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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 (författare)
- Karolinska Inst, Dept Physiol & Pharmacol, Sect Pharmacogenet, Nanna Svartz Vag 2, S-17177 Stockholm, Sweden.
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- Kals, Mart (författare)
- Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.;Univ Tartu, Inst Math & Stat, J Liivi 2, EE-50409 Tartu, Estonia.
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- Lauschke, Volker (författare)
- Karolinska Institutet
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- Barragan, Isabel (författare)
- Karolinska Institutet
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- Ewels, Philip (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-10691 Stockholm, Sweden.
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- Kaller, Max (författare)
- KTH,Genteknologi,Royal Inst Technol, Sch Biotechnol, Div Gene Technol, Sci Life Lab, S-17121 Stockholm, Sweden.
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- Axelsson, Tomas (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab
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- Lehtio, Janne (författare)
- Karolinska Institutet
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- Milani, Lili (författare)
- Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.
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- Ingelman-Sundberg, Magnus (författare)
- Karolinska Institutet
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Karolinska Inst, Dept Physiol & Pharmacol, Sect Pharmacogenet, Nanna Svartz Vag 2, S-17177 Stockholm, Sweden Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.;Univ Tartu, Inst Math & Stat, J Liivi 2, EE-50409 Tartu, Estonia. (creator_code:org_t)
- 2016-04-29
- 2016
- Engelska.
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 44:14, s. 6756-6769
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
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