Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1175408 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31051400.fastq.gz | Fastqsanger.gz | |||
| SRR31052500.fastq.gz | Fastqsanger.gz | |||
| SRR31052600.fastq.gz | Fastqsanger.gz | |||
| SRR31051401.fastq.gz | Fastqsanger.gz | |||
| SRR31052501.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 257 |
Similar Datasets
Project description:Tissue nanotransfection (TNT) based topical electrophoretic delivery of Etv2, Foxc2, and Fli1 (EFF) plasmids achieve induced vasculogenesis (iV) in the skin by inducing vasculogenic fibroblasts (VF). scRNA-seq analysis revealed TET-dependent gain of VF in dermal fibroblasts in response to EFF. Emergence of VF required TET-dependent demethylation of fibroblast-borne endothelial genes in vivo. Fibroblast-specific inducible overexpression of EFF in TARGATT mice caused induction of TET1/2/3, followed by transition of fibroblast to VF in vivo. TET induction was associated with elevated 5-hmC abundance in VF. TET-dependent demethylation of fibroblast-borne endothelial genes caused the formation of VF and rescued perfusion in diabetic ischemic limbs. TNTEFF rescued perfusion and closure of diabetic wounds. TET enzymes, suppressed in diabetics, play a pivotal role in causing endogenous EFF-induced VF state change of skin fibroblasts. TNT delivery of EFF transcription factors upregulate TET expression. This work is the first to recognize the significance of TET in the inducible formation of blood vessels to rescue diabetic ischemic tissue.
2024-12-05 | GSE268094 | GEO
Project description:Tet-mediated DNA oxidation is a new type of epigenetic modification in mammals and its role in the regulation of cell fate transition remains poorly understood. Here, we derive mouse embryonic fibroblasts (MEFs) deleted in all three Tet genes and examine their capability to be reprogrammed into iPS cells. We demonstrate that these Tet-deficient MEFs cannot be reprogrammed due to a blockage in the mesenchymal-to-epithelial transition (MET). Reprogramming of MEFs deficient in TDG is similarly blocked. The blockage is caused by impaired activation of crucial microRNAs, which depends on oxidative demethylation promoted by Tet and TDG. Reintroduction of either miR-200c or catalytically active Tet and TDG restores reprogramming to the respective knockout MEFs. Thus, oxidative demethylation is essential for somatic cell reprogramming. These findings provide mechanistic insights into the operation of epigenetic barriers in cell lineage conversion. Reduced Representation Bisulfite (RRBS, MspI,~75-400bp size fraction) and Tet-Assisted RRBS (TARRBS) of MEFs & reprogramming MEFs at Day 5
2014-02-19 | E-GEOD-52741 | biostudies-arrayexpress
Project description:Adaptive cellular reprogramming is an emerging field to study promotion of a host’s intrinsic healing strategies through changing one somatic cell type into another state or fate; tissue injury is known to enhance such cell conversions. Here we identify a molecular pathway in injured skin, whereby a subset of dermal fibroblasts displays a novel vasculogenic state change with gain in vasculogenic transcripts and endothelial cell-like functions without losing core fibroblast lineage fate phenotypic, functional, and transcriptional characteristics. Removal of microRNA suppression of FLI1 transcription in fibroblasts results in upregulation of a cascade of vasculogenic molecules that heralds the vasculogenic state change in some fibroblasts. FLI1 dependent vasculogenic fibroblast subset emergence in injured skin is blunted in poorly healing skin wounds of diabetic animals but can be restored through topical tissue nanotransfection of a single anti-microRNA oligonucleotide, to rescue tissue perfusion and wound healing. Augmenting a physiologic tissue injury adaptive response mechanism that produces vasculogenic fibroblasts opens new avenues for therapeutic tissue vascularization of ischemic conditions.
2022-12-27 | GSE167406 | GEO
Project description:Tet-mediated DNA oxidation is a new type of epigenetic modification in mammals and its role in the regulation of cell fate transition remains poorly understood. Here, we derive mouse embryonic fibroblasts (MEFs) deleted in all three Tet genes and examine their capability to be reprogrammed into iPS cells. We demonstrate that these Tet-deficient MEFs cannot be reprogrammed due to a blockage in the mesenchymal-to-epithelial transition (MET). Reprogramming of MEFs deficient in TDG is similarly blocked. The blockage is caused by impaired activation of crucial microRNAs, which depends on oxidative demethylation promoted by Tet and TDG. Reintroduction of either miR-200c or catalytically active Tet and TDG restores reprogramming to the respective knockout MEFs. Thus, oxidative demethylation is essential for somatic cell reprogramming. These findings provide mechanistic insights into the operation of epigenetic barriers in cell lineage conversion.
2014-02-19 | GSE52741 | GEO
Project description:TET-Mediated DNA Demethylation is Required for Inducible Vasculogenic Reprogramming of the Skin
| PRJNA1114656 | ENA
Project description:Active DNA demethylation via Ten-eleven Translocation (TET) family enzymes is essential for epigenetic reprogramming in cell state transitions. TET enzymes catalyze up to three successive oxidations of 5-methylcytosine (5mC), generating 5- hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). Although these bases are known to contribute to distinct demethylation pathways, the lack of tools to uncouple these sequential oxidative events has constrained our mechanistic understanding of TET’s role in reprogramming. Here, we employ biochemically engineered TET mutants to examine their effects on the reprogramming efficiency of mouse embryonic fibroblasts (MEFs). We show that only TET mutants proficient for oxidation to 5fC/5caC are able to rescue the reprogramming potential of Tet2 -deficient MEFs. This effect correlated with an increased capacity to drive DNA demethylation at reprogramming enhancers, ultimately accelerating chromatin opening in these regions. Together, these experiments demonstrate that DNA demethylation through 5fC/5caC intermediates is critical for iPSC reprogramming.
2021-12-21 | GSE150964 | GEO
Project description:Active DNA demethylation via Ten-eleven Translocation (TET) family enzymes is essential for epigenetic reprogramming in cell state transitions. TET enzymes catalyze up to three successive oxidations of 5-methylcytosine (5mC), generating 5- hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). Although these bases are known to contribute to distinct demethylation pathways, the lack of tools to uncouple these sequential oxidative events has constrained our mechanistic understanding of TET’s role in reprogramming. Here, we employ biochemically engineered TET mutants to examine their effects on the reprogramming efficiency of mouse embryonic fibroblasts (MEFs). We show that only TET mutants proficient for oxidation to 5fC/5caC are able to rescue the reprogramming potential of Tet2 -deficient MEFs. This effect correlated with an increased capacity to drive DNA demethylation at reprogramming enhancers, ultimately accelerating chromatin opening in these regions. Together, these experiments demonstrate that DNA demethylation through 5fC/5caC intermediates is critical for iPSC reprogramming.
2021-12-21 | GSE158333 | GEO
Project description:Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA demethylation requires TET activity but mostly occurs at sites where TET proteins are not bound suggesting a rather indirect mechanism. Among the few specific genes bound and activated by TET proteins was the naïve pluripotency and germline marker Dppa3 (Pgc7, Stella), which undergoes TDG dependent demethylation. The requirement of TET proteins for genome-wide DNA demethylation could be bypassed by ectopic expression of Dppa3. We show that DPPA3 binds and displaces UHRF1 from chromatin and thereby prevents the recruitment and activation of the maintenance DNA methyltransferase DNMT1. We demonstrate that DPPA3 alone can drive global DNA demethylation when transferred to amphibians (Xenopus) and fish (medaka), both species that naturally do not have a Dppa3 gene and exhibit no post-fertilization DNA demethylation. Our results show that TET proteins are responsible for active and - indirectly also for - passive DNA demethylation; while TET proteins initiate local and gene-specific demethylation in vertebrates, the recent emergence of DPPA3 introduced a unique means of genome-wide passive demethylation in mammals and contributed to the evolution of epigenetic regulation during early mammalian development.
2020-10-12 | PXD019794 | Pride
Project description:Oncogenic imbalance of DNA methylation is well-recognized in cancer development. Ten-eleven translocation (TET) family of dioxygenases, which facilitate DNA demethylation, are frequently dysregulated in cancers. How such dysregulation contributes to tumorigenesis remains poorly understood, especially in solid tumors which present infrequent mutational incidence of TET genes. Here we identify TET mutations in 7.4% of human lung adenocarcinoma (LUAD), which frequently co-occur with oncogenic KRAS mutations, and this co-occurrence is predictive of poor survival in LUAD patients. Using autochthonous mouse model of KrasG12D-driven LUAD, we show that individual or combinational loss of Tet genes markedly promotes tumor development. In this Kras-mutant and Tet-deficient model, pre-malignant lung epithelium undergoes neoplastic reprogramming of DNA methylation and transcription, with a particular impact on Wnt signaling. Among the Wnt-associated components that undergo reprogramming, multiple canonical Wnt antagonizing genes present impaired expression arising from elevated DNA methylation, triggering aberrant activation of Wnt signaling. These impairments can be largely reversed upon the restoration of TET activity. Correspondingly, genetic depletion of β-catenin, the transcriptional effector of Wnt signaling, substantially reverts the malignant progression of Tet-deficient LUAD. These findings reveal TET enzymes as critical epigenetic barriers against lung tumorigenesis and highlight the therapeutic vulnerability of TET-mutant lung cancer through targeting Wnt signaling.
2022-02-23 | GSE185615 | GEO
Project description:Dynamic DNA methylation and demethylation regulate gene expression during development. While DNA methyltransferases (DNMTs) establish and maintain cytosine methylation patterns, Ten-eleven translocation (Tet) dioxygenases catalyze sequential oxidation of 5-methylcytosine (5mC) to promote demethylation. Target-specific 5mC oxidation requires precise regulation of the Tet enzymatic activity. However, the mechanism underlying their activity control remains largely unexplored. Here we show a large low-complexity domain (LCD), present within the catalytic domain of Tet3, functions to repress the dioxygenase activity. Recombinant LCD-deleted Tet3 exhibits enhanced activity to convert 5mC into oxidized species. Deletion of the Tet3 LCD in mouse oocytes renders 5mC oxidation indiscriminately across the genome, leading to most prominently the derepression of ERVK retrotransposons and upregulation of adjacent genes. The extensive 5mC oxidation is associated with impairments in oocyte development. These findings suggest an intrinsic auto-regulatory mechanism of Tet3 dioxygenase operating to ensure a tight regulation of its enzymatic activity to achieve spatiotemporal specificity of methylome reprogramming during oocyte development.
2023-08-24 | GSE222498 | GEO