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Reposted by Marieke Oudelaar

Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 3d

🚨 Paper alert: Using liver organoids and in vivo models, the Akhtar lab and first-author @mwiese.bsky.social revealed how the epigenetic regulator KANSL3 shapes transcriptional programs driving liver function and development.

More in @lsajournal.org:
www.life-science-alliance.org/content/8/12...

KANSL3 controls hepatocyte differentiation and metabolism via histone acetylation. Loss of this epigenetic regulator leads to hyperplasia and liver fibrosis.

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Reposted by Marieke Oudelaar

Till Schwämmle @tschwammle.bsky.social · 3d

Happy to share the 2nd part of my PhD @natsmb.nature.com!

Using CRISPR screens, we uncover the TF-RE wiring underlying Xist regulation. Since the preprint, we've added a titration of Xist, showing that XCI is directly dependent on Xist levels.

Check the Bluetorial by @eddaschulz.bsky.social 👇

Edda Schulz @eddaschulz.bsky.social · 3d

⚠️ 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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Scaffidi Lab @scaffidilab.bsky.social · 9d

Histone acetylation - not always about transcriptional activation: H4K16ac safeguards the genome replication program by repressing premature replication of heterochromatin. Well done Marta Milan! tinyurl.com/yuy9m8t3

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Vijay Ramani @vram142.bsky.social · 19d

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers

DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

www.biorxiv.org

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Francesca Mattiroli @fmattiroli.bsky.social · 19d

The latest work from ours and @vram142.bsky.social lab is out! True teamwork to visualize nascent chromatin with strand resolution, using a fully reconstituted system. Very proud of superstar-PhD student Bruna, and @palindromephd.bsky.social. Learning so much from Vijay’s amazing technologies! RT

Vijay Ramani @vram142.bsky.social · 19d

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers

DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

www.biorxiv.org

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Reposted by Marieke Oudelaar

Job Dekker @jobdekker.bsky.social · 16d

New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan.
www.biorxiv.org/content/10.1...

Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons

We have investigated changes in chromosome conformation, nuclear organization, and transcription during differentiation and maturation of control and mutant motor neurons harboring hexanucleotide expa...

www.biorxiv.org

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Reposted by Marieke Oudelaar

Bas van Steensel lab (NKI) @basvansteensellab.bsky.social · 15d

Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights: 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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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15d

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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Jop Kind @jopkind.bsky.social · 22d

1/ 🧵 I am excited to share a new preprint from our group:
Single-cell Dam&T-seq during mouse corticogenesis reveals how genome–lamina interactions regulate long neuronal genes.
doi.org/10.1101/2025...
#Neurodevelopment #Epigenetics @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social

MeCP2 binding and genome–lamina reorganization precede long gene activation during mouse corticogenesis

During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders[1][1]–[4][2]. The role of spatial...

doi.org

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Jamie Hackett @jamiehackett.bsky.social · 13d

❓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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Jop Kind @jopkind.bsky.social · 28d

Very proud of Kim to be featured by MIT Technology Review as one of this year's innovators under 35 for her pioneering work on mapping DNA repair in single cells! @oncodeinstitute.bsky.social @hubrechtinstitute.bsky.social

Hubrecht Institute @hubrechtinstitute.bsky.social · 28d

Kim de Luca, Hubrecht alumna from the Kind group, was featured by MIT Technology Review in this year's Innovators Under 35! Swipe to read more.

The full list can be found here: http://www.technologyreview.com/innovators-under-35/2025/.

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Marc Bühler @marcbuhler.bsky.social · Sep 8

We are hiring-join us!

FMI science @fmiscience.bsky.social · Sep 8

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

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janeskok.bsky.social @janeskok.bsky.social · Sep 9

Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...

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Annual Reviews @annualreviews.bsky.social · Sep 9

The latest Annual Review of Genomics and Human Genetics is now online 🧬 Most read article so far is "Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome" @akispapantonis.bsky.social @mariekeoudelaar.bsky.social Check it out arevie.ws/47BZEJp
Full TOC: arevie.ws/4plCaPe

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Lorenz Lab @sonjalorenzlab.bsky.social · Sep 4

We’re excited that our article on the ubiquitination of drug-like small molecules in cells has been selected as an Editorial Highlight in #NatureCommun! 🎉
Check it out here 👉 www.nature.com/ncomms/edito...

Editors' Highlights | Nature Communications

Editors' Highlights

www.nature.com

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Craig Kaplan @triggerloop.bsky.social · Aug 28

Final version of Bingbing Duan’s main thesis work is out now now in Nature Communications @natureportfolio.nature.com www.nature.com/articles/s41... I’m so pleased with this study that we’ve been working on for so long #epistasis #transcription #geneexpression 1/

Widespread epistasis shapes RNA polymerase II active site function and evolution - Nature Communications

The active site of RNA Polymerase II is highly conserved. Here the authors show that mutations can propagate effects across the enzyme and alter genetic behavior of distal residues, demonstrating plas...

www.nature.com

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Sarah Hainer @hainerlab.bsky.social · Aug 28

Our collaborative paper with the Arndt lab is out today: doi.org/10.1093/nar/... (originally bioRxiv: www.biorxiv.org/content/10.1...). Here we asked the question of how CHD1 localizes to chromatin.

A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes

Abstract. The nucleosome remodeler Chd1 is required for the re-establishment of nucleosome positioning in the wake of transcription elongation by RNA Polym

doi.org

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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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Romain Koszul @rkoszul.bsky.social · Aug 11

New work from @beckof.bsky.social and our lab's collaboration, with @alengronne.bsky.social! Multifaceted influence of transcription on yeast chromosome folding... loop extrusion of course but also active promoters making loops, bypassing centromeres boundaries
www.sciencedirect.com/science/arti...

RNA Pol II-based regulations of chromosome folding

The spatial organization of eukaryotic genomes and its dynamics are of functional importance for gene expression, DNA replication, and segregation. St…

www.sciencedirect.com

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Johannes Stein @jmstein.bsky.social · Aug 13

(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!

Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵

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Eric Joyce @ericjoyce.bsky.social · Aug 14

🚨New preprint from the lab🚨
🧬 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...

Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen

The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their ...

www.biorxiv.org

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Abby Buchwalter @abbybuch.bsky.social · Jul 22

Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...

The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology

Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...

www.nature.com

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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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Schubeler Lab @schubelerlab.bsky.social · Aug 7

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Aug 11

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression

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

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts

Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...

www.biorxiv.org

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