• We found that cellular senescence and tumor regression upon MYC inactivation in T-ALL was associated with genome-wide changes in 5mC and 5hmC patterns. (biomedcentral.com)
  • Knockdown of TET1 or ectopic expression of TET2 in T-ALL was associated with genome-wide changes in 5mC and 5hmC enrichment and decreased cell proliferation, suggesting a tumor promoting function of TET1, and a tumor suppressing role for TET2. (biomedcentral.com)
  • Reduced-Representation Methylation Sequencing (RRMS) with Oxford Nanopore enables cost-effective, genome-wide characterisation of methylation patterns across regions of interest. (nanoporetech.com)
  • Methods: Generation and maintenance of Tet2 conditional knockout MiceAnalysis of 5-hmC and 5-mC levels using dot blotFlow cytometry analysis, cell sorting, and hematopoietic progenitor cell (HPC) assayMSC Culture and long-term coculture with HSPCsReal-time PCR and RAN-Seq AnalysisMeDIP-seq to profile the genome-wide distribution of 5hmC. (ox.ac.uk)
  • Comparable genome-wide serial DNA methylation studies could be conducted in models of severe PAH models to establish patterns of altered 5mC and 5hmC patterns. (mergullo.net)
  • It has been proved that BaP reduced genome-wide DNA methylation, and activated proto-oncogene by hypomethylation in the promoter region, but silenced tumor suppressor genes by promoter hypermethylation, resulting in cancer initiation and progression. (biomedcentral.com)
  • Additionally, downgrading TET1 has decreased levels of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) in both cell cultures and mice. (wikipedia.org)
  • This is not the case for 5hmc as it is glucosylated in the initial step inhibiting its oxidation by TET1. (wikipedia.org)
  • Patients with schizophrenia or bipolar disorder have shown increased levels of TET1 mRNA and protein expression in the inferior parietal lobule, indicating these diseases may be caused by mistakes in gene expression regulation. (wikipedia.org)
  • Colon, breast, prostate and liver tumors have significantly reduced levels of TET1 compared to the healthy colon cells and normal epithelial colon cells with downgraded TET1 levels have greater levels of proliferation. (wikipedia.org)
  • Additionally, increasing TET1 expression levels in colon cancer cells decreased cell proliferation in both cell cultures and mice through demethylation of promoters of the WNT signaling pathway. (wikipedia.org)
  • Breast cancer cell lines with silenced TET1 expression have increased rates of invasion and breast cancers that spread to the lymph nodes are characterized by lower TET1 levels. (wikipedia.org)
  • TET1 levels could be used to detect breast cancer metastasis. (wikipedia.org)
  • A histone deacetylase inhibitor Trichostatin A increased levels of TET1 in breast cancer tissues but was a less effective tumor suppressor in patients with low TET1 expression. (wikipedia.org)
  • Breast cancer patients with high TET1 levels had significantly higher survival probabilities than patients with low TET1 levels. (wikipedia.org)
  • Degradation of TET1 in hypoxia-induced EMT lung cancer cells led to reduced metastasis rates and cells. (wikipedia.org)
  • Healthy cells transitioning to cancer cells have decreased levels of TET1 but decreasing TET1 expression does not lead to malignancy. (wikipedia.org)
  • Cancer cells using the KRAS pathway had decreased invasive potential after reintroducing TET1, likewise downgrading KRAS increased TET1 levels. (wikipedia.org)
  • Hinokitiol (5, 10 μM) decreases DNMT1 and UHRF1 mRNA and protein expression, and increases TET1 expression via enhancement of 5hmC level in HCT-116 cells. (boykyo.com.cn)
  • Here, we report that in T cell acute lymphoblastic leukemia (T-ALL) the MYC oncogene controls the expression of TET1 and TET2 to maintain 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) patterns, which is associated with tumor cell-specific gene expression. (biomedcentral.com)
  • Consequently, MYC inactivation led to an inverse expression pattern, decreasing TET1 , while increasing TET2 levels. (biomedcentral.com)
  • First author Sarah Moyon explains , "We found that TET1 levels progressively decline in older mice, and with that, DNA can no longer be properly modified to guarantee the formation of functional myelin. (epigenie.com)
  • DNA methylation (5mC, mediated by the DNA methyltransferases DNMT1, 3A, and 3B) and DNA hydroxymethylation (5hmC, mediated by the ten-eleven translocation TET1, 2, 3 family) are extensively disrupted in GBM. (woofahs.com)
  • The TET family of enzymes (TET1, TET2, and TET3) plays a critical role in DNA demethylation by converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a precursor step. (aacrjournals.org)
  • Two years ago, his group published a method called oxidative bisulfite sequencing, or oxBS-seq, for quantifying and distinguishing 5-methylcytosine (5mC), and 5-hydroxymethylcytosine (5hmC) at single-base resolution. (genomeweb.com)
  • The enzyme is also utilized as part of TET-Assisted Bisulfite Sequencing (TAB-seq) to quantify levels of hydroxymethylation in the genome and to distinguish 5-hydroxymethylcytosine (5hmc) from 5-methylcytosine (5mc) at single base resolution. (wikipedia.org)
  • We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. (biomedcentral.com)
  • Furthermore, hinokitiol reduces methylation status and restores mRNA expression of MGMT , CHST10 , and BTG4 genes [2] . (boykyo.com.cn)
  • Chromatin immunoprecipitation and sequence analysis showed that increased succinate levels led to reduced accumulation of the transcriptional marker 5hmC and transcriptionally repressed EMT-related genes. (frontlinegenomics.com)
  • The majority of TET2-dependent 5hmC modifications in MSCs are located within genes. (ox.ac.uk)
  • For example, there is no information on DNA 5mC and 5hmC methylation status of proinflammatory genes in humans with PAH. (mergullo.net)
  • Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. (babraham.ac.uk)
  • Analyzing 5′-upstream non-protein-encoding regions of the human mitochondrial function-associated genes, we speculate that mitochondrial functions could be recovered or improved at a transcriptional level. (intechopen.com)
  • Expression levels of bioactive sphingolipid genes might be novel markers for determination of drug resistance in CML pat. (nobleresearch.org)
  • The role and effect of 5hmC on 5mC turnover and hence DNA demethylation, on gene expression per se and stem cell fate and differentiation is a topic of vigorous interest. (stanford.edu)
  • In mouse, a unidirectional demethylation process from the zygote stage to blastocyst stage is observed using either reduced representation bisulfite sequencing (RRBS) or single-base resolution whole-genome bisulfite sequencing (WGBS) method. (nature.com)
  • Ten Eleven Translocation (TET) protein-catalyzed 5mC oxidation not only creates novel DNA modifications, such as 5hmC, but also initiates active or passive DNA demethylation. (researchgate.net)
  • The 5mC in DNA is hydroxylated to 5-hydroxymethylcytosine (5hmC) by TET enzymes, which can also catalyze the oxidation of 5hmC to 5-formyl cytosine (5fC) and ultimately to 5-carboxy cytosine (5caC). (troscriptions.com)
  • TET2 mutations have been associated with reduced patient survival in acute myeloid leukemia. (aacrjournals.org)
  • Along with 5-carboxyl-cytosine (5caC) both modifications are present at low levels in the genome and are widely considered to be intermediates en route from methylated to unmethylated cytosine. (genomeweb.com)
  • There's been a tendency to [say] 'these rarer modifications can't possibly be important because they're present at such low levels,'" he said, but some appear to occur at relatively high levels in specific areas of the genome and might have biological functions. (genomeweb.com)
  • To gain insights into this process on the molecular level, we have employed both bulk and single-nucleus next-generation sequencing technologies to identify stress-induced epigenetic modifications from individual neuronal cell types and followed up on potential targets using novel genetically modified mice. (upenn.edu)
  • Using nanopore sequencing, researchers have directly identified DNA and RNA base modifications at single-nucleotide resolution, including 5mC, 5hmC, 6mA, and BrdU in DNA, and m6A in RNA, with detection of further natural or synthetic epigenetic modifications possible through training basecalling algorithms. (nanoporetech.com)
  • SEs are defined as large clusters of active enhancers in large clusters that are enriched with high levels of transcription factors (TFs), master co-factors, mediator complexes, RNA polymerase II (RNA pol II), and epigenetic modifications [ 5 , 7 ]. (ijbs.com)
  • The approach, called reduced bisulfite sequencing, or redBS-seq, provides an alternative to another method, fCAB-seq, that was published by researchers in the US last year. (genomeweb.com)
  • To map 5fC, Balasubramanian and his colleagues performed bisulfite sequencing on natural DNA and on DNA where 5fC had been chemically reduced to 5hmC. (genomeweb.com)
  • Results We isolate GSCs from well-characterized GBM patient-derived xenografts (PDX), characterize their stemness properties using immunofluorescence staining, profile their epigenome including 5mC, 5hmC, 5fC/5caC, and two Alantolactone enhancer marks, and define their transcriptome. (woofahs.com)
  • Our integrative study reveals that abnormal expression of ten-eleven-translocation (TET) family members correlates with global levels of 5mC and 5fC/5caC and may be responsible for the distinct levels of these marks between glioma and neural stem cells. (woofahs.com)
  • Another exciting discovery is that of the 'sixth base' in DNA i.e. hydroxylation of methylated cytosines (5mC) by enzymes leading to '5hmC' that is present in many tissues. (stanford.edu)
  • In the brain of stressed mouse and autistic human patients, reduced MeCP2 expression is correlated with Mecp2 / MECP2 promoter hypermethylation. (biomedcentral.com)
  • Patients with scleroderma may be predisposed to PAH due to promoter methylation and reduced BMPR2 expression. (mergullo.net)
  • One study of peripheral blood cell DNA reported no methylation of the promoter [24], but a more recent study did find increased methylation and reduced expression of BMPR2 protein in heritable PAH [25]. (mergullo.net)
  • These results indicate that PLOD2 promotes cancer progression at least in part by altering succinate levels. (frontlinegenomics.com)
  • There is an increasing body of literature that identifies the potential anti-tumour effects of vitamin C. Research documented in the Journal of Scientific Reports found that vitamin C increases the activity of a chemical compound known as 5hmC, which promotes cell death in breast cancer cells. (abundanceandhealth.co.uk)
  • The disruption of ncRNA expression in cancer cells may also alter histone PTMs and DNA methylation levels (Church 2014). (diagenode.com)
  • In addition, the level of methylation of the HpaII sites (CCGG) within CGIs demonstrates a correlation with average CGI methylation levels [ 10 ]. (biomedcentral.com)
  • Hinokitiol is a component of essential oils isolated from Chymacyparis obtusa , reduces Nrf2 expression, and decreases DNMT1 and UHRF1 mRNA and protein expression, with anti-infective, anti-oxidative, and anti-tumor activities. (boykyo.com.cn)
  • The mRNA levels of several metabolic dioxygenases were induced during the EMT of mammary epithelial cells, of which PLOD2 had the highest expression. (frontlinegenomics.com)
  • Here, we characterized the whole-genome distribution of methyl-CpG and 5-hydroxymethylcytosine (5hmC) in mouse innate lymphoid cell 3 (ILC3), ILC2 and natural killer (NK) cells. (stanford.edu)
  • The study also showed that the enzyme PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2) regulates succinate levels during breast cancer progression. (frontlinegenomics.com)
  • To find out how succinate regulates cancer progression, the authors used isotope-resolved metabolomic analysis to measure metabolite levels during the epithelial-to-mesenchymal transition (EMT) - the process that mobilises cancer cells. (frontlinegenomics.com)
  • When PLOD2 expression was silenced in mammary epithelial cells, levels of succinate decreased, the mesenchymal phenotype and stemness were abolished, and 5hmC levels increased. (frontlinegenomics.com)
  • Cancer patients, unlike non-cancer patients, have a higher level of cfDNA in plasma or serum, and epigenetic alterations can be detected in these samples. (diagenode.com)
  • Hinokitiol also reduces Nrf2 expression in glioma stem cells in a dose-dependent manner [1] . (boykyo.com.cn)
  • Further studies confirmed that PLOD2 expression was increased during the EMT process, and that this increased PLOD2 expression caused cytoplasmic succinate levels to increase. (frontlinegenomics.com)
  • These mutations decrease the binding of MeCP2 to methylated DNA and concomitantly reduce MeCP2 protein stability, leading to gene expression and cellular morphological changes in a neuronal cell type-specific manner. (upenn.edu)
  • As ChIP-seq cannot establish physical co-occurrence of two marks on the same allele, admixture of cells that either express (green) or do not express (red) the gene in focus could explain the occurrence of both marks as well as the low expression level in the overall population. (researchgate.net)
  • Equipped with foremost technologies and PhD-level scientists with years of experience, Creative BioMart is capable of providing flexible solutions to settle various kinds of problems in analytic project of histone PTMs available for the scientific community. (creativebiomart.net)
  • Detection of the phosphorylation levels in histone would afford valuable information for better understanding of the pathological process of some diseases, and for the development protein kinase-targeted drug. (creativebiomart.net)
  • During PCR amplification, DHU is recognized as thymine, resulting in a 5mC/5hmC-to-T transition. (biomedcentral.com)
  • They detected changes in the levels of hundreds of metabolites in mammary epithelial cells, including increased cytoplasmic succinate levels. (frontlinegenomics.com)
  • Relative quiescence coupled with low levels of apoptosis and slow cell cycling contribute to CSC resistance to chemotherapy, while their asymmetric division gives rise to poorly differentiated daughter cells that facilitate tumor recurrence [6, 7]. (woofahs.com)
  • Treatment of cells with mTOR inhibitors may lead to reduced synthesis of RPL11 and thereby destabilize p53. (hif-signal.com)
  • The manifestation levels in control cells were arranged to 1 1. (synanet2020.com)
  • Pyk2 inactivation by its specific inhibitor or repression by RNAi inhibited the localization of LSR and downstream tricellulin to tTJs without changing their manifestation level in EpH4 cells. (synanet2020.com)
  • recipient mice exhibited a higher incident of myeloid malignancies and a significantly reduced survival rate compare with WT recipient mice. (ox.ac.uk)
  • 5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5′-monophosphate (hmCMP) by an N-glycosidase MilB. (hif-signal.com)
  • However, the extent to which the levels of p53 and RPL11 were reduced by rapamycin varied between cell lines. (hif-signal.com)
  • Indeed, rapamycin increased the levels of endogenous MDM2 despite inhibition of its phosphorylation at Ser-166. (hif-signal.com)
  • Shortly after 5hmC was discovered, 5-formyl-cytosine (5fC) was reported in the literature, "so we immediately started thinking about ways of sequencing that modification as well," Balasubramanian told In Sequence . (genomeweb.com)
  • As PhD students, we found it difficult to access the research we needed, so we decided to create a new Open Access publisher that levels the playing field for scientists across the world. (intechopen.com)
  • In fact, evidence shows that because of the unique liposomal technology, Altrient vitamin C is able to produce serum levels nearly double those thought theoretically possible with other oral forms of vitamin C - making Altrient a highly recommend supplement. (abundanceandhealth.co.uk)
  • Conversely, elevating malonyl-CoA levels in MCD KO mice does not induce browning. (biomed.news)
  • Even more selective agents should be created, with some lung-restricted distribution to reduce off-target effects preferably. (mergullo.net)
  • For 5hmC, studies over the last year or so have already shown its importance in biology and a number of disease areas. (genomeweb.com)
  • To meet multiple research goals, we offer a complete range of arrays for whole-transcriptome-, gene-, exon-, or short noncoding (snc)RNA-level analysis. (cd-genomics.com)
  • In agreement, senotherapeutics have had success in reducing the detrimental effects in experimental models of cardiovascular aging and disease. (oaepublish.com)
  • The idea of redBS-seq and fCAB-seq is similar − reducing 5fC to 5hmC prior to sequencing − but He and his colleagues used EtONH 2 instead of borohydride, which they found to result in lower background, according to Peng Jin, a professor of human genetics at Emory University School of Medicine and the co-senior author of last year's study. (genomeweb.com)