Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes implications for hepatic gene expression

doi:10.1093/nar/gkw316

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Ivanov, Maxim (author)

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes implications for hepatic gene expression

E-article/E-chapterEnglish2016

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2016

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LIBRIS-ID:20187838
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-307889uri
urn:nbn:se:uu:diva-307889urn
10.1093/nar/gkw316doi

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Language:English

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deldatabas:Eplk_tEPLK

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Vetenskapsrådet
EU, FP7, Sjunde ramprogrammet [267038]
EU, Europeiska forskningsrådet [MJD71]
Carl Tryggers stiftelse för vetenskaplig forskning [CTS15:41]
Karolinska Institutets Forskningsstiftelse [C331601172]
gratis
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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Kals, Mart (author)
Lauschke, Volker (author)
Barragan, Isabel (author)
Ewels, Philip (author)
Kaller, Max (author)
Axelsson, Tomas (author)
Lehtio, Janne (author)
Milani, Lili (author)
Ingelman-Sundberg, Magnus (author)
Uppsala universitetMedicinska och farmaceutiska vetenskapsområdet (publisher)
Uppsala universitetScience for Life Laboratory, SciLifeLab (publisher)

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In:VärdpublikationNucleic Acids Research44:14, 6756-67690305-1048

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By the author/editor: Ivanov, Maxim; Kals, Mart; Lauschke, Volker; Barragan, Isabel; Ewels, Philip; Kaller, Max; show more...; Axelsson, Tomas; Lehtio, Janne; Milani, Lili; Ingelman-Sundber ...; show less...

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