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Karsten Rippe @karsten-rippe.bsky.social · 09/09/2026

🧬 1/ HP1α marks silenced heterochromatin, but how does it repress, and what happens when transcription is switched on? On mouse fibroblast chromocenters, HP1α stays bound, its barrier is local, and the domain reorganizes nanodomain by nanodomain. 👉 @cp-molcell.bsky.social doi.org/10.1016/j.mo...

Schematic of the two experimental systems. Left, activators recruited to chromocenters of wild-type and Suv39h dn mouse fibroblasts, with DAPI and anti-HP1α images showing HP1α enrichment and loss. Right, the U2OS 2-6-3 reporter array with an activator recruited alone or together with HP1α.

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Karsten Rippe @karsten-rippe.bsky.social · 14/05/2026

1/ Some cancers can proliferate without telomerase. They recombine and extend their telomeres inside ALT-associated PML bodies (APBs). @emmakoeleman.bsky.social @dkfz.bsky.social mapped where proteins and single-stranded telomeric repeats sit in APBs: doi.org/10.64898/202... 🧵

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Karsten Rippe @karsten-rippe.bsky.social · 20/04/2026

1/ Philipp Mallm from the @dkfz.bsky.social Single-cell Open Lab just broke the news at #AACR26: the first results on colorectal cancer (CRC) tissue analysis with the new Atera spatial transcriptomics platform from @10xgenomics.bsky.social. Is it "making the impossible possible?" 🧵

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Karsten Rippe @karsten-rippe.bsky.social · 24/12/2025

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

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Karsten Rippe @karsten-rippe.bsky.social · 21/08/2025

Happy to report that the Xenium system for spatial transcriptomics in the Single Cell Open Lab www.dkfz.de/en/single-ce... @dkfz.bsky.social was the first one worldwide to pass the mark of 100 runs according to @10xgenomics.bsky.social. And it keeps on running with another one, so stay tuned...

dkfz.de

Single-cell Open Lab - German Cancer Research Center

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Karsten Rippe @karsten-rippe.bsky.social · 13/08/2025

Glad that the preprint on identifying and characterizing rare tumor-reactive T cells in multiple myeloma & AML patients is out now doi.org/10.1101/2025.... Single-cell TCR and transcriptome profiling & immunopeptidomics revealed conserved programs and shared non-canonical antigens.

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Karsten Rippe @karsten-rippe.bsky.social · 11/07/2025

Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse. doi.org/10.1038/s414...

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Karsten Rippe @karsten-rippe.bsky.social · 20/06/2025

1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...

doi.org

Comparison of spatial transcriptomics technologies using tumor cryosections - Genome Biology

Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within the...

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Karsten Rippe @karsten-rippe.bsky.social · 19/06/2025

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

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Karsten Rippe @karsten-rippe.bsky.social · 12/04/2025

From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏

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Karsten Rippe @karsten-rippe.bsky.social · 31/03/2025

“We all rely on science.” U.S. scientists are speaking out for scientific integrity and academic freedom. What they’re doing matters. We owe them our solidarity and a clear stand beside them. www.nytimes.com/2025/03/31/s...

nytimes.com

Trump Administration Has Begun a War on Science, Researchers Say (Gift Article)

Nearly 2,000 scientists urged that Congress restore funding to federal agencies decimated by recent cuts.

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Karsten Rippe @karsten-rippe.bsky.social · 25/01/2025

A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...

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Karsten Rippe @karsten-rippe.bsky.social · 22/01/2025

Fakten sind das Rückgrat unserer Demokratie Facts are the backbone of our democracy When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation. www.openpetition.de/!ychtb

openpetition.de

Fakten sind das Rückgrat unserer Demokratie - Online-Petition

Liebe Mitbürgerinnen und Mitbürger, als Wissenschaftlerinnen und Wissenschaftler arbeiten wir täglich daran, die Grundlagen für fundierte Entscheidungen und Innovationen zu schaffen – basierend auf üb...

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Karsten Rippe @karsten-rippe.bsky.social · 13/12/2024

🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...

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Reposted by Karsten Rippe

Rob Schneider @robertife.bsky.social · 08/12/2024

Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup. ➡️Register now www.grc.org/histone-and-...

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Reposted by Karsten Rippe

Christa Buecker @chribue.bsky.social · 02/12/2024

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

doi.org

Redirecting

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Reposted by Karsten Rippe

Marieke Oudelaar @mariekeoudelaar.bsky.social · 22/11/2024

📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10 www.biorxiv.org/content/10.1...

biorxiv.org

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Karsten Rippe @karsten-rippe.bsky.social · 02/12/2024

📢 Join us for the 26th Single Cell Center Heidelberg Workshop! 📍 EMBL, Large Operon 📅 Thursday, December 5, 2024 🌟 Register: indico.dkfz.de/event/871/ organized by @karsten-rippe.bsky.social, @eileen-furlong.bsky.social, Josephine Bageritz, Charles Girardot & Natalia Gabrielli

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