas Gschwind@argschwind.bsky.social · 3w ago

Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/

(1/5) Excited to share our new paper in Advanced Science! We combine genome editing, super-resolution microscopy, and single-molecule tracking to investigate the endogenous oncogenic fusion transcription factor EWS::FLI1 in Ewing sarcoma cells. advanced.onlinelibrary.wiley.com/doi/full/10....

Dynamic Regulation of Endogenous Transcription Factor Hubs at Single‐Molecule Resolution

This study combines single-molecule microscopy and genome editing to characterize the dynamic behaviors of endogenous oncofusion transcription factor EWS::FLI1 in Ewing sarcoma cells. EWS::FLI1 forms...

advanced.onlinelibrary.wiley.com

MIT ACCESS is an opportunity for undergraduates to explore cutting-edge research and graduate education in science and engineering. See for yourself what grad life is like at MIT! Applications due Aug 1: access.mit.edu @mitcheme.bsky.social @mitchemistry.bsky.social

Excited to share the first preprint from my lab! Transcription has been implicated in regulating SMC complex function, but how this works has been unclear. Here, we use a yeast quiescence model to examine how transcription targets condensin.

bioRxivpreprint@biorxivpreprint.bsky.social · 3w ago

Asymmetric condensin loop extrusion is regulated by RPA-coated single-stranded DNA in quiescent cells https://www.biorxiv.org/content/10.64898/2026.07.10.737861v1

Very interesting and comprehensive study using synthetic activation of enhancers to probe the rules of distal vs. proximal gene regulations:

Elias Friman@eliasfriman.bsky.social · 3mo ago

Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...

@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 · 3w ago

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

Got a Zombie Fly? MCB Scientists Want Your Help Mapping a Mind-Controlling Fungus 🧪 🧬 🔬 #AcademicSky #higherEd www.mcb.harvard.edu/department/n... @zombiflied.bsky.social @naoshigeuchida.bsky.social @harvardmuseums.bsky.social @boschildmuseum.bsky.social @museumofscience.bsky.social @harvard.edu

Got a Zombie Fly? MCB Scientists Want Your Help Mapping a Mind-Controlling Fungus - Harvard University - Department of Molecular & Cellular Biology

A dead fly perched high on a blade of grass, wings raised, glued in place by its own mouthparts, might look like something out of a horror movie. […]

mcb.harvard.edu

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...

rdcu.be

Popularity of the first name Kenzie correlates with UFO sightings in South Dakota (r=0.939)

New paper! 🚀 A high-affinity anti- #mNeonGreen #nanobody turns #mNG into a #multifunctional Tag. @nanotag.bsky.social decided to openly share the #nanobody for research use. Not common, but we strongly believe well-defined reagents are key for reproducible science. We hope you find it useful! 💚

It was an absolute pleasure to write a News&Views for @andersshansen.bsky.social lab's newest paper in NSMB. Here, the authors provide absolute quantification of chromatin loops genome-wide: www.nature.com/articles/s41...

Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology

By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...

nature.com

@dimitristypas.bsky.social · last mo.

In an associated News & Views, @fenaochs.bsky.social provides what I at least found an eloquent, insighftul and broad exemplification and contextualisation of what the study could mean for the field and what could follow. www.nature.com/articles/s41...

Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.

Our evil ORFeome paper is out! In collaboration with @alex-stark.bsky.social, we screened ~4,000 viral proteins and secreted effectors from bacteria and parasites, covering hundreds of diverse pathogens, for phenotypes in human cells.

In an associated News & Views, @fenaochs.bsky.social provides what I at least found an eloquent, insighftul and broad exemplification and contextualisation of what the study could mean for the field and what could follow. www.nature.com/articles/s41...

Putting numbers on chromatin looping - Nature Structural & Molecular Biology

Chromatin looping is a fundamental feature of genome organization that contributes to gene regulation and genome stability. Yet how often loops form in living cells has remained difficult to answer. J...

nature.com

I am on paternity leave but I need to talk about this work by the @andersshansen.bsky.social lab that was published @natsmb.nature.com. The authors provide absolute quantification of chromatin loops across the genome. www.nature.com/articles/s41... Putting actual numbers in E-P, P-P and all loops!

Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology

By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...

nature.com

And thanks so much to Adrian Henggeler and @fenaochs.bsky.social for writing such a thoughtful News&Views: www.nature.com/articles/s41...

Anders Sejr Hansen@andersshansen.bsky.social · last mo.

Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates

Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates

Anders Sejr Hansen@andersshansen.bsky.social · 2y ago

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...