Browsing by Author "Rathert, Philipp"

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Open Access
Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2
(2018) Rajavelu, Arumugam; Lungu, Cristiana; Emperle, Max; Dukatz, Michael; Bröhm, Alexander; Broche, Julian; Hanelt, Ines; Parsa, Edris; Schiffers, Sarah; Karnik, Rahul; Meissner, Alexander; Carell, Thomas; Rathert, Philipp; Jurkowska, Renata Z.; Jeltsch, Albert
Despite their central importance in mammalian development, the mechanisms that regulate the DNA methylation machinery and thereby the generation of genomic methylation patterns are still poorly understood. Here, we identify the 5mC-binding protein MeCP2 as a direct and strong interactor of DNA methyltransferase 3 (DNMT3) proteins. We mapped the interaction interface to the transcriptional repression domain of MeCP2 and the ADD domain of DNMT3A and find that binding of MeCP2 strongly inhibits the activity of DNMT3A in vitro. This effect was reinforced by cellular studies where a global reduction of DNA methylation levels was observed after overexpression of MeCP2 in human cells. By engineering conformationally locked DNMT3A variants as novel tools to study the allosteric regulation of this enzyme, we show that MeCP2 stabilizes the closed, autoinhibitory conformation of DNMT3A. Interestingly, the interaction with MeCP2 and its resulting inhibition were relieved by the binding of K4 unmodified histone H3 N-terminal tail to the DNMT3A-ADD domain. Taken together, our data indicate that the localization and activity of DNMT3A are under the combined control of MeCP2 and H3 tail modifications where, depending on the modification status of the H3 tail at the binding sites, MeCP2 can act as either a repressor or activator of DNA methylation.
Open Access
Epigenomic profiling of immune cell subtypes reveals H3K27ac-marked stress signatures after long-duration spaceflight
(2025) Fullstone, Tabea L.; Fischer, Lukas F.J.; Bohmeier, Maria; Frings-Meuthen, Petra; Crucian, Brian E.; Rathert, Philipp
Long-duration spaceflight imposes significant physiological stress on astronauts, including profound alterations in immune function. This study investigated epigenetic changes in immune cells following prolonged orbital spaceflight by analysing histone modifications in CD4+ and CD8+ T-cells from astronauts before, immediately after, and during recovery from spaceflight. Using Cleavage Under Targets and Tagmentation (Cut&Tag) to assess H3K27ac modifications, we identified significant alterations in chromatin accessibility, predominantly involving immune response pathways, gene regulation, and cellular adaptation mechanisms. While some epigenetic changes were transient, others persisted beyond 50 days post-return, suggesting long-term effects. These findings enhance our understanding of immune adaptation to spaceflight and have implications for mitigating spaceflight-associated health risks. Furthermore, they provide valuable insights into immune system regulation under high-stress conditions, potentially informing research on immunodeficiency disorders, cancer epigenetics, and aging-related immune decline on Earth. This study underscores the critical role of epigenetics in long-term space missions and terrestrial health applications.
Open Access
G protein-coupled estrogen receptor correlates with Dkk2 expression and has prognostic impact in ovarian cancer patients
(2021) Fraungruber, Patricia; Kaltofen, Till; Heublein, Sabine; Kuhn, Christina; Mayr, Doris; Burges, Alexander; Mahner, Sven; Rathert, Philipp; Jeschke, Udo; Trillsch, Fabian
Wnt pathway modulator Dickkopf 2 (Dkk2) and signaling of the G protein-coupled estrogen receptor (GPER) seem to have essential functions in numerous cancer types. For epithelial ovarian cancer (EOC), it has not been proven if either Dkk2 or the GPER on its own have an independent impact on overall survival (OS). So far, the correlation of both factors and their clinical significance has not systematically been investigated before. Expression levels of Dkk2 were immunohistochemically analyzed in 156 patient samples from different histologic subtypes of EOC applying the immune-reactivity score (IRS). Expression analyses were correlated with clinical and pathological parameters to assess for prognostic relevance. Data analysis was performed using Spearman’s correlations, Kruskal-Wallis-test and Kaplan-Meier estimates. Highest Dkk2 expression of all subtypes was observed in clear cell carcinoma. In addition, Dkk2 expression differed significantly (p<0.001) between low and high grade serous ovarian cancer. A significant correlation of Dkk2 with the cytoplasmic GPER expression was noted (p=0.001) but not for the nuclear estrogen receptor alpha (ERα) or beta (ERβ). Patients exhibiting both, high expression Dkk2 (IRS>4) and GPER (IRS>8), had a significantly better overall survival compared to patients with low expression (61 months vs. 33 months; p=0.024). Dkk2 and GPER expression correlates in EOC and combined expression of both is associated with improved OS. These findings underline the clinical significance of both pathways and indicate a possible prognostic impact as well as a potential for treatment strategies addressing interactions between estrogen and Wnt signaling in ovarian cancer.
Open Access
The GEF‐H1/PKD3 signaling pathway promotes the maintenance of triple‐negative breast cancer stem cells
(2019) Lieb, Wolfgang S.; Lungu, Cristiana; Tamas, Raluca; Berreth, Hannah; Rathert, Philipp; Storz, Peter; Olayioye, Monilola A.; Hausser, Angelika
Open Access
The kinase NEK6 positively regulates LSD1 activity and accumulation in local chromatin sub-compartments
(2024) Knodel, Franziska; Eirich, Jürgen; Pinter, Sabine; Eisler, Stephan A.; Finkemeier, Iris; Rathert, Philipp
LSD1 plays a crucial role in mammalian biology, regulated through interactions with coregulators and post-translational modifications. Here we show that the kinase NEK6 stimulates LSD1 activity in cells and observe a strong colocalization of NEK6 and LSD1 at distinct chromatin sub-compartments (CSCs). We demonstrate that LSD1 is a substrate for NEK6 phosphorylation at the N-terminal intrinsically disordered region (IDR) of LSD1, which shows phase separation behavior in vitro and in cells. The LSD1-IDR is important for LSD1 activity and functions to co-compartmentalize NEK6, histone peptides and DNA. The subsequent phosphorylation of LSD1 by NEK6 supports the concentration of LSD1 at these distinct CSCs, which is imperative for dynamic control of transcription. This suggest that phase separation is crucial for the regulatory function of LSD1 and our findings highlight the role of NEK6 in modulating LSD1 activity and phase separation, expanding our understanding of LSD1 regulation and its implications in cellular processes.
Open Access
Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites
(2017) Lungu, Cristiana; Pinter, Sabine; Broche, Julian; Rathert, Philipp; Jeltsch, Albert
Investigation of the fundamental role of epigenetic processes requires methods for the locus-specific detection of epigenetic modifications in living cells. Here, we address this urgent demand by developing four modular fluorescence complementation-based epigenetic biosensors for live cell microscopy applications. These tools combine engineered DNA-binding proteins with domains recognizing target epigenetic marks, both fused to non-fluorescent fragments of a fluorescent protein. The presence of the epigenetic mark at the target DNA sequence leads to the reconstitution of a functional fluorophore. With this approach, we could for the first time directly detect DNA methylation and histone 3 lysine 9 trimethylation at endogenous genomic sites in live cells and follow dynamic changes in these marks upon drug treatment, induction of epigenetic enzymes and during the cell cycle. We anticipate that this versatile technology will improve our understanding of how specific epigenetic signatures are set, erased and maintained during embryonic development or disease onset.
Open Access
Structure, activity and function of the NSD3 protein lysine methyltransferase
(2021) Rathert, Philipp
NSD3 is one of six H3K36-specific lysine methyltransferases in metazoans, and the methylation of H3K36 is associated with active transcription. NSD3 is a member of the nuclear receptor-binding SET domain (NSD) family of histone methyltransferases together with NSD1 and NSD2, which generate mono- and dimethylated lysine on histone H3. NSD3 is mutated and hyperactive in some human cancers, but the biochemical mechanisms underlying such dysregulation are barely understood. In this review, the current knowledge of NSD3 is systematically reviewed. Finally, the molecular and functional characteristics of NSD3 in different tumor types according to the current research are summarized.