A5051622432- Epigenetics and DNA Methylation
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- Dietary Effects on Health
- Pluripotent Stem Cells Research
- Cancer-related gene regulation
- CRISPR and Genetic Engineering
- Phagocytosis and Immune Regulation
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Genetics and Neurodevelopmental Disorders
- PARP inhibition in cancer therapy
- Genetic Syndromes and Imprinting
- Immune cells in cancer
- Advanced Fluorescence Microscopy Techniques
- Cancer Cells and Metastasis
- Advanced Electron Microscopy Techniques and Applications
- Plant Genetic and Mutation Studies
- Photosynthetic Processes and Mechanisms
- Ferroptosis and cancer prognosis
- Telomeres, Telomerase, and Senescence
- Birth, Development, and Health
- Cancer Genomics and Diagnostics
- Diet and metabolism studies
- Cancer Research and Treatments
Queen Mary University of London
2015-2024
Cancer Research UK
2023
Broadata Communications (United States)
2021
Babraham Institute
2006-2020
University of London
2014
Cancer Institute (WIA)
2014
University of Cambridge
2010
Max Planck Institute for Biophysical Chemistry
2005
Max Planck Society
2005
5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. We introduce oxidative bisulfite sequencing (oxBS-Seq), first method for quantitative mapping of 5hmC genomic at single-nucleotide resolution. Selective chemical oxidation 5-formylcytosine (5fC) enables conversion 5fC uracil. demonstrate utility oxBS-Seq map and quantify CpG islands (CGIs) mouse embryonic stem (ES) cells identify 800 5hmC-containing CGIs that...
Current human pluripotent stem cells lack the transcription factor circuitry that governs ground state of mouse embryonic (ESC). Here, we report short-term expression two components, NANOG and KLF2, is sufficient to ignite other elements network reset state. Inhibition ERK protein kinase C sustains a transgene-independent rewired Reset self-renew continuously without signaling, are phenotypically stable, karyotypically intact. They differentiate in vitro form teratomas vivo. Metabolism...
DNA methylation patterns are reprogrammed in primordial germ cells and preimplantation embryos by demethylation subsequent de novo methylation. It has been suggested that epigenetic reprogramming may be necessary for the embryonic genome to return a pluripotent state. We have carried out genome-wide promoter analysis of mouse stem (ES) cells, (EG) sperm, trophoblast (TS) primary fibroblasts (pMEFs). Global clustering shows ES EG sperm surprisingly similar, suggesting while is highly...
Data Resource Profile: Accessible for Integrated Epigenomic Studies (ARIES) Caroline L Relton, Tom Gaunt, Wendy McArdle, Karen Ho, Aparna Duggirala, Hashem Shihab, Geoff Woodward, Oliver Lyttleton, David M Evans, Wolf Reik, Yu-Lee Paul, Gabriella Ficz, Susan E Ozanne, Anil Wipat, Keith Flanagan, Allyson Lister, Bastiaan T Heijmans, Ring and George Davey Smith MRC Integrative Epidemiology Unit, School of Social Community Medicine, University Bristol, UK, Institute Genetic Newcastle...
DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) DNA. These derivatives a role demethylation but addition may signaling functions their own right. A recent study identified proteins which showed preferential binding 5-methylcytosine its oxidised forms, where readers for 5hmC little overlap, bound further oxidation...
Methylation of cytosine in DNA (5mC) is an important epigenetic mark that involved the regulation genome function. During early embryonic development mammals, methylation landscape dynamically reprogrammed part through active demethylation. Recent advances have identified key players demethylation pathways, including oxidation 5mC to 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) by TET enzymes, excision 5fC base repair enzyme thymine glycosylase (TDG). Here, we provide first...
Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan diverse species, including rodents. However, the mechanisms by which DR interacts with process to improve old age are poorly understood. DNA methylation could play an important role mediating effects because it is sensitive nutrition can affect gene expression memory over time. Here, we profile genome-wide changes methylation, lipidomics response...
Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos is linked with pluripotency. Inhibition Erk1/2 Gsk3β signalling mouse embryonic stem (ESCs) by small molecule inhibitors (called 2i) has recently been shown to induce hypomethylation. We show whole-genome bisulphite sequencing that 2i induces rapid genome-wide demethylation on a scale pattern similar migratory PGCs embryos. Major satellites, intracisternal A particles (IAPs) imprinted genes...
Epigenetic memory, in particular DNA methylation, is established during development differentiating cells and must be erased to create naïve (induced) pluripotent stem cells. The ten-eleven translocation (TET) enzymes can catalyze the oxidation of 5-methylcytosine (5mC) 5-hydroxymethylcytosine (5hmC) further oxidized derivatives, thereby actively removing this memory. Nevertheless, mechanism by which TET are regulated, extent they manipulated, poorly understood. Here we report that retinoic...
Fertilization triggers global erasure of paternal 5-methylcytosine as part epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding its targets and wider context demethylation is limited a small fraction genome. We employed an optimized bisulfite strategy generate genome-wide methylation profiles control TET3-deficient zygotes, using SNPs access alleles. revealed that in addition pervasive removal...
Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this sufficient to drive cellular transformation not clear. To investigate question, we use CRISPR-dCas9 epigenetic editing tool, where an inactive form Cas9 fused methyltransferase effectors. Using system, here show simultaneous de novo methylation genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN primary breast cells isolated from healthy human tissue. We find that maintained even the absence...
Fluorescence recovery after photobleaching (FRAP) microscopy was used to determine the kinetic properties of Polycomb group (PcG) proteins in whole living Drosophila organisms (embryos) and tissues (wing imaginal discs salivary glands). PcG genes are essential higher eukaryotes responsible for maintenance spatially distinct repression developmentally important regulators such as homeotic genes. Their absence, well overexpression, causes transformations axial organization body. Although...
Transcription factors (TFs) are proteins that affect gene expression by binding to regulatory regions of DNA in a sequence specific manner. The TFs is controlled many factors, including the sequence, concentration TF, chromatin accessibility and co-factors. Here, we systematically investigated mechanism hundreds analysing ChIP-seq data with our explainable statistical model, ChIPanalyser. This tool uses as inputs motif; capacity distinguish between strong weak sites; TF; accessibility. We...
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<p>Survival genes identified by whole genome CRISPR/Cas9 screening in INK128-treated mESCs and vehicle mESCs.</p>