Thank you Benjamin 😊

Thanks a lot Graham, I am looking forward to any question that may come up and hope that you and your lab enjoy the read 🙏

Thank you Kumar, this means a lot 🤩

Thanks a lot, hope you like where the story went since you last saw it in Sounio!

Thanks Marcel, I hope you like the paper :)

I hope we will get another chance for collaboration, this was great!! 💪

I am sure we will! Thank you for helping me refine this tweetorial 💪

Our latest collaboration with the talented Susi @sbantele.bsky.social and Jiri Lukas is out now @science.org 🤩. We reveal the hidden price for DNA repair, with potential implications for genome function, gene therapy and ageing👇

Shoutout to @zonderlandg.bsky.social and our fantastic collaborators from @grothlab.bsky.social @biranalva.bsky.social, Nicolas Alcaraz, Alice Wenger and @nilskrietenstein.bsky.social, Irene Mordini, who took our discoveries to the next level, great team effort 🙌🙌🙌#ScienceResearch 12/12

Can a repaired locus still do its job? We challenged DSB-recovered cells with growth factor signaling.
Live-cell imaging revealed a 𝗯𝗹𝘂𝗻𝘁𝗲𝗱 𝗰-𝗠𝗬𝗖 𝗿𝗲𝘀𝗽𝗼𝗻𝘀𝗲 𝘁𝗼 𝗘𝗚𝗙 — both short- and long-term induction were defective. 11/n

Are 3D chromatin changes after DNA repair tied to 𝘄𝗲𝗮𝗸𝗲𝗻𝗲𝗱 𝗥𝗡𝗔 𝗵𝘂𝗯𝘀?
Using RNA FISH at the c-MYC locus, we found they are — local RNA compartments stay compromised even after repair, mirroring structural chromatin changes. 10/n

𝗔𝗿𝗲 𝟯𝗗 𝗰𝗵𝗿𝗼𝗺𝗮𝘁𝗶𝗻 𝗰𝗵𝗮𝗻𝗴𝗲𝘀 𝗮 𝗵𝗲𝗿𝗶𝘁𝗮𝗯𝗹𝗲 𝗰𝗼𝗻𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗲 𝗼𝗳 𝗗𝗡𝗔 𝗿𝗲𝗽𝗮𝗶𝗿?Labelling both ends of the c-MYC TAD revealed a stable increase in probe distance. @nilskrietenstein.bsky.social took a closer look with Region-Capture Micro-C and found heritable 3D structural changes in the entire c-MYC TAD! 9/n

𝗜𝘀 𝘁𝗵𝗲 𝗶𝗺𝗽𝗮𝗶𝗿𝗺𝗲𝗻𝘁 𝘁𝗲𝗺𝗽𝗼𝗿𝗮𝗿𝘆? Not at all. Even after >two rounds of replication, c-MYC TAD genes stay repressed after a single DSB!
And our collaborators @grothlab.bsky.social took it further — editing the Mcm2 locus in mESCs showed deregulation inherited over multiple passages. 8/n

𝗛𝗼𝘄 𝗺𝘂𝗰𝗵 𝗰𝗵𝗿𝗼𝗺𝗮𝘁𝗶𝗻 𝗶𝘀 𝗮𝗰𝘁𝘂𝗮𝗹𝗹𝘆 𝗮𝗳𝗳𝗲𝗰𝘁𝗲𝗱 𝗯𝘆 𝗮 𝘀𝗶𝗻𝗴𝗹𝗲 𝗗𝗦𝗕? As a first surprise, a single Cas9-induced DSB anywhere in the c-MYC TAD (>2.5 MB) affects local gene expression! Even when most of the cells have completed DNA repair and the break was over a megabase distant from the c-MYC ORF! 7/n

We used the >2.5 MB c-MYC TAD as our model targeting it by single Cas9 cuts, across the entire TAD. Next, we measure the c-MYC protein levels during and after DNA repair (marked by 53BP1 at the DSB) using high content single-cell microscopy of thousands of cells to generate population data. 6/n

These findings shift how we think about ageing, cancer, and the hidden “cost” of genome integrity.
It also raises big questions👇
• Which genes are most vulnerable to chromatin fatigue?
• How does chromatin refold after repair —and why isn’t it always perfect?
• How can we safely use CRISPR/Cas9? 5/n

IN SUM, post-repair chromatin shows deregulated genes, altered 3D structure, impaired RNA compartments and gene induction. IMPORTANTLY, all is inherited by daughter cells, so we term this post-repair state “𝗰𝗵𝗿𝗼𝗺𝗮𝘁𝗶𝗻 𝗳𝗮𝘁𝗶𝗴𝘂𝗲”, the 𝗰𝗼𝘀𝘁 𝗼𝗳 𝗗𝗡𝗔 𝗿𝗲𝗽𝗮𝗶𝗿 enabling survival and proliferation. 4/n

BACKGROUND: during DNA double-strand break (DSB) damage response and repair, large (>Mb) chromatin regions surrounding the DSB are modified and reshaped. The big Q: 𝗖𝗮𝗻 𝗰𝗵𝗿𝗼𝗺𝗮𝘁𝗶𝗻 𝗳𝘂𝗹𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝘁𝗵𝗲𝘀𝗲 𝗹𝗮𝗿𝗴𝗲-𝘀𝗰𝗮𝗹𝗲 𝗰𝗵𝗮𝗻𝗴𝗲𝘀 𝘄𝗶𝘁𝗵𝗼𝘂𝘁 𝗰𝗼𝗻𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗲 𝘁𝗼 𝗰𝗲𝗹𝗹𝘂𝗹𝗮𝗿 𝗽𝗵𝘆𝘀𝗶𝗼𝗹𝗼𝗴𝘆? 3/n

WHY? Targeted cleavage of DNA is routinely used for experimental and therapeutical genome editing ✂️ 🧬 But we show long-term consequences of CRISPR-Cas9 go beyond mutations and challenge the assumption that mutations are the only consequence of DNA breaks. 2/n

Repair of DNA double-strand breaks leaves heritable impairment to genome function Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...

𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n