Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression
2016 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no 14, 6756-6769 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2016. Vol. 44, no 14, 6756-6769 p.
IdentifiersURN: urn:nbn:se:uu:diva-307889DOI: 10.1093/nar/gkw316ISI: 000382999900024PubMedID: 27131363OAI: oai:DiVA.org:uu-307889DiVA: diva2:1048807
FunderSwedish Research CouncilEU, FP7, Seventh Framework Programme, 267038EU, European Research Council, MJD71Carl Tryggers foundation , CTS15:41The Karolinska Institutet's Research Foundation, C331601172