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Single base resolut...
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes implications for hepatic gene expression
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Ivanov, Maxim (author)
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Kals, Mart (author)
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Lauschke, Volker (author)
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Barragan, Isabel (author)
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Ewels, Philip (author)
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Kaller, Max (author)
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Axelsson, Tomas (author)
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Lehtio, Janne (author)
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Milani, Lili (author)
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Ingelman-Sundberg, Magnus (author)
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(publisher)
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(publisher)
- 2016
- 2016
- English.
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In: Nucleic Acids Research. - 0305-1048. ; 44:14, 6756-6769
Abstract
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- 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.
Subject headings
- Medical and Health Sciences (hsv)
- Basic Medicine (hsv)
- Medical Genetics (hsv)
- Medicin och hälsovetenskap (hsv)
- Medicinska grundvetenskaper (hsv)
- Medicinsk genetik (hsv)
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