Andreas Panagopoulos

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰

Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs:

www.biorxiv.org/content/10.6...

1/n Have you ever wondered whether an amplified oncogene in a patient’s tumor (HER2/EGFR/CCND1/…) is carried on extrachromosomal DNA (ecDNA) vs embedded within a chromosome? Bulk WGS + genome graph can hint, but in practice it’s often hard to resolve. Here is our new preprint.

Most genetic interaction studies measure gene relationships in one condition, but environment can reshape which genes depend on each other.

Today in Molecular Cell, Luke Gilbert & team deliver the first systematic, multi-condition map of genetic rewiring in human cells.

To kickstart this new Bluesky account: We're hiring!
The Bertolin Lab @dundee.ac.uk is looking for a postdoc to work on DNA-end homeostasis & genome stability, funded by Wellcome Trust Award. Exciting science, fantastic environment, founding role in the lab.
Details in the flyer — get in touch! 👇

🧵 Thread: What happens when transcription isn’t properly shut off during mitosis? Our new preprint explores just that 👇
www.biorxiv.org/content/10.6...

Excited to share our latest study in Nature Communications ✨

We map how cells clear DNA damage–stalled RNA polymerase II using a stepwise TFIIH → ubiquitin/VCP mechanism, keeping transcription and genome stability on track.

Paper: www.nature.com/articles/s41...

#Genomics #DNADamage #CellBiology

Our paper on visualising influenza A virus in live cells with single viral RNA resolution is now out in Cell Systems 🥳

For more details about what we did, see the thread about the preprint below ⬇️

Pre-incision structures reveal principles of DNA nucleotide excision repair - Nature Cryo-electron microscopy structures of nucleotide excision repair complexes reveal the roles of the constituent proteins XPA, XPB, XPC, XPD, XPF, XPG and RPA in DNA bubble formation and excision ...

Our great collaboration with the lab of Wei Yang and Kaoru Sugasawa is now online in Nature. We’re glad we could contribute some cell biology to complement this beautiful structural and biochemical work.

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

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding - Nature Genetics Acute perturbation of histone acetylation induces changes in chromatin organization that are only partially reversed once the perturbation is removed and are associated with transcriptional memory eff...

TSA treatment may induce cellular and structural memory !! Happy to have been part of this beautiful story, lead by @fpaldi.bsky.social in Giacomo Cavalli's lab. Now published in @natgenet.nature.com 👏.
www.nature.com/articles/s41...

Last days to apply this position in our group! Do join us in this great Institute @crg.eu, with great colleagues, and help shaping the science and culture of our lab!

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Beautiful work, Nibal!!! Congratulations 🥳🥳👏👏

Happy to share the results from my PhD thesis, in which we uncovered a function for FANCD2 on maintaining fork stability upon re-replication, now out in Nat. Commun!

📖 Read the full story here: 

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

Thanks to everyone who supported me along the way!

Precise control of transcription condensates across S phase balances linker histone expression with DNA replication, ensuring genome stability Marmolejo et al. uncover transcription condensate dynamics at histone locus bodies across the cell cycle. These dynamics are governed by cell cycle (DDK and CDK1/2) and checkpoint (ATR-CHK1) kinases t...

I am excited to share the first paper from the Saldivar lab! A special thank you to all who contributed.

Precise control of transcription condensates across S phase balances linker histone expression with DNA replication, ensuring genome stability: Molecular Cell www.cell.com/molecular-ce...

Don't miss the opportunity to attend exciting virtual talks from leading scientists in genome integrity, provided by the @genomeiinetwork.bsky.social! Next one is in a few days 👇

PAF15–PCNA exhaustion governs the strand-specific control of DNA replication Nature - PCNA–PAF15 has a key role in determining replisome dynamics during genome replication and protecting against genome instability.

Dear Colleagues,

Delighted to share that our first lab paper is now published in Nature.!!! 😊😊😊

We identify a previously concealed “safety limit” in DNA replication program: cells intrinsically rate-limit PCNA via PAF15, shaping strand-specific and global replication dynamics.

👉 rdcu.be/e1bBt

Site-saturation functional screens identify PALB2 missense variants associated with increased breast cancer risk - Nature Communications The impact of variants of uncertain significance (VUS) on protein function and cancer risk remain unclear. Here, the authors focus on the functional impact of VUS of the PALB2 gene and identify defect...

We present a site‑saturation functional screens of missense variants in the high-risk breast cancer susceptibility gene PALB2. Damaging missense variants confer a high risk of breast cancer! Thanks to all co-authors and to KWF for financially supporting our work!

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

CytoTape in a neuron

Our CytoTape work is published today in Nature @nature.com! CytoTape is a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo. www.nature.com/articles/s41...

PARP1 and PARP2 are dispensable for DNA repair by microhomology-mediated end-joining at double-ended DSBs Abstract. Poly ADP-ribose polymerase (PARP) inhibitors are standard of care treatment for cancers with homologous-recombination deficiencies. Yet, as tumou

new PARP paper from our neigbhors in the Arnoult lab at CU Boulder: indicates that PARP inhibitors alone are not good enough; we need combo therapy by adding inhibitors of MMEJ. academic.oup.com/nar/article/....

We are seeking a motivated postdoctoral fellow to investigate mechanisms of DNA damage response, APOBEC-mediated mutagenesis, innate immunity, and double-stranded RNA sensing. Located in Southern California, UCI offers an outstanding scientific environment and exceptional quality of life.

🔔 New paper alert 🔔 www.nature.com/articles/s41...
Some regions in the genome replicate early and some late, but the why and how remain poorly understood. DNA replication and 3D genome organization appear linked, raising the question if one may regulate the other? (1/n)

Description Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

We are recruiting a Postdoc in computational biology, together with @mariasecrier.bsky.social

4yr, fully funded by @cancerresearchuk.org, ideal for Postdocs wanting to develop their independence

Applications open now: www.imperial.ac.uk/jobs/search-...

Preprint alert! 🥸

Yajie Zhu (PhD graduate) and Mariano Barbieri (postdoc, @spp2202.bsky.social Accelerator award) produced a package that will classify loops in your #3Dgenomics data based on (whichever) epigenomic data you have available. Keep reading...

1/n

www.biorxiv.org/content/10.6...

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

We are hiring! Join the Gerlich lab as a scientific programmer/bioinformatician and join an interdisciplinary team studying fundamental mechanisms of chromosome organization, DNA repair, and cell division.

A genetically encoded device for transcriptome storage in mammalian cells Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and s...

🧬🔬@science.org A genetically encoded device for #transcriptome storage in mammalian cells | Science www.science.org/doi/10.1126/... @broadinstitute.org

Excited to share our new Nature study! 🧬

We (sidrituruci.bsky.social et al) discovered that CFAP20 helps clear stalled RNAPII, preventing harmful clashes with DNA replication machinery. This protects cells from R-loops and genome instability.

Full paper: www.nature.com/articles/s41...

Happy to share our work on RPA exhaustion activating SLFN11 published in @natcellbio.nature.com today!

Read in Nature: nature.com/articles/s41586-025-09899-8

Stress controls epigenetic inheritance!

A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8

Insights from three decades of BRCA1/2 modeling in mice - Nature Genetics This Perspective highlights the insights into the biology of BRCA1/2 afforded by mouse models and patient-derived tumor xenografts and emphasizes their value in addressing unresolved questions and pre...

🐭 In vivo veritas 🐭

Now out in Nature Genetics: @josjonkers.bsky.social and I describe currently available mouse models of BRCA1/2 and their roles in understanding BRCA1/2 biology, particularly in normal development, tumor suppression and therapy response.

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