Ilya Flyamer

Congrats Noura! 🎉

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Terrific paper on a new chromosomal
compartment where extensive loop
extrusion isolates domains from
other such domains

Have you wondered how the rules of chromatin folding have evolved? Well, this task is not easy to formalize. But here is our take on it: train species-specific DNA-to-chromatin encoder, apply to DNA of unseen species, and build chromatin rules-based tree of life. Have a look:
doi.org/10.1093/nar/...

That sounds amazing!

Ah wow, I'm not a protein person, but that sounds easy😅 Thanks, I'll reach out if I decide to try it!

Well, a while ago was a few months ago... So I doubt it. Actually in this paper there is a custom more convenient version

Yeah I wanted to try this enzyme a while ago too, saw some papers using it for ChIP or something like that... but you have to purify it yourself😅 I wish it was available commercially, I would like to try it

Would anyone out there be able to share some Mus Spretus DNA with us? 🐀🧬 Any tissue of origin, for PCR amplification of selected genomic regions. Many thanks in advance!

In this specific paper there is a focus on two loci, one is I think >100kb. I offered you to try modeling this data many years ago😂

Far!

Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity - PubMed How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to st …

Nuclear hormone receptor enhancers activate gene expression within like 15 min, at this sort of distance... E.g. see here, but there is a ton of literature pubmed.ncbi.nlm.nih.gov/38781242/

🚨 Want to do a #Phd using high-throughput mutagenesis and CRISPR screens to understand how gene body methylation impacts transcription in collaboration with Greg Kudla's group? Do apply, deadline in a week! www.findaphd.com/phds/project...
Deadline 15th December 2025
#epigenetics Please share 🙏

📢 Last days to apply for our #PhD and #MDPhD programs! Become part of Basel, Europe’s #LifeScience hub, and grow in a dynamic, international, and supportive community. Apply by Nov 15: www.fmi.ch/education-ca...

📣 Paper alert!

I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...

Last chance to become a mentor in Sci.STEP, the call is about to close!

Congrats Wendy and team! Great news!

We are looking for mentors for the Sci.STEPS program! Please apply if you want to help your junior colleagues around the globe navigate their career path in any science related field.

Hi Marc, "minutes" is correct :) The CTCF and cohesin mediated loops, at least measured in those studies, are very stable

If you are curious about how cohesin regulates chromosome contact dynamics and its role in enhancer-promoter communication, check out our latest work. It’s been really fun to work with @nesslfy.bsky.social and @lucagiorgetti.bsky.social. Hope you enjoy reading it!

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇

Congrats, Charlene, amazing news!

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

New preprint with @gfudenberg.bsky.social

We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.

This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇

www.biorxiv.org/content/10.1...

Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development The spatial organization of chromosomes in the nucleus is fundamental to cellular processes. Contact frequency maps from Hi-C and related chromosome conformation capture assays are increasingly availa...

We're excited to share our new preprint, "Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development", led by Thomas Reimonn. www.biorxiv.org/content/10.1...

Very excited to share the first preprint of the lab! We show that the nuclear pore protein TPR forms biomolecular condensates which keep heterochromatin away from the nuclear pore complexes and maintains global chromatin organization. Check it out, share it, tell us what you think!!

You have to add it just 1 cell cycle before fixing the cells.

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

following this week's JC - this latest preprint from Giorgetti lab is *extremely* intriguing! TLDR: enhancers wake up promoters from their rare-bursting sleep and put them into a frequent-bursting state. The timescale is surprising - an Enh 150kb away activates the gene once a day!!

H2AK119ub Safeguards Against Ectopic Transcription Factor Mediated Gene Activation in the Developing Forebrain The PRC1 complex regulates developmental gene expression in mammals by ubiquitinating histones (H2AK119ub) and nucleating repressive chromatin interactions. Human genetic data and functional experimen...

Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...

Calling all aspiring Postdocs! One extra week to apply to join our exciting HFSP-funded project to uncover how chromatin moves to function.

Deadline July 15th.

www.mdc-berlin.de/career/jobs/...