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Reposted by Elphege Nora Lab at UCSF

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 Elphege Nora Lab at UCSF

Camille Moore @camille-moore.bsky.social · 5d

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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David Suter @davidsuter.bsky.social · 12d

📣 New preprint from the lab - Endogenous fluctuations of transcription factor levels shape their occupancy in unexpected ways
www.biorxiv.org/content/10.1...

Endogenous variability in transcription factor concentrations shapes their genome-wide occupancy

The control of transcription factor (TF) concentrations is crucial for the precise regulation of gene expression and cell fate decisions during development. Yet, TF concentrations can display substant...

www.biorxiv.org

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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13d

How do enhancers activate genes?

Confused about how cohesin contributes?

Physics uncovers a molecular scenario that explains the biological data across labs

Truly exciting findings from @lucagiorgetti.bsky.social 💪

Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 13d

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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Reposted by Elphege Nora Lab at UCSF

Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 13d

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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Reposted by Elphege Nora Lab at UCSF

Anders Sejr Hansen @andersshansen.bsky.social · 14d

Really enjoyed reading the new @lucagiorgetti.bsky.social lab preprint that makes the case that not all E-P interactions are created equal - it is the subset of long-lived extrusion-mediated E-P interactions that are most transcriptionally important:
www.biorxiv.org/content/10.1...

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Reposted by Elphege Nora Lab at UCSF

Serena Sanulli Lab at Stanford Genetics @serenasanulli.bsky.social · 16d

Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!

bioRxiv Genetics @biorxiv-genetic.bsky.social · 16d

An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates https://www.biorxiv.org/content/10.1101/2025.09.21.676939v1

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

That was >40 years ago!

So many of John's papers still read incredibly prescient to this day.

Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.

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

As early as 1984 they reported pairwise distances between loci across they could recognize thanks their cytological patterns.

They were already using distance heatmaps, looking at contact between heterochromatin & the periphery and making polymers models, all with data from single live cells (!)

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

Not sure that's what you want but group of John Sedat was mapping polytene chromosome folding in the mid-80s.

www.nature.com/articles/308...
rupress.org/jcb/article/...

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Reposted by Elphege Nora Lab at UCSF

Vijay Ramani @vram142.bsky.social · 18d

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 Elphege Nora Lab at UCSF

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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Reposted by Elphege Nora Lab at UCSF

janeskok.bsky.social @janeskok.bsky.social · 29d

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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janeskok.bsky.social @janeskok.bsky.social · Sep 3

We’re back! Registration is NOW OPEN for the 6th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer. Don’t miss insights from leading experts in the field. Join us online on Nov 25, 2025—register for free: bit.ly/chromatin-2025 #chromatin2025

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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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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · Aug 31

Excitingly, the lab of Jan-Michael Peters just reported
largely concordant findings:

The PDS5:NIPBL balance in cells tunes the rate/velocity of cohesin loop extrusion, shaping chromosomes from loops to compartments 🚅➰

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

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Nature Biotechnology @natbiotech.nature.com · Aug 26

In Brief: A new center in San Francisco will offer tailor-made CRISPR therapies to cure children with rare diseases www.nature.com/articles/s41...

Children with rare genetic diseases get CRISPR Cures center - Nature Biotechnology

Nature Biotechnology - Children with rare genetic diseases get CRISPR Cures center

www.nature.com

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bioRxiv Genomics @biorxiv-genomic.bsky.social · Aug 1

Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1

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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · Aug 19

29 / and this one illustrates the dramatic differences in loop dynamics after depleting
NIPBL (slow rate, normal lifetime)
WAPL (very high lifetime)
PDS5 (high lifetime, high rate)

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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · Aug 19

28/ and some movies!

This one illustrates the difference in loop dynamics between high lifetime v.s. high rate, at equal processivity.

LEFT - High lifetime: loops take time to grow but remain for very long

RIGHT - High rate: loops grow super fast but eventually dissociate to reform

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Elzo de Wit lab @ NKI @dewitlab.bsky.social · Aug 18

We all know that cancers -even from the same subtype- are highly heterogeneous right? In a new study we asked whether this was also the case for the three-dimensional organization of the genome in breast cancer. The answer: it’s complicated. www.cell.com/iscience/ful...

A 3D genome compendium of breast cancer progression

Genomics; Chromosome organization; Molecular Genetics; Cancer

www.cell.com

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

27/ Co-authors on bluesky include @erikacanderson.bsky.social @karissalhansen.bsky.social

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

26/ This was a hand in hand collaboration between experimentalists in our group, led by @rini-shah.bsky.social ocial, and physicists in @gfudenberg.bsky.social ’s lab, led by Max Tortora, with help from @nesslfy.bsky.social in @lucagiorgetti.bsky.social ’s lab.

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

25/ There is more in the manuscript 📖 - including

▶️ calibration of models to experiments
▶️ how to titrate & measure chromatin bound cohesin
▶️ how extrusion rate affect compartmentalization & transcription
▶️ speculations about cell types that change expression levels of cohesin co-factors 💭

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

24/ On the other hand, quantitative titrations showed that extrusion rates scale with NIPBL dosage 📐

This is a whole new way to think about the molecular origin of NIPBL haploinsufficiency in Cornelia de Lange patients, who suffer from partial reduction of NIPBL levels.

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