{"entity": "publication", "iuid": "7d3a9a83444049e8b4d26652d57f1ad6", "timestamp": "2026-05-19T00:52:13.039Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6"}}, "title": "Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.", "authors": [{"family": "Ivanov", "given": "Maxim", "initials": "M"}, {"family": "Kals", "given": "Mart", "initials": "M"}, {"family": "Lauschke", "given": "Volker", "initials": "V"}, {"family": "Barragan", "given": "Isabel", "initials": "I"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2016-08-19", "journal": {"volume": "44", "issn": "1362-4962", "issue": "14", "pages": "6756-6769", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "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.", "doi": "10.1093/nar/gkw316", "pmid": "27131363", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Clinical Proteomics Mass spectrometry": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw316"}, {"db": "pmc", "key": "PMC5001587"}], "notes": [], "created": "2017-05-03T13:00:08.926Z", "modified": "2024-01-16T13:48:49.630Z"}