6/n Equally strikingly, many of these splicing changes manifesting upon senescence induction can be recorded in RNA-seq data from aging human tissues, while interventions that hinder CTCF clustering extended the replicative lifespan of human cells nearing senescence!

5/n The net result of all these genomic changes is not transcriptional, but rather splicing-centric, with most effects manifesting in speckle-associated genes. Strikingly, interventions preventing CTCF clustering almost fully revert splicing patterns to those seen in proliferating cells!

4/n ...which we further validated at the single cell-level using high-resolution DNA tracing in collaboration with Jan Ellenberg and Kai Beckwith and their powerful LoopTrace approach, thanks to intramural @spp2202.bsky.social funding.

3/n CTCF clustering leads to the 3D reorganisation of chromatin with the emergence of new and longer CTCF-anchored loops predominantly in the speckle-associated A1 subcompartment of the genome.

2/n Here, we find that a protein of the nuclear periphery important in mitosis, BANF1 (see PMID: 28841419) and the key speckle component, SRRM2, are both necessary for this clustering. In fact, 62 aa of the SRRM2 RNA-binding domain suffice to induce CTCF clusters even in proliferating cells!

Yours truly staring at a picture of the historical Sternwarte during Day 2 of the great CLEPIC2026 meeting, followed by @dewitlab.bsky.social, @radaiglesiaslab.bsky.social with amazing talks.

And here is the (Greek) back cover for an extra taste of the book.

I know that this might only concern my Greek friends and colleagues, and I know that it has nothing to do with my science… but I always so thrilled when I get to see my fiction in print — this time, a collection of 26 short stories about losing and finding affection at different life stages.

4/n We then used MD simulations to test whether these loop classes are the result of the same or different underlying mechanisms with some surprising conclusions ― so do read the preprint and lets us know! This work was supported by the DFG SPP2202 priority program (@spp2202.bsky.social).

3/n ...which allowed the automated and unbiased clustering of >20,000 loops into 6 well-separated clusters, with distinct epigenomic and physical attributes. The key here is that raw signal structure is considered (not peaks) allowing the neural network to identify differences in signal structure.

2/n Yajie and Mariano implemented a variational deep embedding (VaDE) neural network trained on Micro-C loop signal structure and concatenated CUT&Tag signal overlapping the anchors of these loops...

By coincidence, this year my 100th peer-reviewed paper was published―on the subject closest to my heart. Although scientific output is not a mere reflection of the number of papers published (or so we hope), looking back at these two decades…

As 2025 comes to a close, I am realising that it has been 20(!) years since the publication of the very first article featuring me as a co-author…

Last day of the @spp2202.bsky.social Closing Retreat in Goettingen ending in a high note with Stavros Lomvardas discussing the peculiar 3D attributes of the OR chromatin landscape!

@karsten-rippe.bsky.social rocking down memory lane and along single cell genomics data in Day 2 of the @spp2202.bsky.social Closing Retreat in Goettingen!

The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.

Science-peripheral post (ignore unless you read in Greek or French): I was surprised and truly honored to receive the Aix-Marseille Metropolitain for the French translation of my novel ‘The last bear of the woods’ (Kichli 2023)—a great thanks to my translators M. Volkich and H. Zervas.

In our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n

...and in doing so, we also discuss how formations such as "factories" and "condensates" can mediate the communication of genes with their cognate cis-regulatory elements to tune their output in different scenarios. 5/n

In our new review, we critically approach both the historical and current nomenclatures, as well as evidence from molecular and cell biology assays since the early '90s to highilght the (many) points where the two concepts align as well as those that still require further work to settle.

The great pace of the "condensate" field has offered frameworks that can be used to explain earlier, but still very valid experimental observations. Thus, we set out to compare and contrast (and synthesize) the "transcription factory" model with what is known about "transcriptional condensates" 2/n

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u A short thread follows 1/n

Hear, hear! Since last week, I have the honor of serving as a Scout for the Henriette Herz program of the Humboldt Foundation. 1/n

Mario Nicodemi kicking off SIBBM2025 with an elegant talk on phase transitions in 3D genome folding in front a wall-to-wall full house in Naples.

Here’s the thing: the 2025 German Pathology Congress is kicking off in a huge room with a non-pathologist as first speaker. Let’s see how Hi-C in cancer fairs today :-)

Always an emotional moment when one of your trainees graduates. Here, Dr. Adi Mackay (Danieli), 10th PhD from our lab, after an impeccable defense and a well-deserved "summa cum laude" distinction. ...paper will hopefully follow soon and it will become very clear why the distinction was awarded.

Hear, hear! The Universtiy Medical Center Goettingen is inviting applications to its new Medical Scientist Program “Genomic responses to disease plasticity” funded by the EKF Stiftung. The program will support early-career bioscientists with a PhD eager to do clinically-oriented research... 1/n

Our CRU5002 friends and collaborators in the Singh lab published (yet another) thorough paper dissecting how PDAC subtypes lose uniformity due to regional immune pressure, leading to the intratumoral subtype co-existence. Happy to have contributed some genomics to this - read on: t.co/tqT4g9d39B

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky #BookChallenge Day 11

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky #BookChallenge Day 8