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Reposted by Simon Gaudin

Dr. Sedona Murphy @sedonamurphy.bsky.social · 19h

If you’re interested in exploring the relationship between chromatin organization and epigenetic memory using chromatin tracing microscopy, my group is recruiting a talented PhD student 🥳

Max Planck Institute for Molecular Genetics @molgen.mpg.de · 23h

🚨 Please share! We are seeking motivated PhD students who wish to work at the intersection of molecular life sciences and computational sciences.
#IMPRS #IMPRSBAC @freieuniversitaet.bsky.social @maxplanck.de
Check out our projects and apply by Jan 7th, 2026!
www.molgen.mpg.de/IMPRSPhDproj...

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Reposted by Simon Gaudin

Edda Schulz @eddaschulz.bsky.social · 2d

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology

Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

www.nature.com

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Reposted by Simon Gaudin

Mikhail Spivakov @mspivakov.bsky.social · 5d

Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.

In a new preprint, we share some clues about when, how, and why this happens!

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

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...

www.biorxiv.org

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Reposted by Simon Gaudin

Camille Moore @camille-moore.bsky.social · 6d

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

www.science.org

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Reposted by Simon Gaudin

Raquel Fueyo @fueyoraquel.bsky.social · 7d

Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD

A human-specific regulatory mechanism revealed in a pre-implantation model

Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.

rdcu.be

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Jamie Hackett @jamiehackett.bsky.social · 12d

❓Can a father’s environmental exposures before conception influence their offspring?

We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences

www.embopress.org/doi/full/10....

Embryonic signatures of intergenerational epigenetic inheritance across paternal environments and genetic backgrounds | The EMBO Journal

imageimagePaternal environmental exposures have been linked with modulation of phenotype and disease risk in offspring via largely unclear mechanisms. This study employs in vitro fertilization and sin...

www.embopress.org

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Daniel Jost - Physical Biology of Chromatin group @djost-physbiol.bsky.social · 9d

New preprint from the lab !! Loop extrusion may provide mechanical robustness to chromatin. Great work by Hossein Salari. @cnrs.fr @lbmcinlyon.bsky.social
www.biorxiv.org/content/10.1...

Loop extrusion provides mechanical robustness to chromatin

Chromosomes are complex biopolymers folded into dynamic loops via a loop extrusion process and may experience various mechanical forces in vivo . We develop a force-dependent model of chromatin loop e...

www.biorxiv.org

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Reposted by Simon Gaudin

Géraldine Laloux @lalouxlab.bsky.social · 14d

📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

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

Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle

The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...

www.biorxiv.org

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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 14d

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🧵👇

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Maxim Greenberg @maxvcg.bsky.social · 23d

Very excited to share an excellent review from @teresa-urli.bsky.social, published one week before her PhD defense! We did a deep dive into the fascinating biology of the variant Polycomb complex, PRC1.6 (1/5) journals.plos.org/plosgenetics...

Epigenetic relay: Polycomb-directed DNA methylation in mammalian development

In mammals, repression of germline-specific gene expression is essential for preserving somatic cell identity and preventing disease. Germline gene silencing is often dependent on the presence of prom...

journals.plos.org

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Reposted by Simon Gaudin

Anders Sejr Hansen @andersshansen.bsky.social · 17d

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...

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Reposted by Simon Gaudin

mathiaseder.bsky.social @mathiaseder.bsky.social · 19d

✨Exciting news: the main story of my PhD is out in Science!

Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.

📖 Read the full story here: www.science.org/doi/10.1126/...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

www.science.org

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Simon Gaudin @simongaudin.bsky.social · 19d

We observe that loci search kinetics are generally in agreement with a « crumpled globule » model, but deviate at submegabase scale, where cohesin accelerates search and gives rise to « kinetically associated domains »; and put a number on extrusion speed based on v rare *processive* events in cells

Simon Gaudin @simongaudin.bsky.social · 19d

Our Boettiger lab paper on live-cell imaging of DNA motion across genomic scales is out! www.science.org/doi/10.1126/...

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging

Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

www.science.org

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Simon Gaudin @simongaudin.bsky.social · 20d

On the mystery of distal enhancer-promoter communication

Anders Sejr Hansen @andersshansen.bsky.social · 22d

Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...

Is enhancer-driven gene regulation all wrapped up? - Nature Reviews Genetics

In this Comment, Wendy Bickmore discusses mechanistic models of how 3D genome organization facilitates communication between distant enhancers and their target promoters to regulate gene expression.

www.nature.com

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Reposted by Simon Gaudin

Jesse Engreitz @jengreitz.bsky.social · 20d

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

👇

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bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

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Manuel Mendoza @longchrom.bsky.social · 20d

Our chromatin scaling paper is now out in its peer-reviewed form! 🎉
We added some controls, statistics, and a new introduction to better contextualise our findings. Overall a much-improved version we hope! (see my earlier thread for the preprint background)
www.sciencedirect.com/science/arti...

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siddhartha jena @epijenatics.bsky.social · 27d

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

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Ed Banigan @irate-physicist.bsky.social · Sep 3

Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters
www.biorxiv.org/content/10.1...
Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5

PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes

Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heter...

www.biorxiv.org

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Bas van Steensel lab (NKI) @basvansteensellab.bsky.social · Sep 2

Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!

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Kazuhiro Maeshima @kazu-maeshima.bsky.social · Aug 28

Is euchromatin really “open”? Our new study @bioRxiv suggests otherwise. Using super-resolution imaging @shiori-iida.bsky.social‬ @masaashimazoe.bsky.social reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing.
www.biorxiv.org/cgi/content/...

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Anders Sejr Hansen @andersshansen.bsky.social · Aug 26

Congratulations to Masahiro Nagano on his new paper on STAG3-cohesin.

STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...

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Reposted by Simon Gaudin

kasitc.bsky.social @kasitc.bsky.social · Aug 18

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

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Simon Gaudin @simongaudin.bsky.social · Aug 16

Absolutely epic

Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · Aug 16

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...

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 ...

www.biorxiv.org

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Reposted by Simon Gaudin

Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Aug 13

#Preprint alert! 📣

We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements

www.biorxiv.org/cgi/content/...

MLL2 facilitates long-range gene regulation through LINE1 elements

Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 d...

www.biorxiv.org

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