Podcasts about dnmt1

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.20.513066v1?rss=1 Authors: Mikaeili, H., Habib, A. M., Yeung, C., Santana-Varela, S., Luiz, A. P., Panteleeva, K., Zuberi, S., Athanasiou-Fragkouli, A., Houlden, H., Wood, J. N., Okorokov, A. L., Cox, J. J. Abstract: Chronic pain affects millions of people worldwide. Studying pain insensitive individuals helps to identify novel analgesic strategies. Here we report how the recently discovered FAAH-OUT lncRNA-encoding gene, which was found from studying a pain insensitive patient with reduced anxiety and fast wound healing, regulates the adjacent key endocannabinoid system gene FAAH, which encodes the anandamide-degrading fatty acid amide hydrolase enzyme. We demonstrate that the disruption in FAAH-OUT lncRNA transcription leads to DNMT1-dependent DNA methylation within the FAAH promoter. In addition, FAAH-OUT contains a conserved regulatory element, FAAH-AMP, that acts as an enhancer for FAAH expression. Furthermore, using transcriptomic analyses we have uncovered a network of genes that are dysregulated from disruption of the FAAH-FAAH-OUT axis, thus providing a coherent mechanistic basis to understand the human phenotype observed and a platform for development of future gene and small molecule therapies. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.20.513009v1?rss=1 Authors: Zhao, Z., Hong, L., Huang, G., He, Y., Zuo, X., Han, W. Abstract: Cells sense physical cues, such as changes in extracellular matrix (ECM) stiffness, and translate these stimuli into biochemical signals that control various aspects of cellular behavior, thereby facilitating physiological and pathological processes in various organs. Evidence from multiple studies suggests that the anterior vaginal wall stiffness is higher in POP patients than in non-POP patients. Our experiments found that the expression of -smooth muscle actin (-SMA) in the anterior vaginal wall of patients with POP was increased, and the expression of DNMT1 was decreased. We used polyacrylamide gel to simulate matrix stiffening in vitro, and substrate stiffening induced the high expression of myofibroblast markers -SMA and CTGF in L929 cells. Inhibition of DNMT1 promotes fibroblast differentiation into myofibroblasts in vitro. The results of bioinformatics analysis showed that the expression of DNMT1 was significantly correlated with microtubule polymerization-related proteins. The experiment showed that the microtubule polymerization inhibitor nocodazole could eliminate the decrease of DNMT1 expression in fibroblasts induced by high stiffness. We conclude that fibroblasts sense an increase in the stiffness of the surrounding matrix and regulate fibroblast differentiation by regulating the expression of DNA methyltransferase 1 (DNMT1) through the regulation of microtubule polymerization. This study may help to elucidate the complex crosstalk between vaginal fibroblasts and their surrounding matrix in both healthy and pathological conditions, and provide new insights into the implications of potentially targeted phenotypic regulation mechanisms in material-related therapeutic applications. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

In this episode, Senta Georgia joins Monica Westley to discuss her research at USC. Dr. Georgia's research involves the regeneration of insulin-producing, pancreatic beta cells as a potential therapeutic for patients with type 1 diabetes. Her research on how the enzyme, DNMT1, is critical to stem cells differentiating into pancreatic beta cells was featured on the cover of the journal Genes & Development.To learn more about Dr. Georgia's research and the ongoing research in her lab click on the link below.Georgia Lab

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.10.197442v1?rss=1 Authors: Cathrin Bayer, Georg Pitschelatow, Nina Hannemann, Jenice Linde, Julia Reichard, Daniel Pensold, Geraldine Zimmer-Bensch Abstract: The limited regenerative capacity of neuronal cells requires tight orchestration of cell death and survival regulation in the context of longevity, as well as age-associated and neurodegenerative diseases. Subordinate to genetic networks, epigenetic mechanisms, like DNA methylation and histone modifications, are involved in the regulation of neuronal functionality, and emerge as key contributors to the pathophysiology of neurodegenerative diseases. DNA methylation, a dynamic and reversible process, is executed by DNA methyltransferases (DNMTs). DNMT1 was previously shown to regulate neuronal survival in the aged brain, whereby a DNMT1-dependent modulation of processes relevant for protein degradation was proposed as underlying mechanism. Functional proteostasis networks are a mandatory prerequisite for the functionality and long-term survival of neurons. Malfunctioning proteostasis is found, inter alia, in neurodegenerative contexts. Here, we investigated whether DNMT1 affects critical aspects of the proteostasis network by a combination of expression studies, life cell imaging and biochemical analyses. We found that DNMT1 negatively impacts retrograde trafficking and autophagy, both being involved in the clearance of aggregation-prone proteins by the aggresome-autophagy pathway. In line with this, we found that the transport of GFP-labeled mutant HTT to perinuclear regions, proposed to by cytoprotective, also depends on DNMT1. Depletion of Dnmt1 accelerated HTT perinuclear HTT aggregation and improved the survival of cells transfected with mutant HTT. This suggests that mutant HTT-induced cytotoxicity is at least in part mediated by DNMT1-dependent modulation of degradative pathways.Competing Interest StatementThe authors have declared no competing interest. Copy rights belong to original authors. Visit the link for more info

Hepatoblastoma is a malignant disease of the liver. It accounts for about 1 % of all childhood cancers and is the most common malignant liver tumor in infancy. Hepatoblastoma is assumed to arise from immature liver progenitor cells by aberrant activation of genes important in the embryonic development. Based on its early manifestation it is generally assumed that hepatoblastoma displays a relatively normal genomic background. Whole-exome sequencing performed in our group identified hepatoblastoma as one of the genetically simplest tumors ever described, with recurrent mutations in beta-catenin (CTNNB1) and nuclear factor (erythroid-derived 2)-like 2 (NFE2L2). Based on this finding we performed targeted genotyping of a large cohort of primary hepatoblastomas, hepatoblastoma cell lines and transitional liver cell tumors and identified CTNNB1 and NFE2L2 to be mutated in 72.5 % and 9.8 % of cases, respectively. CTNNB1 is a key effector molecule of canonical WNT signaling pathway, a pathway that is essential in organogenesis and cellular processes such as cell proliferation, differentiation, survival and apoptosis. However, NFE2L2 is involved in the activation of the cellular antioxidant response to combat the harmful effects such as xenobiotics and oxidative stress. Interestingly, all NFE2L2 mutations were located in or adjacent to the DLG and ETGE motifs of the NFE2L2 protein that are needed to get recognized by the KEAP1/CUL3 complex for proteasomal degradation. Functional analysis showed that cells transfected with mutant NFE2L2 were insensitive to KEAP1-mediated downregulation of NFE2L2 signaling and that depletion of the NFE2L2 via siRNA downregulates the NAD(P)H dehydrogenase (quinine) 1 (NQO1), a target gene of NFE2L2, and inhibits proliferation. In the clinical setting, NQO1 overexpression in tumors was significantly associated with metastasis, vascular invasion, the adverse prognostic C2 gene signature as well as poor outcome. RNA sequencing in our group identified the ubiquitin-like with PHD and ring finger domains 1 (UHRF1), a protein known to preferentially bind to hemi-methylated DNA, to be highly overexpressed in hepatoblastoma tumors. UHRF1 is as a key regulator in the epigenetic crosstalk, by controlling DNA methylation and histone modification. Using immunoprecipitation, we were able to show that UHRF1 binds in concert with DNA methyltransferase 1 (DNMT1) and ubiquitin specific peptidase 7 (USP7) as a trimeric complex to promoter regions of tumor suppressor genes (TSG) relevant in hepatoblastoma, such as hedgehog interacting protein (HHIP), insulin-like growth factor binding protein 3 (IGFBP3), and secreted frizzled-related protein 1 (SFRP1). These genes are epigenetically silenced in hepatoblastoma, as evidenced by heavy DNA methylation and enrichment of the repressive H3K27me3 and H3K9me2 chromatin mark. Interestingly, knockdown of UHRF1 expression via RNA interference resulted in promoter demethylation, but no reactivation of TSG gene expression. Additionally, no effect on tumor cell proliferation was observed after UHRF1 knockdown. Chromatin immunoprecipitation experiments revealed a decrease of the repressive chromatin marks H3K27me3 and H3K9me2 after UHRF1 depletion, but neither a clear shift towards the active H3K4me2 chromatin mark nor enrichment of RNA Polymerase at the TSG loci was observed. Statistical analyses revealed that a high expression of UHRF1 was associated with advanced disease state and a worse overall survival. Taken together our study demonstrates that activation of WNT signaling in concert with activation of the NFE2L2-KEAP1 pathway might be the driving force in the development of liver cancers. Moreover, we defined aberrant NQO1 expression as a marker for adverse course of disease and poor outcome. In addition, we showed that an aberrant expression of the epigenetic regulator UHRF1 and its excessive binding on promoter regions results in methylation of TSGs. This may represent an important mechanism in the initial phases of embryonal tumorigenesis. However, UHRF1 depletion alone was not sufficient to re-induce TSG expression. Therefore, UHRF1 might be more useful as a biomarker for the prognosis of hepatoblastoma than a direct anti-cancer target for hepatoblastoma therapy.

Theo Rein explains how the antidepressant paroxetine affects epigenetic regulation of Bdnf.

DNA methylation plays a crucial role in the epigenetic control of gene expression during mammalian development and differentiation. Whereas the de novo DNA methyltransferases (Dnmts), Dnmt3a and Dnmt3b, establish DNA methylation patterns during development; Dnmt1 stably maintains DNA methylation patterns during replication. DNA methylation patterns change dynamically during development and lineage specification, yet very little is known about how DNA methylation affects gene expression profiles upon differentiation. Therefore, we determined genome-wide expression profiles during differentiation of severely hypomethylated embryonic stem cells (ESCs) lacking either the maintenance enzyme Dnmt1 (dnmt1-/- ESCs) or all three major Dnmts (dnmt1-/-; dnmt3a-/-, dnmt3b-/- or TKO ESCs), resulting in complete loss of DNA methylation, and assayed their potential to transit in and out of the ESC state. Our results clearly demonstrate that upon initial differentiation to embryoid bodies (EBs), wild type, dnmt1-/- and TKO cells are able to activate differentiation processes. However, transcription profiles of dnmt1-/- and TKO EBs progressively diverge with prolonged EB culture, with dnmt1-/- EBs being more similar to wild type EBs, indicating a higher differentiation potential of dnmt1-/- EBs compared to TKO EBs. Remarkably though, after dissociation of late EBs and further cultivation under pluripotency promoting conditions, both dnmt1-/- and TKO but not wild type cells rapidly revert to expression profiles typical of undifferentiated ESCs. Thus, while DNA methylation is dispensable for the initial activation of differentiation programs, it seems to be crucial for permanently restricting the developmental fate during differentiation. Based on the essential role of Uhrf1 in maintenance DNA methylation, we investigated the structurally highly similar second member of the Uhrf protein family, Uhrf2, whose function in maintenance methylation or other biological processes is completely unknown. Expression analysis of uhrf1 and uhrf2 in various cell lines and tissues revealed a time- and developmental switch in transcript levels of both genes with uhrf1 being highly expressed in undifferentiated, proliferating cells and uhrf2 being predominately expressed in differentiated, non-dividing cells. These opposite expression patterns together with no detectable effect on DNA methylation levels upon knock down of uhrf2 suggests that Uhrf2 is rather involved in maintaining DNA methylation patterns in differentiated cells and points to non-redundant functions of both proteins. The discovery of the “6th base” of the genome, 5-hydroxymethylcytosine (5hmC), resulting from the oxidation of 5mC by the family of Tet dioxygenases (Tet1-3), once again ignited the debate about how DNA methylation marks can be modified and removed. To gain insights into the biological function of this newly identified modification, we developed a sensitive enzymatic assay for quantification of global 5hmC levels in genomic DNA. Similar to 5mC levels, we found that also 5hmC levels dynamically change during differentiation of ESCs to EBs, which correlates with the differential expression of tet1-3. Furthermore, we characterized a novel endonuclease, PvuRts1I that selectively cleaves 5hmC containing DNA and show first data on its application as a tool to map and analyze 5hmC patterns in mammalian genomes. Finally, we investigated designer transcription activator-like effector (dTALEs) proteins targeting the oct4 locus. Our results show that the epigenetic state of the target locus interferes with the ability of dTALEs to activate transcriptionally silent genes, which however can be overcome using dTALEs in combination with low doses of epigenetic inhibitors. In conclusion, this work gives further insights into the biological roles of methylation mark writers (Dnmts), readers (Uhrfs) and modifiers (Tets) and advances our understanding on the function of DNA methylation in the epigenetic control of gene expression during development and cellular differentiation.

Background: We analyzed prospectively whether MGMT (O(6)-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression. 12 Hide Figures Abstract Introduction Methods Results Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Background We analyzed prospectively whether MGMT (O6-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression. Methodology/Principal Findings: Adult patients with a histologically proven malignant astrocytoma (glioblastoma: N = 53, anaplastic astrocytoma: N = 10) were included. MGMT promoter methylation was determined by methylation-specific PCR (MSP) and sequencing analysis. Expression of MGMT and DNMTs mRNA were analysed by real-time qPCR. Prognostic factors were obtained from proportional hazards models. Correlation between MGMT mRNA expression and MGMT methylation status was validated using data from the Cancer Genome Atlas (TCGA) database (N = 229 glioblastomas). Low MGMT mRNA expression was strongly predictive for prolonged time to progression, treatment response, and length of survival in univariate and multivariate models (p

Fri, 18 Dec 2009 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/11021/ https://edoc.ub.uni-muenchen.de/11021/1/Rottach_Andrea.pdf Rottach, Andrea ddc:570, ddc:500, Fakultät für

Thu, 5 Jun 2008 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/9490/ https://edoc.ub.uni-muenchen.de/9490/1/Kuch_David.pdf Kuch, David ddc:540, ddc:500, Fakultät

DNA lesions arising from environmental and endogenous sources induce various cellular responses including cell cycle arrest, DNA repair and apoptosis. Although detailed insights into the biochemical mechanisms and composition of DNA repair pathways have been obtained from in vitro experiments, a better understanding of the interplay and regulation of these pathways requires DNA repair studies in living cells. In this study we employed laser microirradiation and photobleaching techniques in combination with specific mutants and inhibitors to analyze the real-time accumulation of proteins at laser-induced DNA damage sites in vivo, thus unravelling the mechanisms underlying the coordination of DNA repair in living cells. The immediate and faithful recognition of DNA lesions is central to cellular survival, but how these lesions are detected within the context of chromatin is still unclear. In vitro data indicated that the DNA-damage dependent poly(ADP-ribose) polymerases, PARP-1 and PARP-2, are involved in this crucial step of DNA repair. With specific inhibitors, mutations and photobleaching analysis we could reveal a complex feedback regulated mechanism for the recruitment of the DNA damage sensor PARP-1 to microirradiated sites. Activation of PARP-1 results in localized poly(ADP-ribosyl)ation and amplifies a signal for the subsequent rapid recruitment of the loading platform XRCC1 which coordinates the assembly of the repair machinery. Using similar techniques we could demonstrate the immediate and transient binding of the RNA Polymerase II cofactor PC4 to DNA damage sites, which depended on its single strand binding capacity. This establishes an interesting link between DNA repair and transcription. We propose a role for PC4 in the early steps of the DNA damage response, recognizing and stabilizing single stranded DNA (ssDNA) and thereby facilitating DNA repair by enabling repair factors to access their substrates. After DNA lesions have been successfully detected they have to be handed over to the repair machinery which restores genome integrity. Efficient repair requires the coordinated recruitment of multiple enzyme activities which is believed to be controlled by central loading platforms. As laser microirradiation induces a variety of different DNA lesions we could directly compare the recruitment kinetics of the two loading platforms PCNA and XRCC1 which are involved in different repair pathways side by side. We could demonstrate that PCNA and XRCC1 show distinct recruitment and binding kinetics with the immediate and fast recruitment of XRCC1 preceding the slow and continuous recruitment of PCNA. Introducing consecutively multiple DNA lesions within a single cell, we further demonstrated that these different recruitment and binding characteristics have functional consequences for the capacity of PCNA and XRCC1 to respond to successive DNA damage events. To further study the role of PCNA and XRCC1 as loading platforms in DNA repair, we extended our analysis to their respective interaction partners DNA Ligase I and III. Although these DNA Ligases are highly homologous and catalyze the same enzymatic reaction, they are not interchangeable and fulfil unique functions in DNA replication and repair. With deletion and mutational analysis we could identify domains mediating the specific recruitment of DNA Ligase I and III to distinct repair pathways through their interaction with PCNA and XRCC1. We conclude that this specific targeting may have evolved to accommodate the particular requirements of different repair pathways (single nucleotide replacement vs. synthesis of short stretches of DNA) and thus enhances the efficiency of DNA repair. Interestingly, we found that other PCNA-interacting proteins exhibit recruitment kinetics similar to DNA Ligase I, indicating that PCNA not only serves as a central loading platform during DNA replication, but also coordinates the recruitment of multiple enzyme activities to DNA repair sites. Accordingly, we found that the maintenance methyltransferase DNMT1, which is known to associate with replication sites through binding to PCNA, is likewise recruited to DNA repair sites by PCNA. We propose that DNMT1, like in DNA replication, preserves methylation patterns in the newly synthesized DNA, thus contributing to the restoration of epigenetic information in DNA repair. In summary, we found immediate and transient binding of repair factors involved in DNA damage detection and signalling, while repair factors involved in the later steps of DNA repair, like damage processing, DNA ligation and restoration of epigenetic information, showed a slow and persistent accumulation at DNA damage sites. We conclude that DNA repair is not mediated by binding of a preassembled repair machinery, but rather coordinated by the sequential recruitment of specific repair factors to DNA damage sites.

The genome of mammals harbors chemical modifications at some cytosine residues in the form of a methyl group. These modified residues, termed 5’-methylcytosines, have been discovered more than 50 years ago (Hotchkiss 1948) and have since been shown to play important roles in the regulation of gene expression and in the execution of developmental programs. Patterns of cytosine methylation (also referred to as DNA methylation) are carefully set and preserved during cellular expansion and global methylation levels are well regulated throughout development. Changes in methylation patterns and levels have been associated with disease progression and death (Li et al. 1992; Okano et al. 1999; Ehrlich 2002). Specifically, elevated levels of global genomic methylation have been shown to play a role in the inactivation of tumor suppressor genes in many types of cancer (Ehrlich 2002). In contrast, reduced levels of methylation have been observed in a wide variety of tumors and complete demethylation in vivo causes embryonic death (Li et al. 1992; Ehrlich 2002). In an effort to study the effect of changed methylation levels in vivo and its effect on disease progression, we developed a genetic approach to study the effect of hypomethylation during embryogenesis and adulthood. DNA methyltransferase 1 (Dnmt1) is the major methyltransferase in mammals and genetic inactivation of the Dnmt1 gene causes demethylation that results in cell death in tissue culture and embryonic lethality of homozygous mutant mice at E8.5 (Li et al. 1992). In a first step, the 5’ end of the Dnmt1 gene was characterized to determine the structure of a new oocyte-specific isoform found in oocytes and early embryos. Upon elucidation of the structure of this isoform, assays were developed to test its function in vivo. Loss of this oocyte-specific isoform protein resulted in hypomethylation of an IAP reporter element suggesting a role for this protein in early development. In contrast, the somatic Dnmt1 isoform, which is present in all somatic cells, was important for maintaining this IAP element methylated following implantation of the embryo and throughout adulthood. Reduced levels of Dnmt1 in adults caused global hypomethylation and resulted in the development of thymic lymphomas which displayed a duplication of chromosome 15 (trisomic 15). The c-myc oncogene, which resides on chromosome 15, was overexpressed, and a gene expression array analysis revealed that another oncogene, Notch-1, was also overexpressed in all tumors. Cooperation between those oncogenes has been previously shown to induce thymic lymphomas. Analysis of the Notch-1 locus demonstrated the presence of IAP insertions upstream of the oncogenic cytoplasmic domain capable of activating transcription of truncated oncogenic Notch-1. IAP elements were shown to be activated by hypomethylation albeit not as much as traditional mutagenic retroviruses. These results thus show that hypomethylation may induce tumorigenesis in this model following two mechanisms. First by inducing chromosome instability and second by creating insertional mutagenesis of defective retroviral elements such as IAPs. These results demonstrate for the first time that hypomethylation can directly induce tumorigenesis in mice and induce chromosome instability.