Francesco Cardamone

An integrated view of the structure and function of the human 4D nucleome - Nature The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!

www.nature.com/articles/s41...

FlyBase secures funding for year, but future still uncertain The FlyBase team’s fundraising efforts have proven successful in the short term, but restoration of its federal grant remains uncertain.

🪰 folks! I spoke to the Transmitter about FlyBase. As noted at flybase.org, bridge $ ran out and many staff were laid off.

Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2

tinyurl.com/FlyBase

John Gurdon obituary: Biologist who made cloning possible He showed that specialized cells retain the genes to form an organism.

Obituary: John Gurdon (1933-2025) Biologist who made cloning possible

go.nature.com/3WicRAe

Feeling inspired after presenting some #3Dgenome & #single-cell data at the #EDRC2025 in the beautiful #Alicante🇪🇸🧬🪰
Looking forward to the next amazing sessions to exchange ideas and connect with the community!

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...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...

If you like transcription regulation and its mechanisms, this WIP list is for you.

I'm sure I've forgotten lots of people, so don't hesitate to let me know so I can add you to the list.

go.bsky.app/8vTgeXB

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development - Nature Ecology & Evolution Single-cell comparison of developing bat and mouse limbs reveals conservation of cell populations and gene expression patterns, and suggests repurposing of genes involved in proximal limb development ...

How bats developed their wings? 🦇

Turns out they reutilize existing gene programs 🔧

Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs

www.nature.com/articles/s41...

H3K27me3 expands the epigenetic control of piRNA transcription Nature Structural & Molecular Biology - Constitutive heterochromatin can promote piRNA transcription, a crucial step in genome defense. Two studies now show that piRNA transcription in...

Our News&views with Germano @cecerelab.bsky.social about the role of H3K27me3 in epigenetic control of piRNA transcription in worms 🪱 and flies 🪰 is out in @natsmb.nature.com
rdcu.be/erkld

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Running circles in my head Researchers in Freiburg have identified the protein ELAV as a key regulator of circular RNA production in the nervous system, which is crucial for brain function.

👀 New study: The stability of circular RNAs makes them ideal for long-lasting regulatory tasks in neurons. Researchers from the @hilgerslab.bsky.social have now identified the protein ELAV protein as a master regulator of circular RNA production in the nervous system, crucial for brain function.

The next TriRhena Gene Regulation Club takes place at the MPI-IE #Freiburg. Save your seat & submit a talk. Strengthen your local #epigenetics network & collaborate with peers.

📅 16 Jun 2025 | 14:00
🎟️ Free entry, registration required
✍️ Register by: 6. Jun

www.ie-freiburg.mpg.de/gene-regulat...

Symposium: Epigenetics of early mouse development We are delighted to invite you to to the second symposium, “Epigenetics of Early Mouse Development”, taking place on April 24, 2025, at the Max Planck Institute of Immunobiology and Epigenetics in Fre...

Interested in the latest advancements of #epigenetics of #mammalian early embryogenesis? Then join our upcoming mini-symposium in Freiburg!

📅 April 24, 2025, 14:00-19:00 PM
📌 Max Planck Institute, Freiburg (only on-site!)
🛠️ Organized by: @iovino-lab.bsky.social

Register & join free of charge.

Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis - Nature Communications Germ layer specification during zygotic genome activation is regulated by chromatin state. Here, the authors use single-cell multiome profiling in Drosophila to show that H3K27me3 and H3K27ac at cis-r...

Exciting news! Our latest work in the Nicola Iovino Lab, “Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis,” is now published in Nature Communications!
www.nature.com/articles/s41...

About a week ago, our new story in the #IovinoLab about chromatin factors and germ layer specification during ZGA in Drosophila embryos was published!

Missed it? 🔎 Check out this resume article by our Institute!

#chromatin #epigenetics #development

Amazing piece of work from @ninacabezas.bsky.social Lab! Congratulations Jasmin, Mari & team!