@KarstenRippe
bsky.app/profile/karsten-rippe.bsky.social
Joined November 2014
  • Tweets164
  • Following0
  • Followers1.1K
56Media
🧬 How does HP1α repress, and what happens when transcription is induced? Our new paper in @MolecularCell: HP1α stays bound, its barrier is local, and mouse chromocenters switch nanodomain by nanodomain. Paper: doi.org/10.1016/j.molcel.202… Thread with figures: bsky.app/profile/karsten-rip…
Model scheme. Top, a silenced wild-type chromocenter with H3K9me3 nucleosomes and bound HP1α; VP16 is blocked, p65 and VPR activate it while HP1α and H3K9me3 stay. Bottom, a Suv39h dn chromocenter without HP1α, which p65 and VPR activate with acetylation and VP16 activates without it.

ALT Model scheme. Top, a silenced wild-type chromocenter with H3K9me3 nucleosomes and bound HP1α; VP16 is blocked, p65 and VPR activate it while HP1α and H3K9me3 stay. Bottom, a Suv39h dn chromocenter without HP1α, which p65 and VPR activate with acetylation and VP16 activates without it.

10
1
31
2,990
1/ 🤔 Do #chromatinlooping-mediated promoter-#enhancer interactions drive gene expression? Or is the local enrichment of transcription factors into hubs/#condensates the key factor? Our AC/DC model of gene regulation at bioRxiv doi.org/10.1101/2024.08.03.6… provides a new view on this.
4
72
2
268
29,440
more replies
8/ 🔥 We reconcile findings from previous sequencing and microscopy studies into the genome-wide AC/DC model of #transcription regulation, revealing two co-existing chromatin compartment architectures. For the full story, check out our bioRxiv preprint at doi.org/10.1101/2024.08.03.6….
1
9
985
9/ 🤘 It's a long way to the top if you wanna rock 'n' roll... but @IsabelleSeufert rocked it with help of great PhD/Master's students @DKFZ & BioQuant, and valuable contributions from @AkisPapantonis, @jpmallm1, @s_anders_m & Petros Kolovos labs & funding by @spp2202_dfg. #ACDC
2
11
846
We studied cryosections of medulloblastoma with extensive nodularity, a tumor chosen for its distinct microanatomy. The automated imaging-based ST methods (MC, Merscope, Xenium) resolved its tissue structure and cell-type-specific transcriptome profiles very well.
1
5
1,408
more replies
We demonstrate how reimaging of slides after the ST analysis can markedly improve cell segmentation accuracy and integrate additional transcript and antibody-based protein readouts on the same tissue section to expand the analysis.
1
3
1,123
Great joint effort with @jpmallm1 from the Single Cell Open Lab @DKFZ and driven by Anne Rademacher, @alik_huseyn0v and Michele Bortolomeazzi with valuable contributions from our collaborators @KiTZ_HD and crucial funding from the MULTI-SPACE program of @ResearchLifesci.
1
5
1,042
Which of the different spatial transcriptomics (ST) technologies should you use for your research? The lessons we have learnt from comparing RNAscope, Molecular Cartography (MC), Merscope, Xenium and Visium are now on bioRxiv doi.org/10.1101/2024.04.03.5… 🧵
1
63
1
237
31,536
Registration is open! Join us in October for our quadrennial international #chromatin symposium in Munich. Hear and meet amazing guest speakers, and present your own work. Details at sfb1064.med.uni-muenchen.de/…
13
29
2,846
Karsten Rippe retweeted
DKFZ@DKFZ27 Mar 2024
Do you want to do excellent #postdoc research supported by one of the most prestigious fellowships in 🇪🇺? Do you want to work at a leading institution with world-class scientists from all over the world? Then apply to the DKFZ #MarieCurie MasterClasses via t1p.de/l01hq
1
19
2
24
5,831
Enjoying the work with @IsabelleSeufert and @jpmallm1 to increase the coverage of scATAC-seq for co-accessibility analysis and other applications frontiersin.org/articles/10.…. Our latest data are at 150k unique fragments/cell. Stay tuned...
1
6
24
3,100
Our single cell analysis of MLL/KMT2A fusions in AML with Michael Lübbert's group @Uniklinik_Fr is now out in @BloodAdvances. It shows a progenitor-like phenotype of the novel MLL-EDC4 fusion. Free download link: authors.elsevier.com/sd/arti…. Thanks to DFG FOR2674 for support.
8
37
4,097
Karsten Rippe retweeted
Teif Lab@TeifLab14 Nov 2023
Our paper on nucleosome repositioning in CLL is now published in @genomeresearch! Led by @krissyvalp in our lab, collab with @KostareliLab, @KarstenRippe genome.cshlp.org/content/33/… ▶️Aggressive cancers have shorter nucleosome spacing ▶️Distinguish cancer subtypes from nuc patterns
The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes—the nucleosome repeat length (NRL)—is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF...

ALT The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes—the nucleosome repeat length (NRL)—is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF...

7
40
1
148
21,531
Load more