ArticleNucleic acids research2016
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
Article in Nucleic acids research, 2016. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor.Scientific reports · 2020Article
- Genetic and Epigenetic Biomarkers of Immune Checkpoint Blockade Response.Journal of clinical medicine · 2020Review
- Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity.Pharmacology & therapeutics · 2019Review
- Epigenetic Influences in the Obesity/Colorectal Cancer Axis: A Novel Theragnostic Avenue.Journal of oncology · 2019Review
- Gene-body 5-hydroxymethylation is associated with gene expression changes in the prefrontal cortex of depressed individuals.Translational psychiatry · 2017Article
- Incorporation of an Epigenetic Evaluation into Safety Assessment: What we First Need to Know.Current opinion in toxicology · 2017Article
- Regulation of drug metabolism and toxicity by multiple factors of genetics, epigenetics, lncRNAs, gut microbiota, and diseases: a meeting report of the 21Acta pharmaceutica Sinica. B · 2017Article
- The Importance of Patient-Specific Factors for Hepatic Drug Response and Toxicity.International journal of molecular sciences · 2016Review
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.