5-methylcytosine (mC) can be oxidized by the tet methylcytosine dioxygenase (Tet) family of enzymes to 5-hydroxymethylcytosine (hmC), which is an intermediate of mC demethylation and may also be a stable epigenetic modification that influences chromatin structure. hmC is particularly abundant in mammalian brains but its function is currently unknown. A high-resolution hydroxymethylome map is required to fully understand the function of hmC in the human brain. We present genome-wide and single-base resolution maps of hmC and mC in the human brain by combined application of Tet-assisted bisulfite sequencing and bisulfite sequencing. We demonstrate that hmCs increase markedly from the fetal to the adult stage, and in the adult brain, 13% of all CpGs are highly hydroxymethylated with strong enrichment at genic regions and distal regulatory elements. Notably, hmC peaks are identified at the 5'splicing sites at the exon-intron boundary, suggesting a mechanistic link between hmC and splicing. We report a surprising transcription-correlated hmC bias toward the sense strand and an mC bias toward the antisense strand of gene bodies. Furthermore, hmC is negatively correlated with H3K27me3-marked and H3K9me3-marked repressive genomic regio...Continue Reading
Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain
Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain
Distal regulatory elements from the mouse metallothionein locus stimulate gene expression in transgenic mice.
A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells
DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure
Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum
Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration
Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2
A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1
Behavioral and molecular neuroepigenetic alterations in prenatally stressed mice: relevance for the study of chromatin remodeling properties of antipsychotic drugs
PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype
Aging stem cells. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging
Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression
BDNF DNA methylation changes as a biomarker of psychiatric disorders: literature review and open access database analysis
Global and Site-Specific Changes in 5-Methylcytosine and 5-Hydroxymethylcytosine after Extended Post-mortem Interval
Epigenetic mechanisms underlying the dynamic expression of cancer-testis genes, PAGE2, -2B and SPANX-B, during mesenchymal-to-epithelial transition
Homeostatic maintenance of allele-specific p16 methylation in cancer cells accompanied by dynamic focal methylation and hydroxymethylation
Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice
Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation
Pharmacoepigenetics of the role of DNA methylation in μ-opioid receptor expression in different human brain regions
WITHDRAWN: Global and site-specific changes in 5-methylcytosine and 5-hydroxymethylcytosine after extended post-mortem interval
Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate
Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver
Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling
Increased 5-hydroxymethylation levels in the hippocampus of rat extinguished from cocaine self-administration
Gene-body 5-hydroxymethylation is associated with gene expression changes in the prefrontal cortex of depressed individuals
Chromatin Switches during Neural Cell Differentiation and Their Dysregulation by Prenatal Alcohol Exposure
L1 retrotransposition is activated by Ten-eleven-translocation protein 1 and repressed by methyl-CpG binding proteins
Multiregional analysis of global 5-methylcytosine and 5-hydroxymethylcytosine throughout the progression of Alzheimer's disease
5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4
Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci
5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma
Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription
Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects
Mouse olfactory bulb methylome and hydroxymethylome maps reveal noncanonical active turnover of DNA methylation
Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood
Linking genetics to epigenetics: The role of folate and folate-related pathways in neurodevelopmental disorders
X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions
Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer
Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice
N -Phthalyl-l-Tryptophan (RG108), like Clozapine (CLO), Induces Chromatin Remodeling in Brains of Prenatally Stressed Mice
Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood.
Tamoxifen induction of Cre recombinase does not cause long-lasting or sexually divergent responses in the CNS epigenome or transcriptome: implications for the design of aging studies
Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation
Aberrant hydroxymethylation of ANGPTL4 is associated with selective intrauterine growth restriction in monochorionic twin pregnancies.
Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression
PRDM8 internal promoter hyperhydroxymethylation correlates with increased expression of the corresponding transcript in Down syndrome
Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression
Epigenetic regulation of RELN and GAD1 in the frontal cortex (FC) of autism spectrum disorder (ASD) subjects
DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex
Distal regulatory elements identified by methylation and hydroxymethylation haplotype blocks from mouse brain
Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson's Disease in Mouse Midbrain
A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-Methylcytosine and 5-Hydroxymethylcytosine Data in Neuroepigenetics
The Vast Complexity of the Epigenetic Landscape during Neurodevelopment: An Open Frame to Understanding Brain Function
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing
DNA hydroxymethylation increases the susceptibility of reactivation of methylated P16 alleles in cancer cells.
Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome
5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells
Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array
Interplay between Metabolism, Nutrition and Epigenetics in Shaping Brain DNA Methylation, Neural Function and Behavior.
Age-dependent levels of 5-methyl-, 5-hydroxymethyl-, and 5-formylcytosine in human and mouse brain tissues.
Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain
Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells
DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods
Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing
Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia
Genome-wide 5-hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer.
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits.
5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease.
Epigenetic control of region-specific transcriptional programs in mouse cerebellar and cortical astrocytes.
CREs: Gene & Cell Therapy
Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.
Cardiovascular Disease & TET2
Cardiovascular diseases are the number one cause of deaths globally. Tet methylcytosine dioxygenase 2 (TET2)-mediated hematopoiesis has been implicated in accelerating heart failure. Here is the latest research on cardiovascular diseases and TET2.
Astrocytes are glial cells that support the blood-brain barrier, facilitate neurotransmission, provide nutrients to neurons, and help repair damaged nervous tissues. Here is the latest research.