Epigenome mapping of human normal purified hepatocytes

Personal epigenome variation and genome-epigenome correlation

Eri Arai, Fumihito Miura, Yasushi Totoki, Satoshi Yamashita, Ying Tian, Masahiro Gotoh, Hidenori Ojima, Hiroyuki Nakagawa, Yoriko Takahashi, Hiromi Nakamura, Natsuko Hama, Mamoru Kato, Hiroshi Kimura, Yutaka Suzuki, Takashi Ito, Tatsuhiro Shibata, Yae Kanai

Research output: Contribution to journalArticle

Abstract

Aim: The aim of this study was to reveal the epigenome landscape of human normal hepatocytes. Materials & methods: Cells purified from partial hepatectomy specimens of Japanese patients were subjected to whole-genome bisulfite sequencing using postbisulfite adaptor tagging, chromatin immunoprecipitation sequencing, RNA sequencing and whole-genome sequencing. Results: CHG and CHH methylations were inversely associated with gene expression. Histone modification profiles of personal differentially methylated regions (pDMRs) differed considerably among samples. pDMRs were observed around the transcription start sites of genes whose expression is reportedly regulated by CpG methylation. pDMRs were frequently observed in the vicinity of single-nucleotide variations and insertions/deletions. Conclusion: Genetic variations may induce epigenetic variations, generating individual differences in the phenotypes of normal hepatocytes through variations in expression.

Original languageEnglish
Pages (from-to)955-979
Number of pages25
JournalEpigenomics
Volume10
Issue number7
DOIs
Publication statusPublished - 2018 Jul 1

Fingerprint

Methylation
Hepatocytes
Histone Code
Genome
RNA Sequence Analysis
Gene Expression
Chromatin Immunoprecipitation
Transcription Initiation Site
Hepatectomy
Epigenomics
Individuality
Nucleotides
Phenotype
hydrogen sulfite

Keywords

  • International Human Epigenome Consortium
  • personal differentially methylated region
  • postbisulfite adaptor tagging

ASJC Scopus subject areas

  • Genetics
  • Cancer Research

Cite this

Epigenome mapping of human normal purified hepatocytes : Personal epigenome variation and genome-epigenome correlation. / Arai, Eri; Miura, Fumihito; Totoki, Yasushi; Yamashita, Satoshi; Tian, Ying; Gotoh, Masahiro; Ojima, Hidenori; Nakagawa, Hiroyuki; Takahashi, Yoriko; Nakamura, Hiromi; Hama, Natsuko; Kato, Mamoru; Kimura, Hiroshi; Suzuki, Yutaka; Ito, Takashi; Shibata, Tatsuhiro; Kanai, Yae.

In: Epigenomics, Vol. 10, No. 7, 01.07.2018, p. 955-979.

Research output: Contribution to journalArticle

Arai, E, Miura, F, Totoki, Y, Yamashita, S, Tian, Y, Gotoh, M, Ojima, H, Nakagawa, H, Takahashi, Y, Nakamura, H, Hama, N, Kato, M, Kimura, H, Suzuki, Y, Ito, T, Shibata, T & Kanai, Y 2018, 'Epigenome mapping of human normal purified hepatocytes: Personal epigenome variation and genome-epigenome correlation', Epigenomics, vol. 10, no. 7, pp. 955-979. https://doi.org/10.2217/epi-2017-0111
Arai, Eri ; Miura, Fumihito ; Totoki, Yasushi ; Yamashita, Satoshi ; Tian, Ying ; Gotoh, Masahiro ; Ojima, Hidenori ; Nakagawa, Hiroyuki ; Takahashi, Yoriko ; Nakamura, Hiromi ; Hama, Natsuko ; Kato, Mamoru ; Kimura, Hiroshi ; Suzuki, Yutaka ; Ito, Takashi ; Shibata, Tatsuhiro ; Kanai, Yae. / Epigenome mapping of human normal purified hepatocytes : Personal epigenome variation and genome-epigenome correlation. In: Epigenomics. 2018 ; Vol. 10, No. 7. pp. 955-979.
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