Peter Ly

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...

Henry De Belly, Ph.D., stands in an empty office, with blanks walls and an empty desk, and arms outstretched.

🚨NEW PI ALERT🚨 @henrydebelly.bsky.social is in the house, and look at that *fresh* new office. Clean slate for his next #relentlessdiscovery in CRI's Tissue Regeneration Program (TRP). Onward! Read more about his new lab 👉 cri.utsw.edu/faculty/henr...

🧪 @haozhulab.bsky.social

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

Mitosis has a timing system. If chromosomes attach properly, cells divide on schedule and keep proliferating. If attachment is slow or incomplete, the delay is recorded — and daughter cells stop dividing.
We explore this link in our new preprint.

🔗 www.biorxiv.org/content/10.6...

New preprint🎉
Happy to share our collaborative manuscript, where we provide in vivo and genome-wide evidence linking MCM2-7 helicase activation, DNA extrusion to initial origin melting, thereby adding a new mechanistic layer to how eukaryotic DNA replication is initiated.

👉 doi.org/10.64898/202...

We have two funded postdoctoral positions available. Topics encompass:

-Next gen light-sheet fluorescence microscopy instrumentation

-Structured illumination microscopy and other approaches to extend the resolution limit.

-Nonlinear microscopy combined with adaptive optics / phase conjugation

Effects of ribonucleotides on telomeric G4 formation, dynamics, and initiation of ribonucleotide excision repair by RNase H2 Abstract. Human telomeres are composed of TTAGGG repeats that can fold into G-quadruplexes (G4s). G4s can form several different conformations, including p

🎉Kicking off 2026 with our first paper from the Freudenthal lab in NAR. Ribonucleotides reshape telomeric G4s and are resistant to RNase H2 repair. Congrats to the authors and huge thanks to our collaborator Hui-Ting Lee! academic.oup.com/nar/article/...

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.

First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

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.

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...

Human eggs must segregate their chromosomes with exquisite precision — yet errors rise with maternal age, causing miscarriage & infertility.
Our new article on @biorxivpreprint.bsky.social shows why chromosome cohesion fails in aging eggs & how to improve it.
www.biorxiv.org/content/10.6... (1/10)

We are excited to share that our latest work from the lab aimed at understanding how the tRNA nuclease SLFN11 is activated in response to DNA damage and replication stress has just been published in @natcellbio.nature.com!

Open access link: www.nature.com/articles/s41...

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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...

SMC and recombination enthusiasts: we updated our work describing the loop extrusion properties of budding yeast condensin and its function in biasing donor usage for mating-type switching. Lots of cool new data, check it out!
www.biorxiv.org/content/10.1...

A breakage–replication/fusion process explains complex rearrangements and segmental DNA amplification - Nature Genetics This paper introduces breakage–replication/fusion, a genomic rearrangement process underpinning three patterns of copy-number gains found in cancer and other diseases.

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

Mitotic errors as triggers of cell death and inflammation - Nature Cell Biology Rizzotto et al. discuss the causes and consequences of deregulated mitosis that allow cells arrested in mitosis to escape to the next interphase, where they can initiate inflammatory signalling or und...

Excited to announce a new review article that Andreas Villunger @villungerlab.bsky.social, Dario Rizzotto (not on bsky) and I wrote. In this article, we discuss mitosis as a central cell cycle stage for integrating DNA damage, cell death and inflammatory responses. www.nature.com/articles/s41...

Introducing Cyclically Multiplexed Expansion Microscopy (Cy-ExM): a workflow for 3D nanoscale, high-plex imaging in whole cells. Cryo-preserved ultrastructure + iterative labeling + expansion microscopy → 20 targets in one dataset with ~70 nm lateral resolution.

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

Happy to share our new review on 3D chromatin organisation by cohesin with you. It was a great pleasure to review recent advances and future prospects with @danielgerlich.bsky.social.

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm Nature Cell Biology - Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through...

Happy to share that my postdoc work with @jobdekker.bsky.social is out!
rdcu.be/eWHD2

We characterize interphase chromatin folding programs with distinct modes of mitotic inheritance and identify the chromosome-intrinsic capacity to form a microcompartment of active CREs during mitotic exit.

Congrats Mara! Very well deserved!

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...

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Our latest paper on the molecular mechanisms of XPF-ERCC1 recruitment to SLX4-dependent DNA repair pathways has been published! Congratulations to first author Junjie Feng, and a heartfelt thank you to all our collaborators for their contributions to this study!
www.nature.com/articles/s41...

Cohesin drives chromatin scanning during the RAD51-mediated homology search Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...

Cohesin guides homology search during DNA repair using loops and sister chromatid linkages Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...

I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵

High-fidelity human chromosome transfer and elimination The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...

A key step towards human genome synthesis. With thanks to @wellcometrust.bsky.social @mrclmb.bsky.social #SynHG doi.org/10.1126/scie...

Tracking ongoing chromosomal instability using single-cell whole-genome sequencing Chromosomal instability (CIN) generates aneuploid genomes that are characteristic of most cancers. While bulk genome sequencing reveals historical CIN, it lacks the resolution to identify ongoing CIN ...

📢 New preprint out!

We are thrilled to introduce our framework to track #ongoingCIN by leveraging single-cell genomics and CIN signatures:

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

If you’re interested in aneuploidy, mark your calendar! The FASEB SRC on the Consequences of Aneuploidy will be held Sept 28 - Oct 1, 2026 in Melbourne, Florida. Many speaking slots are reserved for early-career researchers. Please help spread the word!

events.faseb.org/event/Aneupl...

Congrats Hana!! 👍

TODAY! Don’t miss it! 👇