ArticleEpigenetics & chromatin2018
Distal regulatory elements identified by methylation and hydroxymethylation haplotype blocks from mouse brain.
Article in Epigenetics & chromatin, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- Neuroepigenetic programming by the maternal environment: part A-epigenome-wide DNA methylation profile in the offspring's olfactory bulb following preconceptional weight loss in mice.Clinical epigenetics · 2026Article
- MPCI: A novel metric for quantifying DNA methylation patterns in NGS data.PLoS computational biology · 2026Article
- tet2 and tet3 regulate cell fate specification and differentiation events during retinal development.bioRxiv : the preprint server for biology · 2024Article
- DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA.Science advances · 2023Article
- Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade.Clinical epigenetics · 2022Article
- Article
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: Triggering a Lethal Fight to Keep Control of the Ten-Eleven Translocase (TET)-Associated DNA Demethylation?Pathogens (Basel, Switzerland) · 2020Review
- Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
background5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes.
resultsWe applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently have 5mC modification simultaneously and are enriched in gene body regions of neuron development-related genes in brain tissues. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions. Moreover, using a metric called methylation haplotype load, we defined a subset of 1361 tissue-specific MHBs and 3818 shared MHBs. Shared MHBs with low MHL correspond with developmental enhancers, and tissue-specific MHBs resemble the regulatory elements for tissue identity.
conclusionsOur results provide new insights into the role of coordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity.
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